WorldWideScience

Sample records for binding energy shifts

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  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. 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

  9. Energy phase shift as mechanism for catalysis

    KAUST Repository

    Beke-Somfai, Tamás

    2012-05-01

    Catalysts are agents that by binding reactant molecules lower the energy barriers to chemical reaction. After reaction the catalyst is regenerated, its unbinding energy recruited from the environment, which is associated with an inevitable loss of energy. We show that combining several catalytic sites to become energetically and temporally phase-shifted relative to each other provides a possibility to sustain the overall reaction by internal \\'energy recycling\\', bypassing the need for thermal activation, and in principle allowing the system to work adiabatically. Using an analytical model for superimposed, phase-shifted potentials of F 1-ATP synthase provides a description integrating main characteristics of this rotary enzyme complex. © 2012 Elsevier B.V. All rights reserved.

  10. Microfluidic Screening of Electrophoretic Mobility Shifts Elucidates Riboswitch Binding Function

    OpenAIRE

    Karns, Kelly; Vogan, Jacob M.; Qin, Qian; Hickey, Scott F.; Wilson, Stephen C.; Hammond, Ming C.; Herr, Amy E.

    2013-01-01

    Riboswitches are RNA sensors that change conformation upon binding small molecule metabolites, in turn modulating gene expression. Our understanding of riboswitch regulatory function would be accelerated by a high throughput, quantitative screening tool capable of measuring riboswitch-ligand binding. We introduce a microfluidic mobility shift assay that enables precise and rapid quantitation of ligand binding and subsequent riboswitch conformational change. In 0.3% of the time required for be...

  11. 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)

  12. Microfluidic screening of electrophoretic mobility shifts elucidates riboswitch binding function.

    Science.gov (United States)

    Karns, Kelly; Vogan, Jacob M; Qin, Qian; Hickey, Scott F; Wilson, Stephen C; Hammond, Ming C; Herr, Amy E

    2013-02-27

    Riboswitches are RNA sensors that change conformation upon binding small molecule metabolites, in turn modulating gene expression. Our understanding of riboswitch regulatory function would be accelerated by a high-throughput, quantitative screening tool capable of measuring riboswitch-ligand binding. We introduce a microfluidic mobility shift assay that enables precise and rapid quantitation of ligand binding and subsequent riboswitch conformational change. In 0.3% of the time required for benchtop assays (3.2 versus 1020 min), we screen and validate five candidate SAM-I riboswitches isolated from thermophilic and cryophilic bacteria. The format offers enhanced resolution of conformational change compared to slab gel formats, quantitation, and repeatability for statistical assessment of small mobility shifts, low reagent consumption, and riboswitch characterization without modification of the aptamer structure. Appreciable analytical sensitivity coupled with high-resolution separation performance allows quantitation of equilibrium dissociation constants (K(d)) for both rapidly and slowly interconverting riboswitch-ligand pairs as validated through experiments and modeling. Conformational change, triplicate mobility shift measurements, and K(d) are reported for both a known and a candidate SAM-I riboswitch with comparison to in-line probing assay results. The microfluidic mobility shift assay establishes a scalable format for the study of riboswitch-ligand binding that will advance the discovery and selection of novel riboswitches and the development of antibiotics to target bacterial riboswitches.

  13. A New Relation between Lamb Shift Energies

    CERN Document Server

    Kubo, Hiroaki; Kanda, Naohiro; Kato, Hiroshi; Munakata, Yasunori; Oshima, Sachiko; Tsuda, Kazuhiro

    2010-01-01

    We derive a new relation between the observed Lamb shift energies of hydrogen and muonium atoms. The relation is based on the non-relativistic description of the Lamb shift, and the proper treatment of the reduced mass of electron and target particles (proton and muon) leads to the new formula which is expressed as $\\displaystyle{{\\Delta E^{(H)}_{2s_{1/2}}\\over \\Delta E^{(\\mu)}_{2s_{1/2}}} =({1+{m_e\\over m_\\mu}\\over 1+{m_e\\over M_p}})^3}$. This relation achieves an excellent agreement with experiment and presents an important QED test free from the cutoff momentum $\\Lambda$.

  14. Negative Energy: From Lamb Shift to Entanglement

    CERN Document Server

    Bu, Shou-Liang

    2016-01-01

    "Negative energy" has been one of the most enduring puzzles in quantum theory, whereas the present work reveals that it actually plays a central role in clarifying various controversies of quantum theory. The basic idea is contained in a hypothesis on negative energy, and it is shown that the idea: (1)is compatible with both relativistic quantum mechanics and known experimental results; (2)helps to clarify the essence of matter waves, and therefore better understand the reality of the wave function, the so-called 'wave-packet reduction' occurring in quantum measurement, and the ghost like correlations between entangled systems; (3)is helpful for distinguishing the vacuum from the ground state of the quantized field, and may supply a possible way for removing the deep-rooted infinities in quantum field theory. The vacuum energy density of the electromagnetic field is calculated here as an example. By employing the same idea, the Lamb-Shift is recalculated in a different way from conventional renormalization me...

  15. Energy efficiency improvement by gear shifting optimization

    Directory of Open Access Journals (Sweden)

    Blagojevic Ivan A.

    2013-01-01

    Full Text Available Many studies have proved that elements of driver’s behavior related to gear selection have considerable influence on the fuel consumption. Optimal gear shifting is a complex task, especially for inexperienced drivers. This paper presents an implemented idea for gear shifting optimization with the aim of fuel consumption minimization with more efficient engine working regimes. Optimized gear shifting enables the best possible relation between vehicle motion regimes and engine working regimes. New theoretical-experimental approach has been developed using On-Board Diagnostic technology which so far has not been used for this purpose. The matrix of driving modes according to which tests were performed is obtained and special data acquisition system and analysis process have been developed. Functional relations between experimental test modes and adequate engine working parameters have been obtained and all necessary operations have been conducted to enable their use as inputs for the designed algorithm. The created Model has been tested in real exploitation conditions on passenger car with Otto fuel injection engine and On-Board Diagnostic connection without any changes on it. The conducted tests have shown that the presented Model has significantly positive effects on fuel consumption which is an important ecological aspect. Further development and testing of the Model allows implementation in wide range of motor vehicles with various types of internal combustion engines.

  16. 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...

  17. Tight-binding theory of NMR shifts in topological insulators

    Science.gov (United States)

    Garate, Ion; Boutin, Samuel; Ramirez Ruiz, Jorge

    To date, most experiments in topological insulators have focused on probing the surface states of these materials and suppressing the often inevitable contribution from bulk states. However, the latter are of interest on their own and contain useful information that can be extracted with a local probe like nuclear magnetic resonance (NMR). Recently, 77Se NMR experiments on Bi2Se3 single crystals have reported unusual field-independent linewidths and short spin-echo decays. It is likely that an unexpectedly strong indirect internuclear coupling, characteristic of some inverted band structures, is the cause of these peculiar results. Motivated by this hypothesis, we report on a microscopic theory of NMR shifts and linewidths in Bi2Se3 and Bi2Te3. Our theory provides quantitative estimates for the Knight shift, the orbital shift, the Ruderman-Kittel-Kasuya-Yoshida coupling and the Bloembergen-Rowland coupling. We will compare our findings with the available experimental data Funded by the National Science and Engineering Research Council of Canada, Fonds de Recherche Québécois Nature et Technologies, and Mitacs-Globalink.

  18. 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....

  19. 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.

  20. 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.

  1. 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.

  2. High-resolution kinetic energy distributions via doppler shift measurements

    Science.gov (United States)

    Xu, Z.; Koplitz, B.; Buelow, S.; Baugh, D.; Wittig, C.

    1986-07-01

    In photolysis/probe experiments using pulsed sources, time delay produces both spatial and directional bias in the fragment distributions, thus enabling well-resolved kinetic energy distributions to be obtained from Doppler shift measurements. Data are presented for H-atoms detected using two-photon ionization, and high S/N and laser-limited kinetic energy resolution are demonstrated.

  3. 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.

  4. 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.

  5. The Lamb Shift and Ultra High Energy Cosmic Rays

    CERN Document Server

    Xue, S S

    2002-01-01

    On the analogy with the Lamb shift, we study the vacuum effects that a proton interacts with virtual particles when it travels through the vacuum. We find that a moving proton is accelerated by gaining the zero-point energy from the vacuum (~10^{-5} eV/cm). Such an effect possibly accounts for the mysterious origin and spectrum of ultra high-energy cosmic ray events above 10^{20}eV, and explains the puzzle why the GZK cutoff is absent. The candidates of these events could be protons from early Universe.

  6. 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.

  7. Measurement of Nanomolar Dissociation Constants by Titration Calorimetry and Thermal Shift Assay – Radicicol Binding to Hsp90 and Ethoxzolamide Binding to CAII

    Directory of Open Access Journals (Sweden)

    Vilma Michailovienė

    2009-06-01

    Full Text Available The analysis of tight protein-ligand binding reactions by isothermal titration calorimetry (ITC and thermal shift assay (TSA is presented. The binding of radicicol to the N-terminal domain of human heat shock protein 90 (Hsp90aN and the binding of ethoxzolamide to human carbonic anhydrase (hCAII were too strong to be measured accurately by direct ITC titration and therefore were measured by displacement ITC and by observing the temperature-denaturation transitions of ligand-free and ligand-bound protein. Stabilization of both proteins by their ligands was profound, increasing the melting temperature by more than 10 ºC, depending on ligand concentration. Analysis of the melting temperature dependence on the protein and ligand concentrations yielded dissociation constants equal to 1 nM and 2 nM for Hsp90aN-radicicol and hCAII-ethoxzolamide, respectively. The ligand-free and ligand-bound protein fractions melt separately, and two melting transitions are observed. This phenomenon is especially pronounced when the ligand concentration is equal to about half the protein concentration. The analysis compares ITC and TSA data, accounts for two transitions and yields the ligand binding constant and the parameters of protein stability, including the Gibbs free energy and the enthalpy of unfolding.

  8. Detecting electron beam energy shifts with a commercially available energy monitor.

    Science.gov (United States)

    Evans, M D; Moftah, B A; Olivares, M; Podgorsak, E B

    2000-07-01

    Routine electron beam quality assurance requires an accurate, yet practical, method of energy characterization. Subtle shifts in beam energy may be produced by the linac bending magnet assembly, and the sensitivity of a commercially available electron beam energy-monitoring device for monitoring these small energy drifts has been evaluated. The device shows an 11% change in signal for a 2 mm change in the I50 energy parameter for low energy electron beams (in the vicinity of 6 MeV) and a 2.5% change in signal for a 2 mm change in the I50 energy parameter for high energy electron beams (in the vicinity of 22 MeV). Thus the device is capable of detecting small energy shifts resulting from bending magnet drift for all clinically relevant electron beams.

  9. 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.

  10. An atomic clockwork using phase dependent energy shifts

    CERN Document Server

    De Munshi, D; Mukherjee, M

    2011-01-01

    A frequency stabilized laser referenced to an unperturbed atomic two level system acts as the most accurate clock with femtosecond clock ticks. For any meaningful use, a Femtosecond Laser Frequency Comb (FLFC) is used to transfer the atomic clock accuracy to electronically countable nanosecond clock ticks. Here we propose an alternative clockwork based on the phenomenon that when an atomic system is slowly evolved in a cyclic path, the atomic energy levels gather some phase called the geometric phase. This geometric phase dependent energy shift has been used here to couple the two frequency regimes in a phase coherent manner. It has also been shown that such a technique can be implemented experimentally, bypassing the highly involved setup of a FLFC.

  11. 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...

  12. Temperature-Dependent Energy Gap Shift and Thermally Activated Transition in Multilayer CdTe/ZnTe Quantum Dots.

    Science.gov (United States)

    Man, Minh Tan; Lee, Hong Seok

    2015-10-01

    We investigated the influence of growth conditions on carrier dynamics in multilayer CdTe/ZnTe quantum dots (QDs) by monitoring the temperature dependence of the photoluminescence emission energy. The results were analyzed using the empirical Varshni and O'Donnell relations for temperature variation of the energy gap shift. Best fit values showed that the thermally activated transition between two different states occurs due to band low-temperature quenching with values separated by 5.0-6.5 meV. The addition of stack periods in multilayer CdTe/ZnTe QDs plays an important role in the energy gap shift, where the exciton binding energy is enhanced, and, conversely, the exciton-phonon coupling strength is suppressed with an average energy of 19.3-19.8 meV.

  13. 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)

  14. 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).

  15. 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.

  16. Pulse EPR-enabled interpretation of scarce pseudocontact shifts induced by lanthanide binding tags

    Energy Technology Data Exchange (ETDEWEB)

    Abdelkader, Elwy H.; Yao, Xuejun [Australian National University, Research School of Chemistry (Australia); Feintuch, Akiva [Weizmann Institute of Science, Department of Chemical Physics (Israel); Adams, Luke A.; Aurelio, Luigi; Graham, Bim [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Goldfarb, Daniella [Weizmann Institute of Science, Department of Chemical Physics (Israel); Otting, Gottfried, E-mail: gottfried.otting@anu.edu.au [Australian National University, Research School of Chemistry (Australia)

    2016-01-15

    Pseudocontact shifts (PCS) induced by tags loaded with paramagnetic lanthanide ions provide powerful long-range structure information, provided the location of the metal ion relative to the target protein is known. Usually, the metal position is determined by fitting the magnetic susceptibility anisotropy (Δχ) tensor to the 3D structure of the protein in an 8-parameter fit, which requires a large set of PCSs to be reliable. In an alternative approach, we used multiple Gd{sup 3+}-Gd{sup 3+} distances measured by double electron–electron resonance (DEER) experiments to define the metal position, allowing Δχ-tensor determinations from more robust 5-parameter fits that can be performed with a relatively sparse set of PCSs. Using this approach with the 32 kDa E. coli aspartate/glutamate binding protein (DEBP), we demonstrate a structural transition between substrate-bound and substrate-free DEBP, supported by PCSs generated by C3-Tm{sup 3+} and C3-Tb{sup 3+} tags attached to a genetically encoded p-azidophenylalanine residue. The significance of small PCSs was magnified by considering the difference between the chemical shifts measured with Tb{sup 3+} and Tm{sup 3+} rather than involving a diamagnetic reference. The integrative sparse data approach developed in this work makes poorly soluble proteins of limited stability amenable to structural studies in solution, without having to rely on cysteine mutations for tag attachment.

  17. 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.

  18. Energy flux and Goos-Hänchen shift in frustrated total internal reflection.

    Science.gov (United States)

    Chen, Xi; Lu, Xiao-Jing; Zhao, Pei-Liang; Zhu, Qi-Biao

    2012-05-01

    Using Yasumoto and Õishi's energy flux method, a generalized analytical formulation for analyzing the Goos-Hänchen (GH) shift in frustrated total internal reflection is provided, from which the GH shift given by Artman's stationary phase method is shown to equal the GH calculated by Renard's conventional energy flux method plus a self-interference shift. The self-interference shift, originating from the interference between the incident and reflected beams, sheds light on the asymptotic behavior of the GH shift in such optical tunneling process in term of energy flux.

  19. Tight-binding theory of NMR shifts in topological insulators Bi2Se3 and Bi2Te3

    Science.gov (United States)

    Boutin, Samuel; Ramírez-Ruiz, Jorge; Garate, Ion

    2016-09-01

    Motivated by recent nuclear magnetic resonance (NMR) experiments, we present a microscopic s p3 tight-binding model calculation of the NMR shifts in bulk Bi2Se3 and Bi2Te3 . We compute the contact, dipolar, orbital and core polarization contributions to the carrier-density-dependent part of the NMR shifts in 209Bi,125Te, and 77Se. The spin-orbit coupling and the layered crystal structure result in a contact Knight shift with strong uniaxial anisotropy. Likewise, because of spin-orbit coupling, dipolar interactions make a significant contribution to the isotropic part of the NMR shift. The contact interaction dominates the isotropic Knight shift in 209Bi NMR, even though the electronic states at the Fermi level have a rather weak s -orbital character. In contrast, the contribution from the contact hyperfine interaction to the NMR shift of 77Se and 125Te is weak compared to the dipolar and orbital shifts therein. In all cases, the orbital shift is at least comparable to the contact and dipolar shifts, while the shift due to core polarization is subdominant (except for Te nuclei located at the inversion centers). By artificially varying the strength of spin-orbit coupling, we evaluate the evolution of the NMR shift across a band inversion but find no clear signature of the topological transition.

  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. Neural Mechanisms of Context Effects on Face Recognition: Automatic Binding and Context Shift Decrements

    Science.gov (United States)

    Hayes, Scott M.; Baena, Elsa; Truong, Trong-Kha; Cabeza, Roberto

    2011-01-01

    Although people do not normally try to remember associations between faces and physical contexts, these associations are established automatically, as indicated by the difficulty of recognizing familiar faces in different contexts (“butcher-on-the-bus” phenomenon). The present functional MRI (fMRI) study investigated the automatic binding of faces and scenes. In the Face-Face (F-F) condition, faces were presented alone during both encoding and retrieval, whereas in the Face/Scene-Face (FS-F) condition, they were presented overlaid on scenes during encoding but alone during retrieval (context change). Although participants were instructed to focus only on the faces during both encoding and retrieval, recognition performance was worse in the FS-F than the F-F condition (“context shift decrement”—CSD), confirming automatic face-scene binding during encoding. This binding was mediated by the hippocampus as indicated by greater subsequent memory effects (remembered > forgotten) in this region for the FS-F than the F-F condition. Scene memory was mediated by the right parahippocampal cortex, which was reactivated during successful retrieval when the faces were associated with a scene during encoding (FS-F condition). Analyses using the CSD as a regressor yielded a clear hemispheric asymmetry in medial temporal lobe activity during encoding: left hippocampal and parahippocampal activity was associated with a smaller CSD, indicating more flexible memory representations immune to context changes, whereas right hippocampal/rhinal activity was associated with a larger CSD, indicating less flexible representations sensitive to context change. Taken together, the results clarify the neural mechanisms of context effects on face recognition. PMID:19925208

  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. Energy shift estimation of demand response activation on domestic refrigerators – A field test study

    DEFF Research Database (Denmark)

    Lakshmanan, Venkatachalam; Gudmand-Høyer, Kristian; Marinelli, Mattia;

    2014-01-01

    This paper presents a method to estimate the amount of energy that can be shifted during demand response (DR) activation on domestic refrigerator. Though there are many methods for DR activation like load reduction, load shifting and onsite generation, the method under study is load shifting. Ele...

  4. Economic assessment of energy storage for load shifting in Positive Energy Building

    DEFF Research Database (Denmark)

    Dumont, Olivier; Carmo, Carolina; Georges, Emeline

    2016-01-01

    by varying the building envelope characteristics, the power supply system, the climate, the lightning and appliances profiles, the roof tilt, the battery size and the electricity tariffs, leading to 3200 cases. The analysis is performed on an annual basis in terms of self-consumption rate, shifted energy......-in tariff and a 5 kWh battery. Finally, simple correlations (based on the feed-in tariff, the annual electrical consumption and production) to predict the optimal size of battery and the lowest payback period are proposed.......Net Zero Energy Buildings (NZEB) and Positive Energy Buildings (PEB) are gaining more and more interest. In this paper, the impact of the integration of a battery in a positive energy building is assessed in order to increase its self-consumption of electricity. Parametric studies are carried out...

  5. Graphene mediated Stark shifting of quantum dot energy levels

    Science.gov (United States)

    Kinnischtzke, Laura; Goodfellow, Kenneth M.; Chakraborty, Chitraleema; Lai, Yi-Ming; Fält, Stefan; Wegscheider, Werner; Badolato, Antonio; Vamivakas, A. Nick

    2016-05-01

    We demonstrate an optoelectronic device comprised of single InAs quantum dots in an n-i-Schottky diode where graphene has been used as the Schottky contact. Deterministic electric field tuning is shown using Stark-shifted micro-photoluminescence from single quantum dots. The extracted dipole moments from the Stark shifts are comparable to conventional devices where the Schottky contact is a semi-transparent metal. Neutral and singly charged excitons are also observed in the well-known Coulomb-blockade plateaus. Our results indicate that graphene is a suitable replacement for metal contacts in quantum dot devices which require electric field control.

  6. Energy shift of H-atom electrons due to Gibbons-Hawking thermal bath

    CERN Document Server

    Pardy, Miroslav

    2016-01-01

    The electromagnetic shift of energy levels of H-atom electrons is determined by calculating an electron coupling to the Gibbons-Hawking electromagnetic field thermal bath. Energy shift of electrons in H-atom is determined in the framework of the non-relativistic quantum mechanics.

  7. 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).

  8. 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.

  9. 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.

  10. Water–gas shift catalyst development for energy efficient applications

    NARCIS (Netherlands)

    Hakeem, A.A.

    2014-01-01

    The water–gas shift (WGS) is a reversible, moderately exothermic reaction (1) and is used for the production of hydrogen from CO rich gas streams (synthesis gas). CO + H2O ⇆ CO2 + H2 ΔH°= –41 kJ mol−1 (1) This research has focused on the catalyst

  11. 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.

  12. 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....

  13. Zero-Energy and Beyond: A Paradigm Shift in Assessment

    Directory of Open Access Journals (Sweden)

    Ronald Rovers

    2014-12-01

    Full Text Available The world is on the eve of major changes in the way energy and material are used, and the building and construction sector is at the forefront. One of the revolutionary changes is that for 0-energy houses and buildings. Many countries already have some projects established, and legislation is following, first requiring near 0-energy, but undoubtedly this will evolve into 0-energy as basic requirement. Buildings will generate all required energy from within their building lot, from incoming free and renewable energy sources: solar radiation and earth core heat mainly. In other words, there are no polluting or depleting issues anymore related to energy consumed to operate a building. This will change the whole approach in evaluation and optimization of the environmental performance of buildings: while the energy-driven measures for buildings become obsolete, it will be materials needed for this transition that have to become the main focus, as argued in this paper.

  14. Visualising the Global Shift in Energy Demand and Supply

    OpenAIRE

    Muhammad Isma'il

    2012-01-01

    The global energy demand depends on supplies from fossil fuels responsible for climate change. The supply of the fossil fuels required to meet the global energy demand depends on production from the available proved reserves of oil, coal and gas unevenly distributed around the world. On the other hand, the energy demand of a country is determined by its economic growth and population dynamics. The industrialised nations accounted for the rising demand in global primary energy. However, a glob...

  15. Study on shift schedule saving energy of automatic transmission of ground vehicles

    Institute of Scientific and Technical Information of China (English)

    龚捷; 赵丁选; 陈鹰; 陈宁

    2004-01-01

    To improve ground vehicle efficiency, shift schedule energy saving was proposed for the ground vehicle automatic transmission by studying the function of the torque converter and transmission in the vehicular drivetrain. The shift schedule can keep the torque converter working in the high efficiency range under all the working conditions except in the low efficiency range on the left when the transmission worked at the lowest shift, and in the low efficiency range on the right when the transmission worked at the highest shift. The shift quality key factors were analysed. The automatic trans-mission's bench-test adopting this shift schedule was made on the automatic transmission's test-bed. The experimental results showed that the shift schedule was correct and that the shift quality was controllable.

  16. Study on shift schedule saving energy of automatic transmission of ground vehicles

    Institute of Scientific and Technical Information of China (English)

    龚捷; 赵丁选; 陈鹰; 陈宁

    2004-01-01

    To improve ground vehicle efficiency,shift schedule energy saving was proposed for the ground vehicle automatic transmission by studying the function of the torque converter and transmission in the vehicular drivetrain.The shift schedule can keep the torque converter working in the high efficiency range under all the working conditions except in the low efficiency range on the left when the transmission worked at the lowest shift,and in the low efficiency range on the right when the transmission worked at the highest shift.The shift quality key factors were analysed.The automatic transmission's bench-test adopting this shift schedule was made on the automatic transmission's test-bed.The experimental results showed that the shift schedule was correct and that the shift quality was controllable.

  17. Relativistic and Radiative Energy Shifts for Rydberg States

    CERN Document Server

    Jentschura, U D; Evers, J; Mohr, P J; Keitel, C H

    2004-01-01

    We investigate relativistic and quantum electrodynamic effects for highly-excited bound states in hydrogenlike systems (Rydberg states). In particular, hydrogenic one-loop Bethe logarithms are calculated for all circular states (l = n-1) in the range 20 20 to an accuracy of five to seven decimal digits, within the specified manifolds of atomic states. Within the numerical accuracy, the results constitute unified, general formulas for quantum electrodynamic corrections whose validity is not restricted to a single atomic state. The results are relevant for accurate predictions of radiative shifts of Rydberg states and for the description of the recently investigated laser-dressed Lamb shift, which is observable in a strong coherent-wave light field.

  18. 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.

  19. Shift to a low carbon society through energy systems design

    Institute of Scientific and Technical Information of China (English)

    Toshihiko; NAKATA; Mikhail; RODIONOV; Diego; SILVA; Joni; JUPESTA

    2010-01-01

    Concern about global warming calls for an advanced approach for designing an energy system to reduce carbon emissions as well as to secure energy security for each country.Conventional energy systems tend to introduce different technologies with high conversion efficiency,leading to a higher average efficiency.Advanced energy systems can be achieved not by an aggregate form of conversion technologies but by an innovative system design itself.The concept of LCS(low carbon society) is a unique approach having multi-dimensional considerations such as social,economic and environmental dimensions.The LCS aims at an extensive restructuring of worldwide energy supply/demand network system by not only replacing the conventional parts with the new ones,but also integrating all the necessary components and designing absolutely different energy networks.As a core tool for the LCS design,energy-economic models are applied to show feasible solutions in future with alternatives such as renewable resources,combined heat and power,and smart grid operations.Models can introduce changes in energy markets,technology learning in capacity,and penetration of innovative technologies,leading to an optimum system configuration under priority settings.The paper describes recent trials of energy models application related to waste-to-energy,clean coal,transportation and rural development.Although the modelling approach is still under investigation,the output clearly shows possible options having variety of technologies and linkages between supply and demand sides.Design of the LCS means an energy systems design with the modelling approach,which gives solution for complex systems,choices among technologies,technology feasibility,R&D targets,and what we need to start.

  20. Resolving shifting patterns of muscle energy use in swimming fish.

    Directory of Open Access Journals (Sweden)

    Shannon P Gerry

    Full Text Available Muscle metabolism dominates the energy costs of locomotion. Although in vivo measures of muscle strain, activity and force can indicate mechanical function, similar muscle-level measures of energy use are challenging to obtain. Without this information locomotor systems are essentially a black box in terms of the distribution of metabolic energy. Although in situ measurements of muscle metabolism are not practical in multiple muscles, the rate of blood flow to skeletal muscle tissue can be used as a proxy for aerobic metabolism, allowing the cost of particular muscle functions to be estimated. Axial, undulatory swimming is one of the most common modes of vertebrate locomotion. In fish, segmented myotomal muscles are the primary power source, driving undulations of the body axis that transfer momentum to the water. Multiple fins and the associated fin muscles also contribute to thrust production, and stabilization and control of the swimming trajectory. We have used blood flow tracers in swimming rainbow trout (Oncorhynchus mykiss to estimate the regional distribution of energy use across the myotomal and fin muscle groups to reveal the functional distribution of metabolic energy use within a swimming animal for the first time. Energy use by the myotomal muscle increased with speed to meet thrust requirements, particularly in posterior myotomes where muscle power outputs are greatest. At low speeds, there was high fin muscle energy use, consistent with active stability control. As speed increased, and fins were adducted, overall fin muscle energy use declined, except in the caudal fin muscles where active fin stiffening is required to maintain power transfer to the wake. The present data were obtained under steady-state conditions which rarely apply in natural, physical environments. This approach also has potential to reveal the mechanical factors that underlie changes in locomotor cost associated with movement through unsteady flow regimes.

  1. Low energy scattering phase shifts for meson-baryon systems

    CERN Document Server

    Detmold, William

    2015-01-01

    In this work, we calculate meson-baryon scattering phase shifts in four channels using lattice QCD methods. From a set of calculations at four volumes, corresponding to spatial sizes of 2, 2.5, 3, and 4 fm, and a pion mass of m_pi ~ 390 MeV, we determine the scattering lengths and effective ranges for these systems at the corresponding quark masses. We also perform the calculation at a lighter quark mass, m_pi ~ 230 MeV, on the largest volume. Using these determinations, along with those in previous work, we perform a chiral extrapolation of the scattering lengths to the physical point after correcting for the effective range contributions using the multi-volume calculations performed at m_pi ~ 390 MeV.

  2. 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.

  3. 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

  4. 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.

  5. Electromagnetic corrections to the hadronic phase shifts in low energy $\\pi^{+}p$ elastic scattering

    CERN Document Server

    Gashi, A; Oades, G C; Rasche, G; Woolcock, W S

    2001-01-01

    We calculate the s and p-wave electromagnetic corrections which must be subtracted from the nuclear phase shifts obtained from the analysis of low energy pi+p elastic scattering data, in order to obtain hadronic phase shifts. We compare our results with earlier calculations and estimate the uncertainties in the corrections.

  6. 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.

  7. 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.

  8. Extremal energy shifts of radiation from a ring near a rotating black hole

    CERN Document Server

    Karas, Vladimir

    2010-01-01

    Radiation from a narrow circular ring shows a characteristic double-horn profile dominated by photons having energy around the maximum or minimum of the allowed range, i.e. near the extremal values of the energy shift. The energy span of a spectral line is a function of the ring radius, black hole spin, and observer's view angle. We describe a useful approach to calculate the extremal energy shifts in the regime of strong gravity. Then we consider an accretion disk consisting of a number of separate nested annuli in the equatorial plane of Kerr black hole, above the innermost stable circular orbit (ISCO). We suggest that the radial structure of the disk emission could be reconstructed using the extremal energy shifts of the individual rings deduced from the broad wings of a relativistic spectral line.

  9. Dark Energy, Paradigm Shifts, and the Role of Evidence

    CERN Document Server

    Lahav, Ofer

    2014-01-01

    We comment on cases in the history of Astronomy, which may shed some light on the current established but enigmatic concordance model of Cosmology. Should the model be understood by adding new entities such as Dark Matter and Dark Energy, or by modifying the underlying theory? For example, the prediction and discovery of planet Neptune can be regarded as analogous to finding a dark component; while explaining the anomalous perihelion precession of Mercury by General Relativity can be taken as analogous to the possibility that modified gravity is an alternative to dark components of the universe. In this paper, we revise this analogy coming from the history of astronomy with an eye to illustrating some of the similarities and differences between the two cases.

  10. Binding of the auxiliary subunit TRIP8b to HCN channels shifts the mode of action of cAMP.

    Science.gov (United States)

    Hu, Lei; Santoro, Bina; Saponaro, Andrea; Liu, Haiying; Moroni, Anna; Siegelbaum, Steven

    2013-12-01

    Hyperpolarization-activated cyclic nucleotide-regulated cation (HCN) channels generate the hyperpolarization-activated cation current Ih present in many neurons. These channels are directly regulated by the binding of cAMP, which both shifts the voltage dependence of HCN channel opening to more positive potentials and increases maximal Ih at extreme negative voltages where voltage gating is complete. Here we report that the HCN channel brain-specific auxiliary subunit TRIP8b produces opposing actions on these two effects of cAMP. In the first action, TRIP8b inhibits the effect of cAMP to shift voltage gating, decreasing both the sensitivity of the channel to cAMP (K1/2) and the efficacy of cAMP (maximal voltage shift); conversely, cAMP binding inhibits these actions of TRIP8b. These mutually antagonistic actions are well described by a cyclic allosteric mechanism in which TRIP8b binding reduces the affinity of the channel for cAMP, with the affinity of the open state for cAMP being reduced to a greater extent than the cAMP affinity of the closed state. In a second apparently independent action, TRIP8b enhances the action of cAMP to increase maximal Ih. This latter effect cannot be explained by the cyclic allosteric model but results from a previously uncharacterized action of TRIP8b to reduce maximal current through the channel in the absence of cAMP. Because the binding of cAMP also antagonizes this second effect of TRIP8b, application of cAMP produces a larger increase in maximal Ih in the presence of TRIP8b than in its absence. These findings may provide a mechanistic explanation for the wide variability in the effects of modulatory transmitters on the voltage gating and maximal amplitude of Ih reported for different neurons in the brain.

  11. How allosteric effectors can bind to the same protein residue and produce opposite shifts in the allosteric equilibrium.

    Science.gov (United States)

    Abraham, D J; Safo, M K; Boyiri, T; Danso-Danquah, R E; Kister, J; Poyart, C

    1995-11-21

    Monoaldehyde allosteric effectors of hemoglobin were designed, using molecular modeling software (GRID), to form a Schiff base adduct with the Val 1 alpha N-terminal nitrogens and interact via a salt bridge with Arg 141 alpha of the opposite subunit. The designed molecules were synthesized if not available. It was envisioned that the molecules, which are aldehyde acids, would produce a high-affinity hemoglobin with potential interest as antisickling agents similar to other aldehyde acids reported earlier. X-ray crystallographic analysis indicated that the aldehyde acids did bind as modeled de novo in symmetry-related pairs to the alpha subunit N-terminal nitrogens. However, oxygen equilibrium curves run on solutions obtained from T- (tense) state hemoglobin crystals of reacted effector molecules produced low-affinity hemoglobins. The shift in the allosteric equilibrium was opposite to that expected. We conclude that the observed shift in allosteric equilibrium was due to the acid group on the monoaldehyde aromatic ring that forms a salt bridge with the guanidinium ion of Arg 141 alpha on the opposite subunit. This added constraint to the T-state structure that ties two subunits across the molecular symmetry axis shifts the equilibrium further toward the T-state. We tested this idea by comparing aldehydes that form Schiff base interactions with the same Val 1 alpha residues but do not interact across the dimer subunit symmetry axis (a new one in this study with no acid group and others that have had determined crystal structures). The latter aldehydes shift the allosteric equilibrium toward the R-state. A hypothesis to predict the direction in shift of the allosteric equilibrium is made and indicates that it is not exclusively where the molecule binds but how it interacts with the protein to stabilize or destabilize the T- (tense) allosteric state.

  12. 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.

  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. 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.

  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. Improvement in a phenomenological formula for ground state binding energies

    CERN Document Server

    Gangopadhyay, G

    2016-01-01

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

  17. Computing dispersive, polarizable, and electrostatic shifts of excitation energy in supramolecular systems: PTCDI crystal.

    Science.gov (United States)

    Megow, Jörg

    2016-09-07

    The gas-to-crystal-shift denotes the shift of electronic excitation energies, i.e., the difference between ground and excited state energies, for a molecule transferred from the gas to the bulk phase. The contributions to the gas-to-crystal-shift comprise electrostatic as well as inductive polarization and dispersive energy shifts of the molecular excitation energies due to interaction with environmental molecules. For the example of 3,4,9,10-perylene-tetracarboxylic-diimide (PTCDI) bulk, the contributions to the gas-to-crystal shift are investigated. In the present work, electrostatic interaction is calculated via Coulomb interaction of partial charges while inductive and dispersive interactions are obtained using respective sum over states expressions. The coupling of higher transition densities for the first 4500 excited states of PTCDI was computed using transition partial charges based on an atomistic model of PTCDI bulk obtained from molecular dynamics simulations. As a result it is concluded that for the investigated model system of a PTCDI crystal, the gas to crystal shift is dominated by dispersive interaction.

  18. 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 ...

  19. 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.

  20. Lamb shift of non-degenerate energy level systems placed between two infinite parallel conducting plates

    CERN Document Server

    Billaud, B

    2012-01-01

    The issue of the observability of the Lamb shift in systems with non-degenerate energy levels is put to question. To this end, we compute the Lamb shift of such systems in the electromagnetic environment provided by two infinite parallel conducting plates, which is instrumental in demonstrating the existence of the so-called Casimir effect. A formula giving the relative change in the Lamb shift (as compared to the standard one in vacuum) is explicitly obtained for spherical semiconductor Quantum Dots (QD). It suggests a possibility of QD non-degenerate energy spectrum fine-tuning for experimental purposes as well as a {\\it Gedankenexperiment} to observe the Lamb shift in spherical semiconductor quantum dots.

  1. 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

  2. Electromagnetic Corrections to the Hadronic Phase Shifts in Low-Energy $\\pi^{+}p$ Elastic Scattering

    CERN Document Server

    Gashi, A; Oades, G C; Rasche, G; Woolcock, W S

    1999-01-01

    We calculate for the s-, p(1/2)- and p(3/2)-waves the electromagnetic corrections which must be subtracted from the nuclear phase shifts obtained from the analysis of low energy pi+ p elastic scattering data, in order to obtain hadronic phase shifts. The calculation uses relativised Schroedinger equations containing the sum of an electromagnetic potential and an effective hadronic potential. We compare our results with those of previous calculations and qualitatively estimate the uncertainties in the corrections.

  3. 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

  4. 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.

  5. Electrophoretic mobility shift assay identifies vitamin D binding protein (Gc-globulin) in human, rat, and mouse sera.

    Science.gov (United States)

    Tang, W X; Bazaraa, H M; Magiera, H; Cooke, N E; Haddad, J G

    1996-06-01

    Serum vitamin D binding protein (DBP, also known as Gc-globulin) is a multifunctional protein capable of binding both vitamin D metabolites and actin. DBP can be visualized when analyzed by polyacrylamide gel electrophoresis followed by staining. Confirmation of its identity had previously required immunoprecipitation with specific anti-DBP antisera or occupancy of the protein with radioactive vitamin D sterols. We present studies showing that preincubation of G-actin with mammalian sera produced a discernible DBP protein band shift on native gel electrophoresis. Addition of DNaseI, a 33-kDa intracellular protein with an avid actin-binding site, to the incubations resulted in a supershift of DBP-actin complexes to an even more cathodal region of the gels. Following incubations with human, rat, and murine sera the same actin shift occurred as did the actin plus DNaseI supershift. The migrations of each complex were correlated with purified DBP migrations under identical conditions. It was confirmed that the supershifted bands contained DBP by Western blotting and detection of DBP by binding of 25-OH[3H]D3. After intravenous G-actin injections into living mice, a serum DBP-actin complex could be detected on native gels as the uncomplexed DBP band decreased in intensity. This simple, direct-staining technique appears to be suitable for identifying DBP/Gc phenotypes in human populations as well as for semiquantitatively monitoring the plasma actin-scavenger system in vivo in animal models or in human diseases.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Ground-State Energy as a Simple Sum of Orbital Energies in Kohn-Sham Theory: A Shift in Perspective through a Shift in Potential

    CERN Document Server

    Levy, Mel

    2016-01-01

    It is observed that the exact interacting ground-state electronic energy of interest may be obtained directly, in principle, as a simple sum of orbital energies when a universal density-dependent term is added to $w\\left(\\left[ \\rho \\right];\\mathbf{r} \\right)$, the familiar Hartree plus exchange-correlation component in the Kohn-Sham effective potential. The resultant shifted potential, $\\bar{w}\\left(\\left[ \\rho \\right];\\mathbf{r} \\right)$, actually changes less on average than $w\\left(\\left[ \\rho \\right];\\mathbf{r} \\right)$ when the density changes, including the fact that $\\bar{w}\\left(\\left[ \\rho \\right];\\mathbf{r} \\right)$ does not undergo a discontinuity when the number of electrons increases through an integer. Thus the approximation of $\\bar{w}\\left(\\left[ \\rho \\right];\\mathbf{r} \\right)$ represents an alternative direct approach for the approximation of the ground-state energy and density.

  11. 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...... the experimentally observed dependence of the biexciton binding energies....

  12. 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.

  13. Stokes shift and fine structure splitting in composition-tunable ZnxCd1-xSe nanocrystals: Atomistic tight-binding theory

    Science.gov (United States)

    Sukkabot, Worasak

    2017-02-01

    I report on the atomistic correlation of the structural properties and excitonic splitting of ternary alloy ZnxCd1-xSe wurtzite nanocrystals using the sp3s* empirical tight-binding method with the description of the first nearest neighbouring interaction and bowing effect. Based on a successful model, the computations are presented under various Zn compositions (x) and diameters of alloy ZnxCd1-xSe nanocrystals with the experimentally synthesized compositions and sizes. With increasing Zn contents (x), the optical band gaps and electron-hole coulomb energies are improved, while ground electron-hole wave function overlaps, electron-hole exchange energies, stokes shift and fine structure splitting are reduced. A composition-tunable emission from blue to yellow wavelength is obviously demonstrated. The optical band gaps, ground electron-hole wave function overlaps, electron-hole interactions, stokes shift and fine structure splitting are progressively decreased with the increasing diameters. Alloy ZnxCd1-xSe nanocrystal with Zn rich and large diameter is the best candidate to optimistically be used as a source of entangled photon pairs. The agreement with the experimental data is remarkable. Finally, the present systematic study on the structural properties and excitonic splitting predominantly opens a new perspective to understand the size- and composition-dependent properties of ZnxCd1-xSe nanocrystals with a comprehensive strategy to design the optoelectronic devices.

  14. 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.

  15. 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...

  16. Shift and broadening of emission lines in Nd$^{3+}$:YAG laser crystal influenced by input energy

    Indian Academy of Sciences (India)

    POURMAND SEYED EBRAHIM; REZAEI GHASEM

    2016-06-01

    Spectroscopic properties of the flashlamp-pumped Nd$^{3+}$:YAG laser as a function of input energy were studied over the range of 18–75 J. The spectral widths and shifts of quasi-three-level and four-level inter-Stark emissions within the respective intermanifold transitions of $^4$F$_{3/2}$ $\\rightarrow$ $^{4}$I$_{9/2} $ and $^{4}$F$_{3/2}$ $\\rightarrow$ $^{4}$I$_{11/2}$ were investigated. The emission lines of $^{4}$F$_{3/2}$ $\\rightarrow$ $^{4}$I$_{9/2}$ shifted towards longer wavelength (red shift) and broadened, while the positions and linewidths of the $^{4}$F$_{3/2}$ $\\rightarrow$ $^{4}$I$_{11/2}$ transition lines remained constant by increasing the pumping energy. This is attributed to the thermal population as well as one-phonon and multiphonon emission processes in the ground state. This phenomenon degrades the output performance of the lasers.

  17. 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

  18. 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}-...

  19. New technique for phase shift analysis multi-energy solution of inverse scattering problem

    CERN Document Server

    Cooper, S G; MacIntosh, R S; Kuznetsova, E V

    1998-01-01

    We demonstrate a new approach to the analysis of extensive multi-energy data. For the case of d + He-4, we produce a phase shift analysis covering for the energy range 3 to 11 MeV. The key idea is the use of iterative perturbative data-to-potential inversion which can produce potentials which reproduce the data simultaneously over a range of energies. It thus effectively regularizes the extraction of phase shifts from diverse, incomplete and possibly somewhat contradictory data sets. In doing so, it will provide guidance to experimentalists as to what further measurements should be made. This study is limited to vector spin observables and spin-orbit interactions. We discuss alternative ways in which the theory can be implemented and which provide insight into the ambiguity problems. We compare the extrapolation of these solutions to other energies. Majorana terms are presented for each potential component.

  20. Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range

    Science.gov (United States)

    Ventura, Alejandra C.; Bush, Alan; Vasen, Gustavo; Goldín, Matías A.; Burkinshaw, Brianne; Bhattacharjee, Nirveek; Folch, Albert; Brent, Roger; Chernomoretz, Ariel; Colman-Lerner, Alejandro

    2014-01-01

    Cell signaling systems sense and respond to ligands that bind cell surface receptors. These systems often respond to changes in the concentration of extracellular ligand more rapidly than the ligand equilibrates with its receptor. We demonstrate, by modeling and experiment, a general “systems level” mechanism cells use to take advantage of the information present in the early signal, before receptor binding reaches a new steady state. This mechanism, pre-equilibrium sensing and signaling (PRESS), operates in signaling systems in which the kinetics of ligand-receptor binding are slower than the downstream signaling steps, and it typically involves transient activation of a downstream step. In the systems where it operates, PRESS expands and shifts the input dynamic range, allowing cells to make different responses to ligand concentrations so high as to be otherwise indistinguishable. Specifically, we show that PRESS applies to the yeast directional polarization in response to pheromone gradients. Consideration of preexisting kinetic data for ligand-receptor interactions suggests that PRESS operates in many cell signaling systems throughout biology. The same mechanism may also operate at other levels in signaling systems in which a slow activation step couples to a faster downstream step. PMID:25172920

  1. Ab initio surface core-level shifts and surface segregation energies

    DEFF Research Database (Denmark)

    Aldén, Magnus; Skriver, Hans Lomholt; Johansson, Börje

    1993-01-01

    We have calculated the surface core-level energy shifts of the 4d and 5d transition metals by means of local-density theory and a Green’s-function technique based on the linear muffin-tin orbitals method. Final-state effects are included by treating the core-ionized atom as an impurity located...

  2. USE OF SIMULINK(MATLAB FOR ANALYSIS OF ENERGY PERFORMANCE OF CLASSICAL PHASE SHIFT INSTALLATION

    Directory of Open Access Journals (Sweden)

    Kalinin L.P.

    2011-08-01

    Full Text Available Article is devoted to the development of simulation model in Simulink environment of phase shift installation, executed on classical scheme “Marcerau Connection”, test of idle, short-circuit and loading modes on base of this simulation model and determine of energy characteristics of this installation.

  3. Energy shift of interacting non-relativistic fermions in noncommutative space

    Directory of Open Access Journals (Sweden)

    A. Jahan

    2005-06-01

    Full Text Available   A local interaction in noncommutative space modifies to a non-local one. For an assembly of particles interacting through the contact potential, formalism of the quantum field theory makes it possible to take into account the effect of modification of the potential on the energy of the system. In this paper we calculate the energy shift of an assembly of non-relativistic fermions, interacting through the contact potential in the presence of the two-dimensional noncommutativity.

  4. Sharpness-induced energy shifts of quantum well states in Pb islands on Cu(111)

    Science.gov (United States)

    Chan, Wen-Yuan; Lu, Shin-Ming; Su, Wei-Bin; Liao, Chun-Chieh; Hoffmann, Germar; Tsai, Tsong-Ru; Chang, Chia-Seng

    2017-03-01

    We elucidate that the tip sharpness in scanning tunneling microscopy (STM) can be characterized through the number of field-emission (FE) resonances. A higher number of FE resonances indicates higher sharpness. We observe empty quantum well (QW) states in Pb islands on Cu(111) under different tip sharpness levels. We found that QW states observed by sharper tips always had lower energies, revealing negative energy shifts. This sharpness-induced energy shift originates from an inhomogeneous electric field in the STM gap. An increase in sharpness increases the electric field inhomogeneity, that is, enhances the electric field near the tip apex, but weakens the electric field near the sample. As a result, higher sharpness can increase the electronic phase in vacuum, causing the lowering of QW state energies. Moreover, the behaviors of negative energy shift as a function of state energy are entirely different for Pb islands with a thickness of two and nine atomic layers. This thickness-dependent behavior results from the electrostatic force in the STM gap decreasing with increasing tip sharpness. The variation of the phase contributed from the expansion deformation induced by the electrostatic force in a nine-layer Pb island is significantly greater, sufficient to effectively negate the increase of electronic phase in vacuum.

  5. 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-.

  6. Electromagnetic corrections to the hadronic phase shifts in low energy pi sup + p elastic scattering

    CERN Document Server

    Gashi, A; Oades, G C; Rasche, G; Woolcock, W S

    2001-01-01

    We calculate for the s-, p sub 1 sub / sub 2 - and p sub 3 sub / sub 2 -waves the electromagnetic corrections which must be subtracted from the nuclear phase shifts obtained from the analysis of low-energy pi sup + p elastic scattering data, in order to obtain hadronic phase shifts. The calculation uses relativised Schroedinger equations containing the sum of an electromagnetic potential and an effective hadronic potential. We compare our results with those of previous calculations and estimate the uncertainties in the corrections.

  7. Low-Energy Kπ Phase Shifts in Chiral SU(3) Quark Model

    Institute of Scientific and Technical Information of China (English)

    HUANG Fei; ZHANG Zong-Ye; YU You-Wen

    2005-01-01

    The low-energy region kaon-pion S- and P-wave phase shifts with isospin I = 1/2 and I = 3/2 are dynamically studied in the chiral SU(3) quark model by solving a resonating group method equation. The model parameters are taken to be the values fitted by the energies of the baryon ground states and the kaon-nucleon elastic scattering phase shifts of different partial waves. As a preliminary study the s-channel q(-q) annihilation interactions are not included since they only act in the very short range and are subsequently assumed to be unimportant in the low-energy domain. The numerical results are in qualitative agreement with the experimental data.

  8. 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.

  9. 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.

  10. Temperature dependence of the energy-level shift induced by the Bose-Einstein condensation of photons

    Institute of Scientific and Technical Information of China (English)

    Zhang Jian-Jun; Cheng Ze; Yuan Jian-Hui; Zhang Jun-Pei

    2012-01-01

    We investigate the energy-level shift of a hydrogen atom in a two-dimensional optical microcavity,where there exists a Bose-Einstein condensation of photons.It is found that below the critical temperature Tc,the energy-level shift of the bound electron is dependent on temperature,and it is a monotonically increasing function of the absolute temperature T.Especially,at the absolute zero temperature,the energy-level shift entirely comes from the Lamb shift,and the atom can be treated approximately,that is,in vacuum.

  11. Graphene Quantum Dot Layers with Energy-Down-Shift Effect on Crystalline-Silicon Solar Cells.

    Science.gov (United States)

    Lee, Kyung D; Park, Myung J; Kim, Do-Yeon; Kim, Soo M; Kang, Byungjun; Kim, Seongtak; Kim, Hyunho; Lee, Hae-Seok; Kang, Yoonmook; Yoon, Sam S; Hong, Byung H; Kim, Donghwan

    2015-09-02

    Graphene quantum dot (GQD) layers were deposited as an energy-down-shift layer on crystalline-silicon solar cell surfaces by kinetic spraying of GQD suspensions. A supersonic air jet was used to accelerate the GQDs onto the surfaces. Here, we report the coating results on a silicon substrate and the GQDs' application as an energy-down-shift layer in crystalline-silicon solar cells, which enhanced the power conversion efficiency (PCE). GQD layers deposited at nozzle scan speeds of 40, 30, 20, and 10 mm/s were evaluated after they were used to fabricate crystalline-silicon solar cells; the results indicate that GQDs play an important role in increasing the optical absorptivity of the cells. The short-circuit current density was enhanced by about 2.94% (0.9 mA/cm(2)) at 30 mm/s. Compared to a reference device without a GQD energy-down-shift layer, the PCE of p-type silicon solar cells was improved by 2.7% (0.4 percentage points).

  12. New measurements and phase shift analysis of p16O elastic scattering at astrophysical energies

    Science.gov (United States)

    Dubovichenko, Sergey; Burtebayev, Nassurlla; Dzhazairov-Kakhramanov, Albert; Zazulin, Denis; Kerimkulov, Zhambul; Nassurlla, Marzhan; Omarov, Chingis; Tkachenko, Alesya; Shmygaleva, Tatyana; Kliczewski, Stanislaw; Sadykov, Turlan

    2017-01-01

    The results of new experimental measurements of p16O elastic scattering in the energy range of 0.6-1.0 MeV at angles of 40°-160° are given. Phase shift analysis of p16O elastic scattering was made using these and other experimental data on differential cross sections in excitation functions and angular distributions at energies of up to 2.5 MeV. Supported by the Ministry of Education and Science of the Republic of Kazakhstan (0073/PCF-IS-MES)

  13. Superluminal Energy Transmission in the Goos-Hanchen Shift of Total Reflection

    CERN Document Server

    Wang, Z Y

    2011-01-01

    This paper is to give a counter example for the theory of relativity. Firstly, the dispersion relation of surface electromagnetic waves is corresponding to that of a tachyon where the coefficient of proportionality is the squared Planck constant. Then we prove the energy flow velocity S/w of the Goos-Hanchen shift in vacuum is cn.sinI>c as well according to electrodynamics. These two different ways lead to a same conclusion that energy transport in the Goos-Hanchen effect of total reflection is faster than light. It is also helpful to study the tachyon of particle physics and superluminal motion observed in astronomy,etc.

  14. Superluminal energy transmission in the Goos-Hanchen shift of total reflection

    Science.gov (United States)

    Wang, Zhong-Yue

    2011-04-01

    The dispersion relation ω2 = β2c2 - τ2c2 of surface electromagnetic waves is corresponding to that E2 = p2c2 - m02c4 of a tachyon where the coefficient of proportionality is the squared Planck constant ℏ2. Then we prove the energy flow velocity of the Goos-Hanchen shift in vacuum is cn sin θi > c as well according to electrodynamics. These two different ways lead to a same conclusion that energy transport in the Goos-Hanchen effect of total reflection is faster than light.

  15. Consumer response to product-integrated energy feedback: behavior, goal level shifts, and energy conservation

    NARCIS (Netherlands)

    McCalley, L.T.; Vries, de Peter W.; Midden, Cees J.H.

    2011-01-01

    Results of recent experiments suggest that interactive control panels of individual appliances can be used to stimulate energy saving behavior by offering the means for consumers to set a goal and receive immediate energy use feedback. The underlying source of the behavioral response, however, remai

  16. Energy calibration issues in nuclear resonant vibrational spectroscopy: observing small spectral shifts and making fast calibrations.

    Science.gov (United States)

    Wang, Hongxin; Yoda, Yoshitaka; Dong, Weibing; Huang, Songping D

    2013-09-01

    The conventional energy calibration for nuclear resonant vibrational spectroscopy (NRVS) is usually long. Meanwhile, taking NRVS samples out of the cryostat increases the chance of sample damage, which makes it impossible to carry out an energy calibration during one NRVS measurement. In this study, by manipulating the 14.4 keV beam through the main measurement chamber without moving out the NRVS sample, two alternative calibration procedures have been proposed and established: (i) an in situ calibration procedure, which measures the main NRVS sample at stage A and the calibration sample at stage B simultaneously, and calibrates the energies for observing extremely small spectral shifts; for example, the 0.3 meV energy shift between the 100%-(57)Fe-enriched [Fe4S4Cl4](=) and 10%-(57)Fe and 90%-(54)Fe labeled [Fe4S4Cl4](=) has been well resolved; (ii) a quick-switching energy calibration procedure, which reduces each calibration time from 3-4 h to about 30 min. Although the quick-switching calibration is not in situ, it is suitable for normal NRVS measurements.

  17. 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.

  18. Economic assessment of electric energy storage for load shifting in positive energy building

    DEFF Research Database (Denmark)

    Dumont, Olivier; Do Carmo, Carolina Madeira Ramos; Georges, Emeline

    2017-01-01

    Net zero energy buildings and positive energy buildings are gaining more and more interest. This paper evaluates the impact of the integration of a battery in a positive energy building used to increase its self-consumption of electricity. Parametric studies are carried out by varying the buildin...... and a 3.7 kWh battery. Finally, simple correlations (based on the feed-in tariff, the annual electrical consumption and production) to predict the optimal size of battery and the lowest payback period are proposed.......Net zero energy buildings and positive energy buildings are gaining more and more interest. This paper evaluates the impact of the integration of a battery in a positive energy building used to increase its self-consumption of electricity. Parametric studies are carried out by varying the building...... envelope characteristics, the power supply system, the climate, the lighting and appliances profiles, the roof tilt angle, the battery size and the electricity tariffs, leading to 3200 cases. The analysis is performed on an annual basis in terms of self-consumption and self-production rate and payback...

  19. Peripheral and integral membrane binding of peptides characterized by time-dependent fluorescence shifts: focus on antimicrobial peptide LAH₄.

    Science.gov (United States)

    Macháň, Radek; Jurkiewicz, Piotr; Olżyńska, Agnieszka; Olšinová, Marie; Cebecauer, Marek; Marquette, Arnaud; Bechinger, Burkhard; Hof, Martin

    2014-06-03

    Positioning of peptides with respect to membranes is an important parameter for biological and biophysical studies using model systems. Our experiments using five different membrane peptides suggest that the time-dependent fluorescence shift (TDFS) of Laurdan can help when distinguishing between peripheral and integral membrane binding and can be a useful, novel tool for studying the impact of transmembrane peptides (TMP) on membrane organization under near-physiological conditions. This article focuses on LAH4, a model α-helical peptide with high antimicrobial and nucleic acid transfection efficiencies. The predominantly helical peptide has been shown to orient in supported model membranes parallel to the membrane surface at acidic and, in a transmembrane manner, at basic pH. Here we investigate its interaction with fully hydrated large unilamellar vesicles (LUVs) by TDFS and fluorescence correlation spectroscopy (FCS). TDFS shows that at acidic pH LAH4 does not influence the glycerol region while at basic pH it makes acyl groups at the glycerol level of the membrane less mobile. TDFS experiments with antimicrobial peptides alamethicin and magainin 2, which are known to assume transmembrane and peripheral orientations, respectively, prove that changes in acyl group mobility at the glycerol level correlate with the orientation of membrane-associated peptide molecules. Analogous experiments with the TMPs LW21 and LAT show similar effects on the mobility of those acyl groups as alamethicin and LAH4 at basic pH. FCS, on the same neutral lipid bilayer vesicles, shows that the peripheral binding mode of LAH4 is more efficient in bilayer permeation than the transmembrane mode. In both cases, the addition of LAH4 does not lead to vesicle disintegration. The influence of negatively charged lipids on the bilayer permeation is also addressed.

  20. 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.

  1. Energy gap in tunneling spectroscopy: effect of the chemical potential shift

    Science.gov (United States)

    Fedotov, N. I.; Zaitsev-Zotov, S. V.

    2016-12-01

    We study the effect of a shift of the chemical potential level on the tunneling conductance spectra. In the systems with gapped energy spectra, significant chemical-potential dependent distortions of the differential tunneling conductance curves, dI/dV, arise in the gap region. An expression is derived for the correction of the dI/dV, which in a number of cases was found to be large. The sign of the correction depends on the chemical potential level position with respect to the gap. The correction of the dI/dV associated with the chemical potential shift has a nearly linear dependence on the tip-sample separation z and vanishes at z → 0.

  2. 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.

  3. Phase-Shift Analysis of Low-Energy $\\pi^{+}p$ Data

    CERN Document Server

    Gashi, A; Oades, G C; Rasche, G; Woolcock, W S

    1999-01-01

    This work presents the results of a revised analysis of the low-energy (pion laboratory kinetic energy T(sub pi) < 100 MeV) pi+ p data using recently obtained electromagnetic corrections. The measurements are analyzed assuming extended threshold expansions for the hadronic K-matrix elements. With a few exceptions, the description of the experimental data is satisfactory. Several minimization functions have been used, yielding consistent results. The phase-shift values, obtained in the s and p(3/2) partial waves, disagree with those of the most recent VPI global-fit solution (SP98); the largest part of this disagreement is removed if we compare our numbers to their single-energy solutions. The s-wave scattering length a(sub 0+), the p-wave scattering volumes a(sub 1+) and a(sub 1-), as well as the hadronic phase shifts themselves, obtained herein, are in agreement with recent work using older electromagnetic corrections; the output of the present work (including meaningful uncertainties) is tabulated in ord...

  4. Studies of K-shell x-ray energy shifts induced by MeV/u heavy ions

    Institute of Scientific and Technical Information of China (English)

    Song Zhang-Yong; Yang Zhi-Hu; Shao Jian-Xiong; Cui Ying; Zhang Hong-Qiang; Ruan Fang-Fang; Du Juan; Gao Zhi-Min; Yu De-Yang; Chen Xi-Meng; Cai Xiao-Hong

    2009-01-01

    This paper reports that the K x-ray spectra of the thin target 47Ag,48Cd,49In and 50Sn were measured by an HPGe semi-conductor detector in collisions with 84.5 MeV 6C4+ ions.Our experiment revealed the Kα x-ray energy shifts were not obvious and the Kβ1 x-ray energy shifts were about 90~110 eV.The simple model of Burch et al has been previously used to calculate the K x-ray energy shifts due to an additional vacancy in 2p orbit.The present work extends the model of Butch to calculate the x-ray energy shifts of multiple ionized atoms induced by heavy ions with kinetic energy of MeV/u.In addition to our experimental results,many other experimental results are compared with the calculated values by using the model.

  5. Contact and dipolar contributions to lanthanide-induced NMR shifts of amino acid and peptide models for calcium binding sites in proteins

    Science.gov (United States)

    Shelling, Judith G.; Bjornson, Michele E.; Hodges, Robert S.; Taneja, Ashok K.; Sykes, Brian D.

    1H nuclear magnetic resonance has been employed to study the binding of Nα-acetyl- L-aspartic acid and Nα-acetyl- L-aspartyl- L-glycyl- L-aspartylamide to the series of six lanthanide ions Dy 3+ through Lu 3+. Values for the dissociation constants and the maximum lanthanide-induced shifts were obtained by fitting the titration data for each metal ion to appropriate binding curves. The shifts were separated into contact and dipolar terms without prior knowledge of the symmetry of the complex or the orientation of the principle axis system of the magnetic susceptibility tensor. The results indicate the contact shifts in 1H NMR are not always negligible, and that Yb 3+ appears to be the best calcium analog for structural studies when the contact interaction is significant.

  6. The spectral shift function for planar obstacle scattering at low energy

    CERN Document Server

    McGillivray, I E

    2011-01-01

    Let $H$ signify the free non-negative Laplacian on $\\mathbb{R}^2$ and $H_Y$ the non-negative Dirichlet Laplacian on the complement $Y$ of a nonpolar compact subset $K$ in the plane. We derive the low-energy expansion for the Krein spectral shift function (scattering phase) for the obstacle scattering system $\\{\\,H_Y,\\,H\\,\\}$ including detailed expressions for the first three coefficients. We use this to investigate the large time behaviour of the expected volume of the pinned Wiener sausage associated to $K$.

  7. Analysis of Cytosolic Proteins that Bind to the 5' Leader Sequence of the Angiotensin AT1 Receptor by RNA Electromobility Shift Assay.

    Science.gov (United States)

    Wu, Z; Krishnamurthi, K; Mok, K; Sandberg, K

    2001-01-01

    Electromobility shift assays (EMSAs) provide a way to study proteinnucleic acid interactions. This method is based on the observation that the electrophoretic mobility of nucleic acids through polyacrylamide gels is retarded when bound to proteins. The mobility of nucleic acid-protein complexes are thus "shifted" with respect to the free nucleic acids. Typically, the nucleic acids are labeled with (32)P. Once the nucleic acid-protein complexes are separated from free radiolabeled nucleic acids, the electrophoresis is terminated and the gel dried. The radiolabeled nucleic acids in their free and complexed forms are visualized and quantified by phosphor autoradiography or by X-ray autoradiography. DNA-binding proteins are commonly identified by EMSA. EMSA also works well for studying purified RNA-binding proteins (1-3) and this technique is currently being developed for identifying unknown RNA-binding proteins.

  8. Phase-shift analysis of low-energy $\\pi^{\\pm}p$ elastic-scattering data

    CERN Document Server

    Matsinos, E; Oades, G C; Rasche, G; Woolcock, W S

    2006-01-01

    Using electromagnetic corrections previously calculated by means of a potential model, we have made a phase-shift analysis of the $\\pi^\\pm p$ elastic-scattering data up to a pion laboratory kinetic energy of 100 MeV. The hadronic interaction was assumed to be isospin invariant. We found that it was possible to obtain self-consistent databases by removing very few measurements. A pion-nucleon model was fitted to the elastic-scattering database obtained after the removal of the outliers. The model-parameter values showed an impressive stability when the database was subjected to different criteria for the rejection of experiments. Our result for the pseudovector $\\pi N N$ coupling constant (in the standard form) is $0.0733 \\pm 0.0014$. The six hadronic phase shifts up to 100 MeV are given in tabulated form. We also give the values of the s-wave scattering lengths and the p-wave scattering volumes. Big differences in the s-wave part of the interaction were observed when comparing our hadronic phase shifts with t...

  9. 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

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

    Indian Academy of Sciences (India)

    S Haddad

    2013-05-01

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

  11. 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

  12. 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.

  13. Lamb shift in radical-ion pairs produces a singlet-triplet energy splitting in photosynthetic reaction centers

    OpenAIRE

    Vitalis, K. M.; Kominis, I. K.

    2013-01-01

    Radical-ion pairs, fundamental for understanding photosynthesis and the avian magnetic compass, were recently shown to be biological open quantum systems. We here show that the coupling of the radical-pair's spin degrees of freedom to its decohering vibrational reservoir leads to a shift of the radical-pair's magnetic energy levels. The Lamb shift Hamiltonian is diagonal in the singlet-triplet basis, and results in a singlet-triplet energy splitting physically indistinguishable from an exchan...

  14. 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.

  15. 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.

  16. 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)

  17. Smart grids: A paradigm shift on energy generation and distribution with the emergence of a new energy management business model

    Science.gov (United States)

    Cardenas, Jesus Alvaro

    An energy and environmental crisis will emerge throughout the world if we continue with our current practices of generation and distribution of electricity. A possible solution to this problem is based on the Smart grid concept, which is heavily influenced by Information and Communication Technology (ICT). Although the electricity industry is mostly regulated, there are global models used as roadmaps for Smart Grids' implementation focusing on technologies and the basic generation-distribution-transmission model. This project aims to further enhance a business model for a future global deployment. It takes into consideration the many factors interacting in this energy provision process, based on the diffusion of technologies and literature surveys on the available documents in the Internet as well as peer-reviewed publications. Tariffs and regulations, distributed energy generation, integration of service providers, consumers becoming producers, self-healing devices, and many other elements are shifting this industry into a major change towards liberalization and deregulation of this sector, which has been heavily protected by the government due to the importance of electricity for consumers. We propose an Energy Management Business Model composed by four basic elements: Supply Chain, Information and Communication Technology (ICT), Stakeholders Response, and the resulting Green Efficient Energy (GEE). We support the developed model based on the literature survey, we support it with the diffusion analysis of these elements, and support the overall model with two surveys: one for peers and professionals, and other for experts in the field, based on the Smart Grid Carnegie Melon Maturity Model (CMU SEI SGMM). The contribution of this model is a simple path to follow for entities that want to achieve environmental friendly energy with the involvement of technology and all stakeholders.

  18. NMR chemical shift as analytical derivative of the Helmholtz free energy.

    Science.gov (United States)

    Van den Heuvel, Willem; Soncini, Alessandro

    2013-02-07

    We present a theory for the temperature-dependent nuclear magnetic shielding tensor of molecules with arbitrary electronic structure. The theory is a generalization of Ramsey's theory for closed-shell molecules. The shielding tensor is defined as a second derivative of the Helmholtz free energy of the electron system in equilibrium with the applied magnetic field and the nuclear magnetic moments. This derivative is analytically evaluated and expressed as a sum over states formula. Special consideration is given to a system with an isolated degenerate ground state for which the size of the degeneracy and the composition of the wave functions are arbitrary. In this case, the paramagnetic part of the shielding tensor is expressed in terms of the g and A tensors of the electron paramagnetic resonance spin Hamiltonian of the degenerate state. As an illustration of the proposed theory, we provide an explicit formula for the paramagnetic shift of the central lanthanide ion in endofullerenes Ln@C(60), with Ln = Ce(3+), Nd(3+), Sm(3+), Dy(3+), Er(3+), and Yb(3+), where the ground state can be a strongly spin-orbit coupled icosahedral sextet for which the paramagnetic shift cannot be described by previous theories.

  19. Ultrasensitive Characterization of Mechanical Oscillations and Plasmon Energy Shift in Gold Nanorods.

    Science.gov (United States)

    Soavi, Giancarlo; Tempra, Iacopo; Pantano, Maria F; Cattoni, Andrea; Collin, Stéphane; Biagioni, Paolo; Pugno, Nicola M; Cerullo, Giulio

    2016-02-23

    Mechanical vibrational resonances in metal nanoparticles are intensively studied because they provide insight into nanoscale elasticity and for their potential application to ultrasensitive mass detection. In this paper, we use broadband femtosecond pump-probe spectroscopy to study the longitudinal acoustic phonons of arrays of gold nanorods with different aspect ratios, fabricated by electron beam lithography with very high size uniformity. We follow in real time the impulsively excited extensional oscillations of the nanorods by measuring the transient shift of the localized surface plasmon band. Broadband and high-sensitivity detection of the time-dependent extinction spectra enables one to develop a model that quantitatively describes the periodic variation of the plasmon extinction coefficient starting from the steady-state spectrum with only one additional free parameter. This model allows us to retrieve the time-dependent elongation of the nanorods with an ultrahigh sensitivity and to measure oscillation amplitudes of just a few picometers and plasmon energy shifts on the order of 10(-2) meV.

  20. Energy Spectrum of YAG:Cr3+ and Thermal Shifts of Its R Lines

    Institute of Scientific and Technical Information of China (English)

    MADong-Ping; CHENJu-Rong

    2005-01-01

    Traditional ligand-field theory has to be improved by taking into account both “pure electronic” contribution and electron-phonon interaction one (including lattice-vibrational relaxation energy). By means of improved ligand-field theory, R1, R2, R'3 R'2 a, 2, and R1 lines, U band, ground-state zero-field-splitting (GSZFS) and ground-state g factors as well as thermal shifts of R1 line and R2 line of YAG:Cr3+ have been calculated. The results are in very good agreement with the experimental data. In contrast with ruby, the octahedron of ligand oxygen ions surrounding the central Cr3+ ion in YAG:Cr3+ is compressed along the [111] direction. Thus, for YAG:Cr3+ and ruby, the splitting of t23 4 A2 (or t23 2 E) has opposite order, and the trigonal-field parameters of the two crystals have opposite signs. In thermal shifts of R1 and R2 lines of YAG:Cr3+, the temperature-dependent contributions due to EPI are dominant.

  1. 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.

  2. 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.

  3. Transition energies and Stokes shift analysis for In-rich InGaN alloys

    Science.gov (United States)

    Schley, P.; Goldhahn, R.; Winzer, A. T.; Gobsch, G.; Cimalla, V.; Ambacher, O.; Rakel, M.; Cobet, C.; Esser, N.; Lu, H.; Schaff, W. J.

    The absorption and emission properties of In-rich InGaN alloys were studied by spectroscopic ellipsometry and photoluminescence spectroscopy, respectively. Films grown on a GaN buffer layer show a much sharper increase of the imaginary part of the dielectric function around the band gap and a slightly reduced Stokes shift compared to layers grown directly on AlN buffers. It is attributed to a reduced electron concentration and improved structural quality of the films. By fitting the third derivatives of the dielectric functions up to 9.5 eV we determine for the first time the compositional dependences (bowing param-eters) of the transition energies for at least four critical points of the band structure.

  4. Mean-field energy-level shifts and dielectric properties of strongly polarized Rydberg gases

    CERN Document Server

    Zhelyazkova, V; Hogan, S D

    2016-01-01

    Mean-field energy-level shifts arising as a result of strong electrostatic dipole interactions within dilute gases of polarized helium Rydberg atoms have been probed by microwave spectroscopy. The Rydberg states studied had principal quantum numbers $n=70$ and 72, and electric dipole moments of up to 14050 D, and were prepared in pulsed supersonic beams at particle number densities on the order of $10^{8}$ cm$^{-3}$. Comparisons of the experimental data with the results of Monte Carlo calculations highlight effects of the distribution of nearest-neighbor spacings in the pulsed supersonic beams, and the dielectric properties of the strongly polarized Rydberg gases, on the microwave spectra. These observations reflect the emergence of macroscopic electrical properties of the atomic samples when strongly polarized.

  5. Mean-field energy-level shifts and dielectric properties of strongly polarized Rydberg gases

    Science.gov (United States)

    Zhelyazkova, V.; Jirschik, R.; Hogan, S. D.

    2016-11-01

    Mean-field energy-level shifts arising as a result of strong electrostatic dipole interactions within dilute gases of polarized helium Rydberg atoms have been probed by microwave spectroscopy. The Rydberg states studied had principal quantum numbers n =70 and 72, and electric dipole moments of up to 14 050 D, and were prepared in pulsed supersonic beams at particle number densities on the order of 108 cm-3. Comparisons of the experimental data with the results of Monte Carlo calculations highlight effects of the distribution of nearest-neighbor spacings in the pulsed supersonic beams, and the dielectric properties of the strongly polarized Rydberg gases, on the microwave spectra. These observations reflect the emergence of macroscopic electrical properties of the atomic samples when strongly polarized.

  6. Adapting photosynthesis to the near-infrared: non-covalent binding of phycocyanobilin provides an extreme spectral red-shift to phycobilisome core-membrane linker from Synechococcus sp. PCC7335.

    Science.gov (United States)

    Miao, Dan; Ding, Wen-Long; Zhao, Bao-Qing; Lu, Lu; Xu, Qian-Zhao; Scheer, Hugo; Zhao, Kai-Hong

    2016-06-01

    Phycobiliproteins that bind bilins are organized as light-harvesting complexes, phycobilisomes, in cyanobacteria and red algae. The harvested light energy is funneled to reaction centers via two energy traps, allophycocyanin B and the core-membrane linker, ApcE1 (conventional ApcE). The covalently bound phycocyanobilin (PCB) of ApcE1 absorbs near 660 nm and fluoresces near 675 nm. In cyanobacteria capable of near infrared photoacclimation, such as Synechococcus sp. PCC7335, there exist even further spectrally red shifted components absorbing >700 nm and fluorescing >710 nm. We expressed the chromophore domain of the extra core-membrane linker from Synechococcus sp. PCC7335, ApcE2, in E. coli together with enzymes generating the chromophore, PCB. The resulting chromoproteins, PCB-ApcE2(1-273) and the more truncated PCB-ApcE2(24-245), absorb at 700 nm and fluoresce at 714 nm. The red shift of ~40 nm compared with canonical ApcE1 results from non-covalent binding of the chromophore by which its full conjugation length including the Δ3,3(1) double bond is preserved. The extreme spectral red-shift could not be ascribed to exciton coupling: dimeric PCB-ApcE2(1-273) and monomeric-ApcE2(24-245) absorbed and fluoresced similarly. Chromophorylation of ApcE2 with phycoerythrobilin- or phytochromobilin resulted in similar red shifts (absorption at 615 and 711 nm, fluorescence at 628 or 726 nm, respectively), compared to the covalently bound chromophores. The self-assembled non-covalent chromophorylation demonstrates a novel access to red and near-infrared emitting fluorophores. Brightly fluorescent biomarking was exemplified in E. coli by single-plasmid transformation.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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....

  12. 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/.

  13. Condensation on surface energy gradient shifts drop size distribution toward small drops.

    Science.gov (United States)

    Macner, Ashley M; Daniel, Susan; Steen, Paul H

    2014-02-25

    During dropwise condensation from vapor onto a cooled surface, distributions of drops evolve by nucleation, growth, and coalescence. Drop surface coverage dictates the heat transfer characteristics and depends on both drop size and number of drops present on the surface at any given time. Thus, manipulating drop distributions is crucial to maximizing heat transfer. On earth, manipulation is achieved with gravity. However, in applications with small length scales or in low gravity environments, other methods of removal, such as a surface energy gradient, are required. This study examines how chemical modification of a cooled surface affects drop growth and coalescence, which in turn influences how a population of drops evolves. Steam is condensed onto a horizontally oriented surface that has been treated by silanization to deliver either a spatially uniform contact angle (hydrophilic, hydrophobic) or a continuous radial gradient of contact angles (hydrophobic to hydrophilic). The time evolution of number density and associated drop size distributions are measured. For a uniform surface, the shape of the drop size distribution is unique and can be used to identify the progress of condensation. In contrast, the drop size distribution for a gradient surface, relative to a uniform surface, shifts toward a population of small drops. The frequent sweeping of drops truncates maturation of the first generation of large drops and locks the distribution shape at the initial distribution. The absence of a shape change indicates that dropwise condensation has reached a steady state. Previous reports of heat transfer enhancement on chemical gradient surfaces can be explained by this shift toward smaller drops, from which the high heat transfer coefficients in dropwise condensation are attributed to. Terrestrial applications using gravity as the primary removal mechanism also stand to benefit from inclusion of gradient surfaces because the critical threshold size required for

  14. Pressure-Induced Shifts of Energy Spectra of α-Al2O3:Mn4+

    Institute of Scientific and Technical Information of China (English)

    MA Dong-Ping,; CHEN Ju-Rong; MA Ning

    2002-01-01

    By making use of the diagonalization of the complete d3 energy matrix in a trigonally distorted cubic-field and the theory of pressure-induced shifts (PS) of energy spectra, the whole energy spectrum of α-Al2 O3 :Mn4+ and PS of levels have been calculated. All the calculated results are in excellent agreement with the experimental data. The comparison between the results ofα-AlO3:Mn4+ and ruby has been made. It is found that on one hand, R1-line and R2line PS of α-Al2O3:Mn4+ and ruby are linear in pressure over 0 ~ 100 kbar, and their values of the principal parameter for PS are very close to each other. On the other hand, the sensitivities of R1-line and R2-line PS of α-Al2O3:Mn4+are higher than those of ruby respectively, which comes mainly from the difference between the values of parameters at normal pressure of two crystals; moreover, the expansion ofd-electron wavefunctions of α-Al2 O3 :Mn4+ with compression is slightly larger than the one of ruby, and the effective charge experienced by d-electrons of α-Al2O3:Mn4+ decreases with compression more rapidly than the one of ruby. In the final analysis, all these can be explained in terms of the facts that the two crystals are doped α-Al2O3 with two isoelectronic ions; the strengths of the crystal field and covalency of α-Al2O3 :Mn4+ are larger than those of ruby respectively, due to the charge of Mn4+ to be larger than that of Cr3+.

  15. Shifts in the myosin heavy chain isozymes in the mouse heart result in increased energy efficiency

    Science.gov (United States)

    Hoyer, Kirsten; Krenz, Maike; Robbins, Jeffrey; Ingwall, Joanne S.

    2007-01-01

    Cardiac-specific transgenesis in the mouse is widely used to study the basic biology and chemistry of the heart and to model human cardiovascular disease. A fundamental difference between mouse and human hearts is the background motor protein: mouse hearts contain predominantly the αα-myosin heavy chain (MyHC) isozyme while human hearts contain predominantly the ββ-MyHC isozyme. Although the intrinsic differences in mechanical and enzymatic properties of the αα- and ββ-MyHC molecules are well known, the consequences of isozyme shifts on energetic of the intact beating heart remain unknown. Therefore, we compared the free energy of ATP hydrolysis (|ΔG~ATP|) determined by 31P NMR spectroscopy in isolated perfused littermate mouse hearts containing the same amount of myosin comprised of either >95% αα-MyHC or ~83% ββ-MyHC. |ΔG~ATP| was ~2 kJ mol−1 higher in the ββ-MyHC hearts at all workloads. Furthermore, upon inotropic challenge, hearts containing predominantly ββ-MyHC hearts increased developed pressure more than αα-MyHC hearts whereas heart rate increased more in αα-MyHC hearts. Thus, hearts containing predominantly the ββ-MyHC isozyme are more energy efficient than αα-MyHC hearts. We suggest that these fundamental differences in the motor protein energy efficiency at the whole heart level should be considered when interpreting results using mouse-based cardiovascular modeling of normal and diseased human heart. PMID:17054980

  16. 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.

  17. 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.

  18. 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.

  19. NMR chemical shift as analytical derivative of the Helmholtz free energy

    CERN Document Server

    Heuvel, Willem Van den

    2012-01-01

    We present a theory for the temperature-dependent nuclear magnetic shielding tensor of molecules with arbitrary electronic structure. The theory is a generalization of Ramsey's theory for closed-shell molecules. The shielding tensor is defined as a second derivative of the Helmholtz free energy of the electron system in equilibrium with the applied magnetic field and the nuclear magnetic moments. This derivative is analytically evaluated and expressed as a sum over states formula. Special consideration is given to a system with an isolated degenerate ground state for which the size of the degeneracy and the composition of the wave functions are arbitrary. In this case the paramagnetic part of the shielding tensor is expressed in terms of the $g$ and $A$ tensors of the EPR spin Hamiltonian of the degenerate state. As an illustration of the proposed theory, we provide an explicit formula for the paramagnetic shift of the central lanthanide ion in endofullerenes Ln@C$_{60}$, with Ln=Ce$^{3+}$, Nd$^{3+}$, Sm$^{3+...

  20. 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.

  1. 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...

  2. Modal shifts in short-haul passenger travel and the consequent energy impacts. [Intercity travel under 500 miles

    Energy Technology Data Exchange (ETDEWEB)

    1980-03-01

    A study was performed to evaluate the impacts of strategies to effect modal shifts in short-haul passenger travel (defined herein as intercity travel under 500 miles) from energy-intensive modes to those modes that are less energy-intensive. A series of individual strategies, ranging from incentives to the less energy-intensive modes (bus, rail) to penalties to the more energy-intensive modes (auto, air) was examined to determine energy saved and policy implications relative to strategy implementation. The most effective of the individual strategies were then combined in all permutations, and the analysis was repeated. As part of the analytical process, effects of factors other than energy (user cost and time, emissions, government subsidy, and travel fatailities) were examined in a benefit/cost analysis. Finally, energy savings, benefit/cost impacts, implementation considerations, and policy implications were evaluated to arrive at conclusions as to the effectiveness of the more-influential strategies and to the overall effectiveness of induced modal shifts. The principal conclusion of the study is that the maximum 1980 energy saving that might be realized by modal shifts, discounting the concurrent effects of demand suppression and improvement of mode efficiency, is approximately 83 x 10/sup 12/ Btu (46,500 bbl gasoline per day), 3.8% of the total projected 1980 energy consumption in the short-haul transportation sector and 0.23% of the total US petroleum use. It was also concluded that strategies to achieve these small savings by modal shifts would result in significant economic, social, and business disruptions.

  3. 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.

  4. 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.

  5. 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.

  6. Using Electrophoretic Mobility Shift Assays to Measure Equilibrium Dissociation Constants: GAL4-p53 Binding DNA as a Model System

    Science.gov (United States)

    Heffler, Michael A.; Walters, Ryan D.; Kugel, Jennifer F.

    2012-01-01

    An undergraduate biochemistry laboratory experiment is described that will teach students the practical and theoretical considerations for measuring the equilibrium dissociation constant (K[subscript D]) for a protein/DNA interaction using electrophoretic mobility shift assays (EMSAs). An EMSA monitors the migration of DNA through a native gel;…

  7. Regional Differences in Muscle Energy Metabolism in Human Muscle by 31P-Chemical Shift Imaging.

    Science.gov (United States)

    Kime, Ryotaro; Kaneko, Yasuhisa; Hongo, Yoshinori; Ohno, Yusuke; Sakamoto, Ayumi; Katsumura, Toshihito

    2016-01-01

    Previous studies have reported significant region-dependent differences in the fiber-type composition of human skeletal muscle. It is therefore hypothesized that there is a difference between the deep and superficial parts of muscle energy metabolism during exercise. We hypothesized that the inorganic phosphate (Pi)/phosphocreatine (PCr) ratio of the superficial parts would be higher, compared with the deep parts, as the work rate increases, because the muscle fiber-type composition of the fast-type may be greater in the superficial parts compared with the deep parts. This study used two-dimensional 31Phosphorus Chemical Shift Imaging (31P-CSI) to detect differences between the deep and superficial parts of the human leg muscles during dynamic knee extension exercise. Six healthy men participated in this study (age 27±1 year, height 169.4±4.1 cm, weight 65.9±8.4 kg). The experiments were carried out with a 1.5-T superconducting magnet with a 5-in. diameter circular surface coil. The subjects performed dynamic one-legged knee extension exercise in the prone position, with the transmit-receive coil placed under the right quadriceps muscles in the magnet. The subjects pulled down an elastic rubber band attached to the ankle at a frequency of 0.25, 0.5 and 1 Hz for 320 s each. The intracellular pH (pHi) was calculated from the median chemical shift of the Pi peak relative to PCr. No significant difference in Pi/PCr was observed between the deep and the superficial parts of the quadriceps muscles at rest. The Pi/PCr of the superficial parts was not significantly increased with increasing work rate. Compared with the superficial areas, the Pi/PCr of the deep parts was significantly higher (p<0.05) at 1 Hz. The pHi showed no significant difference between the two parts. These results suggest that muscle oxidative metabolism is different between deep and superficial parts of quadriceps muscles during dynamic exercise.

  8. 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.

  9. Distributed energy resources management using plug-in hybrid electric vehicles as a fuel-shifting demand response resource

    DEFF Research Database (Denmark)

    Morais, Hugo; Sousa, Tiago; Soares, J.

    2015-01-01

    In the smart grids context, distributed energy resources management plays an important role in the power systems' operation. Battery electric vehicles and plug-in hybrid electric vehicles should be important resources in the future distribution networks operation. Therefore, it is important...... to develop adequate methodologies to schedule the electric vehicles' charge and discharge processes, avoiding network congestions and providing ancillary services.This paper proposes the participation of plug-in hybrid electric vehicles in fuel shifting demand response programs. Two services are proposed......, namely the fuel shifting and the fuel discharging. The fuel shifting program consists in replacing the electric energy by fossil fuels in plug-in hybrid electric vehicles daily trips, and the fuel discharge program consists in use of their internal combustion engine to generate electricity injecting...

  10. Physical Activity, Energy Expenditure, Nutritional Habits, Quality of Sleep and Stress Levels in Shift-Working Health Care Personnel

    Science.gov (United States)

    Vogt, Lena Johanna; Gärtner, Simone; Hannich, Hans Joachim; Steveling, Antje; Lerch, Markus M.

    2017-01-01

    Background Among health care personnel working regular hours or rotating shifts can affect parameters of general health and nutrition. We have investigated physical activity, sleep quality, metabolic activity and stress levels in health care workers from both groups. Methods We prospectively recruited 46 volunteer participants from the workforce of a University Medical Department of which 23 worked in rotating shifts (all nursing) and 21 non-shift regular hours (10 nursing, 13 clerical staff). All were investigated over 7 days by multisensory accelerometer (SenseWear Bodymedia® armband) and kept a detailed food diary. Physical activity and resting energy expenditure (REE) were measured in metabolic equivalents of task (METs). Quality of sleep was assessed as Pittsburgh Sleeping Quality Index and stress load using the Trier Inventory for Chronic Stress questionnaire (TICS). Results No significant differences were found for overall physical activity, steps per minute, time of exceeding the 3 METs level or sleep quality. A significant difference for physical activity during working hours was found between shift-workers vs. non-shift-workers (ppersonnel (median = 1.5 METs SE = 0.07, p<0.05). Non-shift-working nurses had a significantly lower REE than the other groups (p<0.05). The proportion of fat in the diet was significantly higher (p<0.05) in the office worker group (median = 42% SE = 1.2) whereas shift-working nurses consumed significantly more carbohydrates (median = 46% SE = 1.4) than clerical staff (median = 41% SE = 1.7). Stress assessment by TICS confirmed a significantly higher level of social overload in the shift working group (p<0.05). Conclusion In this prospective cohort study shift-working had no influence on overall physical activity. Lower physical activity during working hours appears to be compensated for during off-hours. Differences in nutritional habits and stress load warrant larger scale trials to determine the effect on implicit health

  11. Chemical shift as a probe of molecular interfaces: NMR studies of DNA binding by the three amino-terminal zinc finger domains from transcription factor IIIA

    Energy Technology Data Exchange (ETDEWEB)

    Foster, Mark P.; Wuttke, Deborah S.; Clemens, Karen R.; Jahnke, Wolfgang; Radhakrishnan, Ishwar; Tennant, Linda; Reymond, Martine; Chung, John; Wright, Peter E. [Scripps Research Institute, Department of Molecular Biology and Skaggs Institute for Chemical Biology (United States)

    1998-07-15

    We report the NMR resonance assignments for a macromolecular protein/DNA complex containing the three amino-terminal zinc fingers (92 amino acid residues) of Xenopus laevis TFIIIA (termed zf1-3) bound to the physiological DNA target (15 base pairs), and for the free DNA. Comparisons are made of the chemical shifts of protein backbone{sup 1} H{sup N}, {sup 15}N,{sup 13} C{sup {alpha}} and{sup 13} C{sup {beta}} and DNA base and sugar protons of the free and bound species. Chemical shift changes are analyzed in the context of the structures of the zf1-3/DNA complex to assess the utility of chemical shift change as a probe of molecular interfaces. Chemical shift perturbations that occur upon binding in the zf1-3/DNA complex do not correspond directly to the structural interface, but rather arise from a number of direct and indirect structural and dynamic effects.

  12. Energy Shift Caused by Non-isotropy of 2-Dimensional Anisotropic Quantum Dot in Presence of Uniform Magnetic Field

    Institute of Scientific and Technical Information of China (English)

    FAN Hong-Yi; XU Xue-Fen

    2005-01-01

    Based on the squeezing mechanism in quantum dots in the presence of uniform magnetic field, we derive the energy shift caused by the non-isotropy of 2-dimensional anisotropic quantum dot. We also study sudden squeezing of the size of the quantum dot. The whole discussion is proceeded smoothly by virtue of the entangled state representation.

  13. 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.

  14. Electromobility Shift Assay Reveals Evidence in Favor of Allele-Specific Binding of RUNX1 to the 5' Hypersensitive Site 4-Locus Control Region.

    Science.gov (United States)

    Dehghani, Hossein; Ghobakhloo, Sepideh; Neishabury, Maryam

    2016-08-01

    In our previous studies on the Iranian β-thalassemia (β-thal) patients, we identified an association between the severity of the β-thal phenotype and the polymorphic palindromic site at the 5' hypersensitive site 4-locus control region (5'HS4-LCR) of the β-globin gene cluster. Furthermore, a linkage disequilibrium was observed between this region and XmnI-HBG2 in the patient population. Based on this data, it was suggested that the well-recognized phenotype-ameliorating role assigned to positive XmnI could be associated with its linked elements in the LCR. To investigate the functional significance of polymorphisms at the 5'HS4-LCR, we studied its influence on binding of transcription factors. Web-based predictions of transcription factor binding revealed a binding site for runt-related transcription factor 1 (RUNX1), when the allele at the center of the palindrome (TGGGG(A/G)CCCCA) was A but not when it was G. Furthermore, electromobility shift assay (EMSA) presented evidence in support of allele-specific binding of RUNX1 to 5'HS4. Considering that RUNX1 is a well-known regulator of hematopoiesis, these preliminary data suggest the importance of further studies to confirm this interaction and consequently investigate its functional and phenotypical relevance. These studies could help us to understand the molecular mechanism behind the phenotype modifying role of the 5'HS4-LCR polymorphic palindromic region (rs16912979), which has been observed in previous studies.

  15. Blue and red shifts of interband transition energy in supported Au nanoclusters on SiO2 and HOPG investigated by reflection electron energy-loss spectroscopy.

    Science.gov (United States)

    Borisyuk, P V; Troyan, V I; Pushkin, M A; Borman, V D; Tronin, V N

    2012-11-01

    Gold nanoclusters supported on SiO2 and HOPG are experimentally investigated by the reflection electron energy-loss spectroscopy. Two different trends in the size-dependence of the position of the energy-loss peak corresponding to the interband Au 5d --> 6s6p transition is observed: a blue shift for Au clusters on SiO2 and a red shift for Au clusters on HOPG. The different behaviors are qualitatively explained by the influence of the substrate on the spectrum of electronic states in Au nanoclusters.

  16. Gold nanoparticles generated through "green route" bind Hg2+ with a concomitant blue shift in plasmon absorption peak.

    Science.gov (United States)

    Radhakumary, C; Sreenivasan, K

    2011-07-21

    We discuss here a quick, simple, economic and ecofriendly method through a completely green route for the selective detection of Hg(2+) in aqueous samples. Here we exploited the ability of chitosan to generate gold nanoparticles and subsequently to act as a stabilizer for the formed nanoparticles. When chitosan stabilized gold nanoparticles (CH-Au NPs) are interacted with Hg(2+) a blue shift for its localized surface plasmon resonance absorbance (LSPR) band is observed. The blue shift is reasoned to be due to the formation of a thin layer of mercury over gold. A concentration as low as 0.01 ppm to a maximum of 100 ppm Hg(2+) can be detected based on this blue shift of the CH-Au NPs. While all other reported methods demand complex reaction steps and costly chemicals, the method we reported here is a simple, rapid and selective approach for the detection of Hg(2+). Our results also show that the CH-Au NPs have excellent selectivity to Hg(2+) over common cations namely, Pb(2+), Cd(2+), Mn(2+), Fe(2+), Ag(1+), Ce(4+), Ni(2+), and Cu(2+).

  17. 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.

  18. Highly emitting near-infrared lanthanide "encapsulated sandwich" metallacrown complexes with excitation shifted toward lower energy.

    Science.gov (United States)

    Trivedi, Evan R; Eliseeva, Svetlana V; Jankolovits, Joseph; Olmstead, Marilyn M; Petoud, Stéphane; Pecoraro, Vincent L

    2014-01-29

    Near-infrared (NIR) luminescent lanthanide complexes hold great promise for practical applications, as their optical properties have several complementary advantages over organic fluorophores and semiconductor nanoparticles. The fundamental challenge for lanthanide luminescence is their sensitization through suitable chromophores. The use of the metallacrown (MC) motif is an innovative strategy to arrange several organic sensitizers at a well-controlled distance from a lanthanide cation. Herein we report a series of lanthanide “encapsulated sandwich” MC complexes of the form Ln3+ [12-MC(Zn(II),quinHA)-4]2[24-MC(Zn(II),quinHA)-8] (Ln3+ [Zn(II)MC(quinHA)]) in which the MC framework is formed by the self-assembly of Zn2+ ions and tetradentate chromophoric ligands based on quinaldichydroxamic acid (quinHA). A first-generation of luminescent MCs was presented previously but was limited due to excitation wavelengths in the UV. We report here that through the design of the chromophore of the MC assembly, we have significantly shifted the absorption wavelength toward lower energy (450 nm). In addition to this near-visible inter- and/or intraligand charge transfer absorption, Ln3+ [Zn(II)MC(quinHA)] exhibits remarkably high quantum yields, long luminescence lifetimes (CD3OD; Yb3+, QLn(L) = 2.88(2)%, τobs = 150.7(2) μs; Nd3+, QLn(L) = 1.35(1)%, τobs = 4.11(3) μs; Er3+, QLn(L) = 3.60(6)·10–2%, τobs = 11.40(3) μs), and excellent photostability. Quantum yields of Nd3+ and Er3+ MCs in the solid state and in deuterated solvents, upon excitation at low energy, are the highest values among NIR-emitting lanthanide complexes containing C–H bonds. The versatility of the MC strategy allows modifications in the excitation wavelength and absorptivity through the appropriate design of the ligand sensitizer, providing a highly efficient platform with tunable properties.

  19. 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.

  20. 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.

  1. 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.

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

    Science.gov (United States)

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

    2016-07-29

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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Energy flux pattern of inverse Goos-Hanchen shift in photonic crystals with negative index of refraction

    CERN Document Server

    Hu, Jinbing; Chen, Jiabi; Jiang, Qiang; Wang, Yan; Zhuang, Songlin

    2015-01-01

    The energy flux patterns of inverse Goos-Hanchen (GH) shift around the interface between air and negatively refractive photonic crystal (NRPhC) with different surface terminations is investigated. Results show that NRPhC exhibits inverse GH shift in TM and TE polarization, and the localization and pattern of energy flux differ in TM and TE polarizations and are strongly affected by surface termination. This is different to the condition of negative permittivity materials (i.e., metal), which only presents inverse GH shift in TM polarization. In the case of TE polarization, the energy flux pattern exhibits the flux of backward wave whose localization changes from the surface to inside of NRPhC with the variation of surface termination. In the case of TM polarization, the energy flux pattern is always confined within the surface of NRPhC, whereas its pattern changes from the flux of backward wave to vortices at the surface of NRPhC, which is different to the energy flux of TM polarization of metal. By properly ...

  8. $\\mu-H$ Lamb shift: dispersing the nucleon-excitation uncertainty with a finite energy sum rule

    CERN Document Server

    Gorchtein, Mikhail; Szczepaniak, Adam P

    2013-01-01

    We assess the two-photon exchange contribution to the Lamb shift in muonic hydrogen with forward dispersion relations. The subtraction constant $\\bar T(0,Q^2)$ that is necessary for a dispersive evaluation of the forward doubly-virtual Compton amplitude, through a finite energy sum rule, is related to the fixed J=0 pole generalized to the case of virtual photons. We evaluated this sum rule using excellent virtual photoabsorption data that are available. We find that the "proton polarizability correction" to the Lamb shift in muonic hydrogen is $-(40\\pm5)\\mu$eV. We conclude that nucleon structure-dependent uncertainty by itself is unlikely to resolve the large (300$\\mu$eV) discrepancy between direct measurement of the Lamb shift in $\\mu H$ and expectations based on conventional Hydrogen measurements.

  9. 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.

  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. 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)

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. What if solar energy becomes really cheap? A thought experiment on environmental problem shifting

    NARCIS (Netherlands)

    Bergh, Van den Jeroen; Folke, Carl; Polasky, Stephen; Scheffer, Marten; Steffen, Will

    2015-01-01

    Solving one environmental problem may often invoke or intensify another one. Such environmental problem shifting (EPS) is a neglected topic in global sustainability research. Indeed, it is difficult to study as it requires the merging of insights from various research areas. Here we identify rele

  17. 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.

  18. 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.

  19. What role for microgeneration in a shift to a low carbon domestic energy sector in the UK?

    Energy Technology Data Exchange (ETDEWEB)

    Bergman, N.; Eyre, N. [Environmental Change Institute, School of Geography and Environment, University of Oxford, South Parks Road, Oxford, OX1 3QY (United Kingdom)

    2011-06-15

    Domestic energy use accounts for more than a quarter of CO2 emissions in the UK. Traditional approaches to energy reduction look at direct emissions savings, and recommend insulation and efficiency as more cost-effective than microgeneration. However, microgeneration has indirect, 'soft' benefits and could play a significant role in emissions reduction. Current uptake of microgeneration in the UK is low, with various barriers-economic, technical, cultural, behavioural and institutional-both to uptake and to maximising energy and emissions savings once installed. Subsidies and spreading information alone do not guarantee maximising uptake, and even if successful, this is not enough to maximise savings. The industry focuses on maximising sales, with no incentives to ensure best installations and use; householders do not have access to the best information, and user behaviour does not maximise energy and emission savings. This is related to a broader state of socio-technical 'lock-in' in domestic energy use; there's a lack of connection between personal behaviour and energy consumption, let alone global climate change. This suggests that a major cultural-behavioural shift is needed to reduce energy/emissions in the home. Transition theory and strategic niche management provide insights into possible systemic change and a suitable framework for future policies, such as supporting a variety of radically innovative niches, both technological and social. Microgeneration, properly employed, has the potential to play a part in such a transition by increasing awareness and energy literacy and empowering people to seriously engage in energy debates as producers, as well as consumers, of energy. This deeper understanding and heightened responsibility are crucial in a shift toward bottom-up emission-reducing behaviour change and better acceptance of top-down energy-saving policy measures, as part of a new domestic energy paradigm. The implications for

  20. A bibliometric analysis of recent energy efficiency literatures. An expanding and shifting focus

    Energy Technology Data Exchange (ETDEWEB)

    Du, Huibin; Wei, Linxue; Wang, Yangyang [College of Management and Economics, Tianjin University, 300072 Tianjin (China); Brown, M.A. [School of Public Policy, Georgia Institute of Technology, Atlanta, 30332, GA (United States); Shi, Zheng [Department of Industrial and Systems Engineering, Lehigh University, Bethlehem, 18015, PA (United States)

    2013-02-15

    To meet the energy requirements of sustainable economic growth, policymakers, analysts, and business leaders have increasingly turned to the role that energy efficiency might play. This has resulted in a growing energy efficiency literature, which is examined in this paper. Using bibliometric techniques, we analyze the database of Science Citation Index Expanded and Social Sciences Citation Index covering the 1991-2010 period. Of the 8,244 publications, 78.8 % were journal articles, and about 95.5 % were published in English. Based on the h-index, an evaluative indicator, the USA has produced the most influential set of publications on energy efficiency, followed by Canada, UK, Japan, and China. In contrast, China is second to the USA in the volume of its publications. Correspondingly, the University of California at Berkeley, Chinese Academy of Sciences, and Tsinghua University were the most productive research organizations. The three most common subjects examined in this body of research were 'energy and fuels', 'environmental sciences', and 'electrical and electronic engineering'. Energy Policy has been the most productive journal, and 'A water and heat management model for proton-exchange-membrane fuel-cells', has had the most citations (587 through May 2012). Based on an analysis of article titles and keywords, we conclude that the hotspots of energy efficiency research have been green communications, renewable energy, and energy sustainability; green communications, in particular, has developed rapidly as a focus of energy efficiency publications in recent years.

  1. 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...

  2. 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...

  3. Effect of temperature-dependent energy-level shifts on a semiconductor's Peltier heat

    Science.gov (United States)

    Emin, David

    1984-11-01

    The Peltier heat of a charge carrier in a semiconductor is calculated for the situation in which the electronic energy levels are temperature dependent. The temperature dependences of the electronic energy levels, generally observed optically, arise from their dependences on the vibrational energy of the lattice (e.g., as caused by thermal expansion). It has been suggested that these temperature dependences will typically have a major effect on the Peltier heat. The Peltier heat associated with a given energy level is a thermodynamic quantity; it is the product of the temperature and the change of the entropy of the system when a carrier is added in that level. As such, the energy levels cannot be treated as explicitly temperature dependent. The electron-lattice interaction causing the temperature dependence must be expressly considered. It is found that the carrier's interaction with the atomic vibrations lowers its electronic energy. However, the interaction of the carrier with the atomic vibrations also causes an infinitesimal lowering (~1N) of each of the N vibrational frequencies. As a result, there is a finite carrier-induced increase in the average vibrational energy. Above the Debye temperature, this cancels the lowering of the carrier's electronic energy. Thus, the standard Peltier-heat formula, whose derivation generally ignores the temperature dependence of the electronic energy levels, is regained. This explains the apparent success of the standard formula in numerous analyses of electronic transport experiments.

  4. Load Shifting Control and Management of Domestic Microgeneration Systems for Improved Energy Efficiency and Comfort

    DEFF Research Database (Denmark)

    Anvari-Moghaddam, Amjad; Quintero, Juan Carlos Vasquez; Guerrero, Josep M.

    2015-01-01

    . Moreover, the superior performance of the proposed energy management system is shown in comparison with the conventional models. The numerical results also indicate that through wise management of demand and generation sides, there is a possibility to reduce domestic energy use and improve the user......In this paper, an intelligent energy management system based on energy saving and user’s comfort is introduced and applied to a residential smart home as a case study. The proposed multi-objective mixed-integer nonlinear programming (MINLP)-based architecture takes the advantages of several key...

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. The Role of Private Actors in Offshore Energy : Shifting Models of Participation

    NARCIS (Netherlands)

    Trevisanut, Seline

    2014-01-01

    The role of private actors in the offshore energy industry has expanded with regard to both the law-making processes and the implementation of the relevant legal framework. This article critically examines the role private actors are playing in the offshore energy sector in order to delineate some t

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  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. The Shifting Landscape of Ratepayer-Funded Energy Efficiency in the U.S.

    Energy Technology Data Exchange (ETDEWEB)

    Barbose, Galen L; Goldman, Charles; Schlegel, Jeff

    2009-07-13

    Over the last two decades, utility ratepayer funding for energy efficiency programs - and the associated energy savings - has seen both booms and busts. Currently, about 35 states implement ratepayer-funded energy efficiency programs, with a total U.S. budget of $3.1 billion in 2008, approximately 80% of which is concentrated in just ten states (CEE 2008).2 However, a proliferation of new state-level policies enacted over the past several years suggests that the next decade may see a dramatic and sustained increase in overall funding levels, and a fundamental re-drawing of the energy efficiency map. These new state energy efficiency policies reflect a variety of concerns, including the increasing cost and siting challenges of building new generation and transmission, fuel cost and supply risks, and the potential cost of future carbon regulations. Within the past three years, for example, eleven states have adopted energy efficiency portfolio (or resource) standards (EEPS or EERS) that establish specific long-term savings targets that utilities are obligated to meet, and at least three other states are currently considering the same. A growing number of states have recently established laws requiring utilities to acquire all available cost-effective energy efficiency. Regulators in several Western states have also recently revised integrated resource planning (IRP) and demand-side management (DSM) planning rules to require more robust analysis of the resource potential and benefits of energy efficiency, which has resulted in increased savings targets for their energy efficiency portfolios (Hopper et al. 2008). Finally, regulators and utilities in many states are beginning to look more closely at regulatory incentive mechanisms to better align utility financial interests with improvements in customer energy efficiency. We examined energy efficiency policies on the books or in the pipeline in all 50 states, along with recent IRPs and DSM plans, and developed low

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. An encodable lanthanide binding tag with reduced size and flexibility for measuring residual dipolar couplings and pseudocontact shifts in large proteins

    Energy Technology Data Exchange (ETDEWEB)

    Barb, Adam W., E-mail: abarb@iastate.edu; Subedi, Ganesh P. [Iowa State University, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology (United States)

    2016-01-15

    Metal ions serve important roles in structural biology applications from long-range perturbations seen in magnetic resonance experiments to electron-dense signatures in X-ray crystallography data; however, the metal ion must be secured in a molecular framework to achieve the maximum benefit. Polypeptide-based lanthanide-binding tags (LBTs) represent one option that can be directly encoded within a recombinant protein expression construct. However, LBTs often exhibit significant mobility relative to the target molecule. Here we report the characterization of improved LBTs sequences for insertion into a protein loop. These LBTs were inserted to connect two parallel alpha helices of an immunoglobulin G (IgG)-binding Z domain platform. Variants A and B bound Tb{sup 3+} with high affinity (0.70 and 0.13 μM, respectively) and displayed restricted LBT motion. Compared to the parent construct, the metal-bound A experienced a 2.5-fold reduction in tag motion as measured by magnetic field-induced residual dipolar couplings and was further studied in a 72.2 kDa complex with the human IgG1 fragment crystallizable (IgG1 Fc) glycoprotein. The appearance of both pseudo-contact shifts (−0.221 to 0.081 ppm) and residual dipolar couplings (−7.6 to 14.3 Hz) of IgG1 Fc resonances in the IgG1 Fc:(variant A:Tb{sup 3+}){sub 2} complex indicated structural restriction of the LBT with respect to the Fc. These studies highlight the applicability of improved LBT sequences with reduced mobility to probe the structure of macromolecular systems.

  9. The Soviet-West European Energy Relationship: Implications of the Shift from Oil to Gas,

    Science.gov (United States)

    1983-06-01

    currency energy exports. (- RESUME Ce rapport examine d’une perspective historique les exportations soviftiques de p6trole et de gaz naturel vers...on shipment of graink phosphates and goods destined for the 1980 Olympic games. With the support of Senator -enrv Jackson, Zbigniew Brzezinski had

  10. 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.

  11. 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.``

  12. 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.

  13. 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.

  14. 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.

  15. Deep layer-resolved core-level shifts in the beryllium surface

    DEFF Research Database (Denmark)

    Aldén, Magnus; Skriver, Hans Lomholt; Johansson, Börje

    1993-01-01

    Core-level energy shifts for the beryllium surface region are calculated by means of a Green’s function technique within the tight-binding linear muffin-tin orbitals method. Both initial- and final-state effects in the core-ionization process are fully accounted for. Anomalously large energy shifts...

  16. 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.

  17. 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.

  18. Seasonal shifting of surplus renewable energy in a power system located in a cold region

    Directory of Open Access Journals (Sweden)

    Jorge Morel

    2014-10-01

    Full Text Available The Fukushima nuclear disaster in 2011 changed Japan's strategy for reducing CO2 emissions. The government is now placing more emphasis on the development of nonCO2-emitting distributed generation systems such as wind, solar, and tidal power to reduce greenhouse gas emissions and guarantee electricity supply in the case of a natural disaster. This paper proposes a strategy for the exploitation of wind, solar, and tidal resources in a cold region in Japan by utilizing surplus energy from the summer and spring during winter. It also aims to determine the most favorable energy mix of these renewable sources and storage system types. The study is performed by calculating hourly demand and renewable energy supply for the city in one year, which is based on actual data of demand, solar irradiation, wind speeds, and tidal current speeds. The costs of the components of the renewable power plants and storage systems are considered, and different proportions of generation outputs are evaluated with different types of storage systems. According to results, the configuration containing the hydrogen storage system using organic chemical hydride methylcyclohexane (OCHM is the most economical but is still more expensive than one using a conventional generation system. Moreover, we confirm that the cost of CO2 emissions is the key element for leveling the playing field between conventional and renewable generation from an economic perspective. The cost of CO2 emissions to public health as well as those costs related to the interruption of services during a catastrophe must be carefully calculated with other issues from conventional power projects to perform a precise comparative evaluation between both types of generation systems.

  19. Energy shifts of K- and L-lines as spectroscopic diagnostic of Z-pinch plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Słabkowska, K.; Szymańska, E.; Polasik, M. [Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń (Poland); Rzadkiewicz, J. [National Centre for Nuclear Research, 05-400 Otwock (Poland); Syrocki, Ł. [Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, 87-100 Toruń (Poland); Pereira, N. R., E-mail: ninorpereira@gmail.com [Ecopulse, Inc., Springfield, VA, 22152 (United States)

    2014-12-15

    Ultrafast molybdenum wire implosions on the Z machine at Sandia produce intense pulses of multi-keV x-rays from partially ionized plasmas. The most intense radiation comes from a hot, dense core of thermal plasma in ionization equilibrium with Mo ionized to within the L-shell. Non-thermal, energetic electrons in the plasma generate Kα and Kβ radiation, whose energy is affected by Mo’s ionization state, and therefore on the plasma temperature. Based on an extensive series of recent computations on this effect, we recalculate the pinch’ Mo x-ray spectrum, with reasonable results.

  20. 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.

  1. 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.

  2. Shift reagents in ion mobility spectrometry: the effect of the number of interaction sites, size and interaction energies on the mobilities of valinol and ethanolamine.

    Science.gov (United States)

    Fernández-Maestre, Roberto; Meza-Morelos, Dairo; Wu, Ching

    2016-05-01

    Overlapping peaks interfere in ion mobility spectrometry (IMS), but they are separated introducing mobility shift reagents (SR) in the buffer gas forming adducts with different collision cross-sections (size). IMS separations using SR depend on the ion mobility shifts which are governed by adduct's size and interaction energies (stabilities). Mobility shifts of valinol and ethanolamine ions were measured by electrospray-ionization ion mobility-mass spectrometry (MS). Methyl-chloro propionate (M) was used as SR; 2-butanol (B) and nitrobenzene (N) were used for comparison. Density functional theory was used for calculations. B produced the smallest mobility shifts because of its small size. M and N have two strong interaction sites (oxygen atoms) and similar molecular mass, and they should produce similar shifts. For both ethanolamine and valinol ions, stabilities were larger for N adducts than those of M. With ethanolamine, M produced a 68% shift, large compared to that using N, 61%, because M has a third weak interaction site on the chlorine atom and, therefore, M has more interaction possibilities than N. This third site overrode the oxygen atoms' interaction energy that favored the adduction of ethanolamine with N over that with M. On the contrary, with valinol mobility shifts were larger with N than with M (21 vs 18%) because interaction energy favored even more adduction of valinol with N than with M; that is, the interaction energy difference between adducts of valinol with M and N was larger than that between those adducts with ethanolamine, and the third M interaction could not override this larger difference. Mobility shifts were explained based on the number of SR's interaction sites, size of ions and SR, and SR-ion interaction energies. This is the first time that the number of interaction sites is used to explain mobility shifts in SR-assisted IMS. Copyright © 2016 John Wiley & Sons, Ltd.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Future energy shifts in historical perspective; Framtida energiomstaellningar i historiskt perspektiv

    Energy Technology Data Exchange (ETDEWEB)

    Kaijser, Arne; Kander, Astrid

    2013-02-15

    The purpose of this report is to summarize the knowledge about historical changes that may be relevant to assess the opportunities and challenges that climate policy faces when it should steer towards future radical changes of infrastructure and energy systems. Scenarios for these transitions and change strategies for implementing them are presented including in the reports 'Two-degree target in sight? Scenarios for Swedish energy and transport by 2050' and 'Choice of path to 2050 - Governance challenges and change strategies for a transition to a carbon constrained society'. In this report, we analyze a number of major changes since the mid-1800s. These changes are of two types: on one hand what we call tailwind changes, on the other hand what we call head wind changes. Tailwind changes have been initiated by fundamental technological innovation and has led to growth opportunities and benefits for both the individual and for the economy. Head wind changes was initiated by crises in the world of various types and can be viewed as the necessity forced conversions where there is in the short and medium term, only losses. Any such change are treated both qualitatively and quantitatively: what institutional conditions were important conditions or obstacles, and how change can be described using different indicators. The main focus is on changes in Sweden, but since these processes are included in international development, we also make outlooks outside Sweden to clarify characteristics in Sweden and to discuss the reasons why some countries were converted faster than others.

  9. 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)

  10. 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.

  11. Ab-inito calculation of energy level alignment and vacuum level shift at CuPc/C60 interfaces

    Science.gov (United States)

    Sai, Na; Zhu, Xiaoyang; Chelikowsky, James; Leung, Kevin

    2012-02-01

    The alignment of the donor and acceptor enegy levels is of crucial importance for organic photovotaic performance. We investigate the interfaical electronic structure and energy level alignment of copper phthalocyanine (CuPc)/fullerene (C60) using ab-inito density functional theory calculations including van der Waals interactions and hybrid density functionals. We show that energy level alignment critically depends on the standing-up and lying-down orientation of the CuPc molecules relative to C60 at the interface. We calculate the magnitude of the interface dipole at different molecular orientations and compare them to the vacuum level shift observed in photoemission spectroscopy. The validity of existing theoretical models which invoke charge transfer on this organic interface will be discussed in light of our predictions. Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Deparment of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  12. Observation of a hole-size-dependent energy shift of the surface-plasmon resonance in Ni antidot thin films

    Energy Technology Data Exchange (ETDEWEB)

    Fang, H.; Akinoglu, E. M.; Fumagalli, P., E-mail: paul.fumagalli@fu-berlin.de [Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin (Germany); Caballero, B.; García-Martín, A. [IMM-Instituto de Microelectrónica de Madrid (CNM-CSIC), Isaac Newton 8, PTM, Tres Cantos, E-28760 Madrid (Spain); Papaioannou, E. Th. [Fachbereich Physik and Landesforschungszentrum OPTIMAS, Technische Universität Kaiserslautern, 67663 Kaiserslautern (Germany); Cuevas, J. C. [Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid (Spain); Giersig, M. [Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin (Germany); Helmholtz Zentrum Berlin, Institute of Nanoarchitectures for Energy Conversion, 14195 Berlin (Germany)

    2015-04-13

    A combined experimental and theoretical study of the magneto-optic properties of a series of nickel antidot thin films is presented. The hole diameter varies from 869 down to 636 nm, while the lattice periodicity is fixed at 920 nm. This results in an overall increase of the polar Kerr rotation with decreasing hole diameter due to the increasing surface coverage with nickel. In addition, at photon energies of 2.7 and 3.3 eV, where surface-plasmon excitations are expected, we observe distinct features in the polar Kerr rotation not present in continuous nickel films. The spectral position of the peaks exhibits a red shift with decreasing hole size. This is explained within the context of an effective medium theory by a change in the effective dielectric function of the Ni thin films.

  13. Improved Ligand-Field Calculation of Energy Spectrum and R-Line Thermal Shift of MgO:Cr3+

    Institute of Scientific and Technical Information of China (English)

    ZHANG Zheng-Jie; MA Dong-Ping

    2007-01-01

    Traditional ligand-field theory has to be improved by taking into account both pure electronic contribution and electron-phonon interaction one (including lattice-vibrational relaxation energy). By means of improved ligand-field theory, the R-line, t322T1 lines, t22(3T1)e4T2, and t22(3T1)e4T1 bands, ground-state g factor, four strain-induced levelsplittings, and R-line thermalshift of MgO:Cr3+ have been calculated. The results are in very good agreement with the experimental data. It is found that for MgO:Cr3+, the contributions due to electron-phonon interaction (EPI) come from the first-order term. In thermal shift of R-line of MgO:Cr3+, the temperature-dependent contribution due to EPI is dominant.

  14. Novel Moessbauer experiment in a rotating system and the extra-energy shift between emission and absorption lines

    CERN Document Server

    Yarman, T; Arik, M; Akkus, B; Oktem, Y; Susam, L A; Missevitch, O V

    2015-01-01

    We present the results of a novel Mossbauer experiment in a rotating system, implemented recently in Istanbul University, which yields the coefficient k=0.69+/-0.02 within the frame of the expression for the relative energy shift between emission and absorption lines dE/E=ku2/c2. This result turned out to be in a quantitative agreement with an experiment achieved earlier on the subject matter (A.L. Kholmetskii et al. 2009 Phys. Scr. 79 065007), and once again strongly pointed to the inequality k>0.5, revealed originally in (A.L. Kholmetskii et al. 2008 Phys. Scr. 77, 035302 (2008)) via the re-analysis of Kundig experiment (W. Kundig. Phys. Rev. 129, 2371 (1963)). A possible explanation of the deviation of the coefficient k from the relativistic prediction k=0.5 is discussed.

  15. Shifting primary energy source and NOx emission location with plug-in hybrid vehicles

    Science.gov (United States)

    Karman, Deniz

    2011-06-01

    Plug-in hybrid vehicles (PHEVs) present an interesting technological opportunity for using non-fossil primary energy in light duty passenger vehicles, with the associated potential for reducing air pollutant and greenhouse gas emissions, to the extent that the electric power grid is fed by non-fossil sources. This perspective, accompanying the article by Thompson et al (2011) in this issue, will touch on two other studies that are directly related: the Argonne study (Elgowainy et al 2010) and a PhD thesis from Utrecht (van Vliet 2010). Thompson et al (2011) have examined air quality effects in a case where the grid is predominantly fossil fed. They estimate a reduction of 7.42 tons/day of NOx from motor vehicles as a result of substituting electric VMTs for 20% of the light duty gasoline vehicle miles traveled. To estimate the impact of this reduction on air quality they also consider the increases in NOx emissions due to the increased load on electricity generating units. The NOx emission increases are estimated as 4.0, 5.5 and 6.3 tons for the Convenience, Battery and Night charging scenarios respectively. The net reductions are thus in the 1.1-3.4 tons/day range. The air quality modelling results presented show that the air quality impact from a ground-level ozone perspective is favorable overall, and while the effect is stronger in some localities, the difference between the three scenarios is small. This is quite significant and suggests that localization of the NOx emissions to point sources has a more pronounced effect than the absolute reductions achieved. Furthermore it demonstrates that localization of NOx emissions to electricity generating units by using PHEVs in vehicle traffic has beneficial effects for air quality not only by minimizing direct human exposure to motor vehicle emissions, but also due to reduced exposure to secondary pollutants (i.e. ozone). In an electric power grid with a smaller share of fossil fired generating units, the beneficial

  16. 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...

  17. 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.

  18. 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.

  19. 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.

  20. Mechanical function of two ankle extensors in wild turkeys: shifts from energy production to energy absorption during incline versus decline running.

    Science.gov (United States)

    Gabaldón, Annette M; Nelson, Frank E; Roberts, Thomas J

    2004-06-01

    (-1) of net work in stance and the PL absorbed 2.4+/-0.9 J kg(-1) of net work. Shifts in muscle mechanical function from energy production during incline running to energy absorption during decline running were observed over a range of running speeds from 1-3 m s(-1) for both the LG and PL. Two fundamentally different mechanisms for changing work output were apparent in the mechanical behavior of the LG and PL. The LG simply altered its length pattern; it actively shortened during incline running to produce mechanical energy and actively lengthened during decline running to absorb mechanical energy. The PL changed mechanical function by altering its length pattern and by shifting the timing of force production across its stretch-shorten cycle. During incline running, the PL produced force during late stance shortening for positive work, but during decline running, the timing of force production shifted into early stance, to align with lengthening for negative work. In addition, during decline running, the PL greatly reduced or eliminated late stance shortening, thus reducing the potential for positive work. Our results show that the changing demands for whole body work during steady speed running are met, at least in part, by an ability of single muscles to shift mechanical function from net energy production to net energy absorption.

  1. 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.

  2. 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.

  3. 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...

  4. 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.

  5. [Enhanced porcine interferon-alpha production by Pichia pastoris by methanol/sorbitol co-feeding and energy metabolism shift].

    Science.gov (United States)

    Wang, Huihui; Jin, Hu; Gao, Minjie; Dai, Keke; Dong, Shijuan; Yu, Ruisong; Li, Zhen; Shi, Zhongping

    2012-02-01

    Porcine interferon-alpha (pIFN-alpha) fermentative production by recombinant Pichia pastoris was carried out in a 10-L bioreactor to study its metabolism changes and effects on fermentation under different inducing strategies, by analyzing the change patterns of the corresponding metabolism and energy regeneration. The results show that the specific activities of alcohol oxidase (AOX), formaldehyde dehydrogenase (FLD) and formate dehydrogenase (FDH) largely increased when reducing temperature from 30 degrees C to 20 degrees C under pure methanol induction, leading significant enhancements in methanol metabolism, formaldehyde dissimilatory energy metabolism and pIFN-alpha antiviral activity. The highest pIFN-alpha antiviral activity reached 1.4 x 10(6) IU/mL, which was about 10-folds of that obtained under 30 degrees C induction. Using methanol/sorbitol co-feeding strategy at 30 degrees C, the major energy metabolism energizing pIFN-alpha synthesis shifted from formaldehyde dissimilatory energy metabolism pathway to TCA cycle, formaldehyde dissimilatory pathway was weakened and accumulation of toxic intermediate metabolite-formaldehyde was relieved, and methanol flux distribution towards to pIFN-alpha synthesis was enhanced. Under this condition, the highest pIFN-alpha antiviral activity reached 1.8 x 10(7) IU/mL which was about 100-folds of that obtained under pure methanol induction at 30 degrees C. More important, enhanced pIFN-alpha production with methanol/sorbitol co-feeding strategy could be implemented under mild conditions, which greatly reduced the fermentation costs and improved the entire fermentation performance.

  6. 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.

  7. Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

    Science.gov (United States)

    Duan, Lili; Liu, Xiao; Zhang, John Z H

    2016-05-04

    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.

  8. 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.

  9. Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure

    Directory of Open Access Journals (Sweden)

    Sarah M. Bahr

    2015-11-01

    Full Text Available Risperidone is a second-generation antipsychotic that causes weight gain. We hypothesized that risperidone-induced shifts in the gut microbiome are mechanistically involved in its metabolic consequences. Wild-type female C57BL/6J mice treated with risperidone (80 μg/day exhibited significant excess weight gain, due to reduced energy expenditure, which correlated with an altered gut microbiome. Fecal transplant from risperidone-treated mice caused a 16% reduction in total resting metabolic rate in naïve recipients, attributable to suppression of non-aerobic metabolism. Risperidone inhibited growth of cultured fecal bacteria grown anaerobically more than those grown aerobically. Finally, transplant of the fecal phage fraction from risperidone-treated mice was sufficient to cause excess weight gain in naïve recipients, again through reduced energy expenditure. Collectively, these data highlight a major role for the gut microbiome in weight gain following chronic use of risperidone, and specifically implicates the modulation of non-aerobic resting metabolism in this mechanism.

  10. Change in the site of electron-transfer reduction of a zinc-quinoxalinoporphyrin/gold-quinoxalinoporphyrin dyad by binding of scandium ions and the resulting remarkable elongation of the charge-shifted-state lifetime.

    Science.gov (United States)

    Ohkubo, Kei; Garcia, Rachel; Sintic, Paul J; Khoury, Tony; Crossley, Maxwell J; Kadish, Karl M; Fukuzumi, Shunichi

    2009-10-12

    The site of electron-transfer reduction of AuPQ(+) (PQ = 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)quino-xalino[2, 3-b']porphyrin) and AuQPQ(+) (QPQ = 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)bisquinoxalino[2,3-b':12,13-b'']porphyrin) is changed from the Au(III) center to the quinoxaline part of the PQ macrocycle in the presence of Sc(3+) in benzonitrile because of strong binding of Sc(3+) to the two nitrogen atoms of the quinoxaline moiety. Strong binding of Sc(3+) to the corresponding nitrogen atoms on the quinoxaline unit of ZnPQ also occurs for the neutral form. The effects of Sc(3+) on the photodynamics of an electron donor-acceptor compound containing a linked Zn(II) and Au(III) porphyrin ([ZnPQ-AuPQ]PF(6)) have been examined by femto- and nanosecond laser flash photolysis measurements. The observed transient absorption bands at 630 and 670 nm after laser pulse irradiation in the absence of Sc(3+) in benzonitrile are assigned to the charge-shifted (CS) state (ZnPQ(*)(+)-AuPQ). The CS state decays through back electron transfer (BET) to the ground state rather than to the triplet excited state. The BET rate was determined from the disappearance of the absorption band due to the CS state. The decay of the CS state obeys first-order kinetics. The CS lifetime was determined to be 250 ps in benzonitrile. Addition of Sc(3+) to a solution of ZnPQ-AuPQ(+) in benzonitrile caused a drastic lengthening of the CS lifetime that was determined to be 430 ns, a value 1700 times longer than the 250 ps lifetime measured in the absence of Sc(3+). Such remarkable prolongation of the CS lifetime in the presence of Sc(3+) results from a change in the site of electron transfer from the Au(III) center to the quinoxaline part of the PQ macrocycle when Sc(3+) binds to the quinoxaline moiety, which decelerate BET due to a large reorganization energy of electron transfer. The change in the site of electron transfer was confirmed by ESR measurements, redox potentials, and UV

  11. 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....

  12. 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.

  13. Communication: Physical origins of ionization potential shifts in mixed carboxylic acids and water complexes

    Science.gov (United States)

    Gu, Quanli; Tang, Zhen; Su, Peifeng; Wu, Wei; Yang, Zhijun; Trindle, Carl O.; Knee, Joseph L.

    2016-08-01

    The ionization potential (IP) of the aromatic alpha hydroxy carboxylic acid, 9-hydroxy-9-fluorene carboxylic acid (9HFCA), is shifted by complexation with hydrogen bonding ligands such as water and formic acid. Generalized Kohn-Sham energy decomposition analysis decomposes the intermolecular binding energies into a frozen energy term, polarization, correlation, and/or dispersion energy terms, as well as terms of geometric relaxation and zero point energy. We observe that in each dimer the attractive polarization always increases upon ionization, enhancing binding in the cation and shifting the IP toward the red. For 9HFCA—H2O, a substantial decrease of the repulsive frozen energy in cation further shifts the IP toward red. For 9HFCA—HCOOH, the increase of the frozen energy actually occurs in the cation and shifts the IP toward blue. Consistent with the experimental measurements, our analysis provides new, non-intuitive perspectives on multiple hydrogen bonds interactions in carboxylic acids and water complexes.

  14. 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...

  15. 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.

  16. 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.

  17. 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).

  18. 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.

  19. 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.

  20. 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.

  1. 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....

  2. 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.

  3. 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.

  4. Field-induced expansion deformation in Pb islands on Cu(111): evidence from energy shift of empty quantum-well states.

    Science.gov (United States)

    Chan, W Y; Huang, H S; Su, W B; Lin, W H; Jeng, H-T; Wu, M K; Chang, C S

    2012-04-06

    We use scanning tunneling microscopy and spectroscopy to measure the energy shift of empty quantum-well (QW) states in Pb islands on the Cu(111) surface. It is found that, with an increase of the electric field, the behavior of the energy shift can be grouped into two different modes for most QW states. In the first mode, the state energy moves toward high energy monotonically. In the second mode, the state energy shifts to a lower energy initially and then turns around to a higher energy. Moreover, we have observed that the QW states of higher energy behave in preference to the first mode, but they gradually change to the second mode as the Pb island becomes thicker. This thickness-dependent behavior reflects the existence of local expansion in the Pb islands, due to the electric field, and that the expansion is larger for a thicker island. QW states can thus be used for studying the localized lattice deformation in the nanometer scale.

  5. 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

  6. Relativistic many-body calculation of energies, lifetimes, polarizabilities, blackbody radiative shift, and hyperfine constants in Lu2 +

    Science.gov (United States)

    Safronova, U. I.; Safronova, M. S.; Johnson, W. R.

    2016-09-01

    Energy levels of 30 low-lying states of Lu2 + and allowed electric-dipole matrix elements between these states are evaluated using a relativistic all-order method in which all single, double, and partial triple excitations of Dirac-Fock wave functions are included to all orders of perturbation theory. Matrix elements are critically evaluated for their accuracy and recommended values of the matrix elements are given together with uncertainty estimates. Line strengths, transition rates, and lifetimes of the metastable 5 d3 /2 and 5 d5 /2 states are calculated. Recommended values are given for static polarizabilities of the 6 s , 5 d , and 6 p states and tensor polarizabilities of the 5 d and 6 p3 /2 states. Uncertainties of the polarizability values are estimated in all cases. The blackbody radiation shift of the 6 s1 /2-5 d5 /2 transition frequency of the Lu2 + ion is calculated with the aid of the recommended scalar polarizabilities of the 6 s1 /2 and 5 d5 /2 states. Finally, A and B hyperfine constants are determined for states of 2+175Lu with n ≤9 . This work provides recommended values of transition matrix elements, polarizabilities, and hyperfine constants of Lu2 +, critically evaluated for accuracy, for benchmark tests of high-precision theoretical methodology and planning of future experiments.

  7. Relativistic many-body calculation of energies, lifetimes, polarizabilities, blackbody radiative shift and hyperfine constants in Lu2+

    CERN Document Server

    Safronova, U I; Johnson, W R

    2016-01-01

    Energy levels of 30 low-lying states of Lu2+ and allowed electric-dipole matrix elements between these states are evaluated using a relativistic all-order method in which all single, double and partial triple excitations of Dirac-Fock wave functions are included to all orders of perturbation theory. Matrix elements are critically evaluated for their accuracy and recommended values of the matrix elements are given together with uncertainty estimates. Line strengths, transition rates and lifetimes of the metastable 5d(3/2) and 5d(5/2) states are calculated. Recommended values are given for static polarizabilities of the 6s, 5d and 6p states and tensor polarizabilities of the 5d and 6p(3/2) states. Uncertainties of the polarizability values are estimated in all cases. The blackbody radiation shift of the 6s(1/2)-5d(5/2) transition frequency of the Lu2+ ion is calculated with the aid of the recommended scalar polarizabilities of the 6s(1/2) and 5d(5/2) states. Finally, A and B hyperfine constants are determined f...

  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. 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...

  10. 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.

  11. 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.

  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. 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

  14. Trends in adsorbate induced core level shifts

    Science.gov (United States)

    Nilsson, Viktor; Van den Bossche, Maxime; Hellman, Anders; Grönbeck, Henrik

    2015-10-01

    Photoelectron core level spectroscopy is commonly used to monitor atomic and molecular adsorption on metal surfaces. As changes in the electron binding energies are convoluted measures with different origins, calculations are often used to facilitate the decoding of experimental signatures. The interpretation could in this sense benefit from knowledge on trends in surface core level shifts for different metals and adsorbates. Here, density functional theory calculations have been used to systematically evaluate core level shifts for (111) and (100) surfaces of 3d, 4d, and 5d transition metals upon CO, H, O and S adsorption. The results reveal trends and several non-intuitive cases. Moreover, the difficulties correlating core level shifts with charging and d-band shifts are underlined.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Comment on "The Lamb Shift and Ultra High Energy Cosmic Rays" and Comment on "Vacuum Polarization Energy Losses of High Energy Cosmic Rays"

    CERN Document Server

    Deligny, O

    2002-01-01

    The cosmic rays spectrum has been shown to extend well beyond 10^20 eV. With nearly 20 events observed in the last 40 years, it is now established that particles with energies near or above 10^21 eV. No nearby astrophysical object has been shown to correlate with the arrival directions of the highest energy events, yet the exponential cut-off in the high energy end of the spectrum one expects to see in the case of far sources is not visible. It was recently pointed out that the influence of the vacuum of quantum electrodynamics on particle propagation could explain qualitatively this mystery. This note is a critic to these ideas.

  20. 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.

  1. 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.

  2. Investigation of energy shift of 4f3 and 4f5d levels in Nd-doped YLF and LLF crystals

    Directory of Open Access Journals (Sweden)

    André Felipe Henriques Librantz

    2006-01-01

    Full Text Available We observed ultraviolet (UV luminescence from 4f25d and 4f3 configuration in Nd-doped YLiF4 (YLF and LuLiF4 (LLF crystals induced by multiphotonic excitation of the three photons (532 nanometers [nm]. The LLF lattice is more compact than the YLF crystal and favours an absorption and emission shift of the main peaks due to crystal field strength. The red and blue shifts of the emission bands towards to lower (and higher energy are different for the transitions from 4f3 and 4f25d levels. The 4f3 transitions have smaller shift (~5 times smaller than the shift of the 4f25d due to 5s25p6 closed-shell shielding effect. On the other hand the 4f25d transitions are more susceptible to lattice change. The effect of the crystalline field was compared for both lattice. The result shows that these emission bands from 4f25d configuration always shift to lower energy when substituting the Y3+ by Lu3+ (i.e., the last one has the ionic radius 5% smaller than Y3+.

  3. 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.).

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  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. Model-Based Design of Energy Efficient Palladium Membrane Water Gas Shift Fuel Processors for PEM Fuel Cell Power Plants

    Science.gov (United States)

    Gummalla, Mallika; Vanderspurt, Thomas Henry; Emerson, Sean; She, Ying; Dardas, Zissis; Olsommer, Benoît

    An integrated, palladium alloy membrane Water-Gas Shift (WGS) reactor can significantly reduce the size, cost and complexity of a fuel processor for a Polymer Electrolyte Membrane fuel cell power system.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. Anomalous center of mass shift gravitational dipole moment

    CERN Document Server

    Jeong, E J

    1996-01-01

    The anomalous, energy dependent shift of the center of mass of an idealized, perfectly rigid, uniformly rotating hemispherical shell which is caused by the relativistic mass increase effect is investigated in detail. It is shown that a classical object on impact which has the harmonic binding force between the adjacent constituent particles has the similar effect of the energy dependent, anomalous shift of the center of mass. From these observations, the general mode of the linear acceleration is suggested to be caused by the anomalous center of mass shift whether it's due to classical or relativistic origin. The effect of the energy dependent center of mass shift perpendicular to the plane of rotation of a rotating hemisphere appears as the non zero gravitational dipole moment in general relativity. Controlled experiment for the measurement of the gravitational dipole field and its possible links to the cylindrical type line formation of a worm hole in the extreme case are suggested. The jets from the black ...

  20. Theoretical calculation of the NMR spin-spin coupling constants and the NMR shifts allow distinguishability between the specific direct and the water-mediated binding of a divalent metal cation to guanine.

    Science.gov (United States)

    Sychrovský, Vladimír; Sponer, Jirí; Hobza, Pavel

    2004-01-21

    The calculated intermolecular and intramolecular indirect NMR spin-spin coupling constants and NMR shifts were used for the discrimination between the inner-shell and the outer-shell binding motif of hydrated divalent cations Mg(2+) or Zn(2+) with a guanine base. The intermolecular coupling constants (1)J(X,O6) and (1)J(X,N7) (X = Mg(2+), Zn(2+)) can be unambiguously assigned to the specific inner-shell binding motif of the hydrated cation either with oxygen O6 or with nitrogen N7 of guanine. The calculated coupling constants (1)J(Mg,O6) and (1)J(Zn,O6) were 6.2 and -17.5 Hz, respectively, for the inner-shell complex of cation directly interacting with oxygen O6 of guanine. For the inner-shell coordination of the cation at nitrogen N7, the calculated coupling constants (1)J(Mg,N7) and (1)J(Zn,N7) were 5.6 and -36.5 Hz, respectively. When the binding of the cation is water-mediated, the coupling constant is zero. To obtain reliable shifts in NMR parameters, hydrated guanine was utilized as the reference state. The calculated change of NMR spin-spin coupling constants due to the hydration and coordination of the cation with guanine is caused mainly by the variation of Fermi-contact coupling contribution while the variation of diamagnetic spin-orbit, paramagnetic spin-orbit, and spin-dipolar coupling contributions is small. The change of s-character of guanine sigma bonding, sigma antibonding, and lone pair orbitals upon the hydration and cation coordination (calculated using the Natural Bond Orbital analysis) correlates with the variation of the Fermi-contact term. The calculated NMR shifts delta(N7) of -15.3 and -12.2 ppm upon the coordination of Mg(2+) and Zn(2+) ion are similar to the NMR shift of 19.6 ppm toward the high field measured by Tanaka for N7 of guanine upon the coordination of the Cd(2+) cation (Tanaka, Y.; Kojima, C.; Morita, E. H.; Kasai. Y.; Yamasaki, K.; Ono, A.; Kainosho, M.; Taira, K. J. Am. Chem. Soc. 2002, 124, 4595-4601). The present data

  1. 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.

  2. L X-ray energy shifts and intensity ratios in tantalum with C and N ions – multiple vacancies in M, N and O shells

    Indian Academy of Sciences (India)

    Y Ramakrishna; K Ramachandra Rao; G J Naga Raju; K Bhaskara Rao; V Seshagiri Rao; P Venkateswarlu; S Bhuloka Reddy

    2002-10-01

    The energy shifts and intensity ratios of different L X-ray components in tantalum element due to 10 MeV carbon and 12 MeV nitrogen ions are estimated. From the observed energy shifts, the possible number of simultaneous vacancies in M shell are estimated. A comparison of L/L 2,15, L 1/L 1 and L 2,3/L 4,4 with the ratios due to Scofield theoretical transition rates indicate that the number of multiple vacancies in N shell are higher than the vacancies in M and O shell. Employing Larkin’s statistical scaling procedure, the number of possible multiple vacancies in N and O shells are estimated quantitatively.

  3. Determination of the cationic amphiphilic drug-DNA binding mode and DNA-assisted fluorescence resonance energy transfer amplification.

    Science.gov (United States)

    Yaseen, Zahid; Banday, Abdul Rouf; Hussain, Mohammed Aamir; Tabish, Mohammad; Kabir-ud-Din

    2014-03-25

    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.

  4. 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.

  5. 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.

  6. 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.

  7. Mitochondrial UCP4 mediates an adaptive shift in energy metabolism and increases the resistance of neurons to metabolic and oxidative stress.

    Science.gov (United States)

    Liu, Dong; Chan, Sic L; de Souza-Pinto, Nadja C; Slevin, John R; Wersto, Robert P; Zhan, Ming; Mustafa, Khadija; de Cabo, Rafael; Mattson, Mark P

    2006-01-01

    The high-metabolic demand of neurons and their reliance on glucose as an energy source places them at risk for dysfunction and death under conditions of metabolic and oxidative stress. Uncoupling proteins (UCPs) are mitochondrial inner membrane proteins implicated in the regulation of mitochondrial membrane potential (Deltapsim) and cellular energy metabolism. The authors cloned UCP4 cDNA from mouse and rat brain, and demonstrate that UCP4 mRNA is expressed abundantly in brain and at particularly high levels in populations of neurons believed to have high-energy requirements. Neural cells with increased levels of UCP4 exhibit decreased Deltapsim, reduced reactive oxygen species (ROS) production and decreased mitochondrial calcium accumulation. UCP4 expressing cells also exhibited changes of oxygen-consumption rate, GDP sensitivity, and response of Deltapsim to oligomycin that were consistent with mitochondrial uncoupling. UCP4 modulates neuronal energy metabolism by increasing glucose uptake and shifting the mode of ATP production from mitochondrial respiration to glycolysis, thereby maintaining cellular ATP levels. The UCP4-mediated shift in energy metabolism reduces ROS production and increases the resistance of neurons to oxidative and mitochondrial stress. Knockdown of UCP4 expression by RNA interference in primary hippocampal neurons results in mitochondrial calcium overload and cell death. UCP4-mRNA expression is increased in neurons exposed to cold temperatures and in brain cells of rats maintained on caloric restriction, suggesting a role for UCP4 in the previously reported antiageing and neuroprotective effects of caloric restriction. By shifting energy metabolism to reduce ROS production and cellular reliance on mitochondrial respiration, UCP4 can protect neurons against oxidative stress and calcium overload.

  8. 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.

  9. 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...

  10. 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 ...

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Effect of temperature-dependent energy-level shifts on a semiconductor's Peltier heat

    Energy Technology Data Exchange (ETDEWEB)

    Emin, D.

    1984-11-15

    The Peltier heat of a charge carrier in a semiconductor is calculated for the situation in which the electronic energy levels are temperature dependent. The temperature dependences of the electronic energy levels, generally observed optically, arise from their dependences on the vibrational energy of the lattice (e.g., as caused by thermal expansion). It has been suggested that these temperature dependences will typically have a major effect on the Peltier heat. The Peltier heat associated with a given energy level is a thermodynamic quantity; it is the product of the temperature and the change of the entropy of the system when a carrier is added in that level. As such, the energy levels cannot be treated as explicitly temperature dependent. The electron-lattice interaction causing the temperature dependence must be expressly considered. It is found that the carrier's interaction with the atomic vibrations lowers its electronic energy. However, the interaction of the carrier with the atomic vibrations also causes an infinitesimal lowering (approx.1/N) of each of the N vibrational frequencies. As a result, there is a finite carrier-induced increase in the average vibrational energy. Above the Debye temperature, this cancels the lowering of the carrier's electronic energy. Thus, the standard Peltier-heat formula, whose derivation generally ignores the temperature dependence of the electronic energy levels, is regained. This explains the apparent success of the standard formula in numerous analyses of electronic transport experiments.

  19. Shifting Attention

    Science.gov (United States)

    Ingram, Jenni

    2014-01-01

    This article examines the shifts in attention and focus as one teacher introduces and explains an image that represents the processes involved in a numeric problem that his students have been working on. This paper takes a micro-analytic approach to examine how the focus of attention shifts through what the teacher and students do and say in the…

  20. Tough Shift

    DEFF Research Database (Denmark)

    Brewer, Robert S.; Verdezoto, Nervo; Holst, Thomas;

    2015-01-01

    in a student dormitory and found that players did not shift their electricity use, because they were unwilling to change their schedules and found it easier to focus on reducing electricity use. Based on our findings, we discuss the implications for encouraging shifting, and also the challenges of integrating...

  1. KK—vacancy sharing and TET energy shift in near—symmetric heavy—ion atom collision

    Institute of Scientific and Technical Information of China (English)

    LiJing-Wen; JiangLi-Yang; 等

    1998-01-01

    The two-electron-one photon transitions(TET) are measured in 75MeV Ni+q+Cu collisons.The KK-vacancy sharing ratio RKK is deduced,which is in agreement with the theoretical prediction of Lennard.The emission energy of TET is slightly larger than twice the correspoding K transition energy.

  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...... exciton and biexciton binding energy changes from 0.23 to 0.3 with increasing inhomogeneous broadening, corresponding to increasing well width. From the temperature dependence of the exciton and biexciton four-wave mixing signal decay, we have deduced the acoustic-phonon scattering of the exciton...

  3. 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.

  4. Predicting paramagnetic 1H NMR chemical shifts and state-energy separations in spin-crossover host-guest systems.

    Science.gov (United States)

    Isley, William C; Zarra, Salvatore; Carlson, Rebecca K; Bilbeisi, Rana A; Ronson, Tanya K; Nitschke, Jonathan R; Gagliardi, Laura; Cramer, Christopher J

    2014-06-14

    The behaviour of metal-organic cages upon guest encapsulation can be difficult to elucidate in solution. Paramagnetic metal centres introduce additional dispersion of signals that is useful for characterisation of host-guest complexes in solution using nuclear magnetic resonance (NMR). However, paramagnetic centres also complicate spectral assignment due to line broadening, signal integration error, and large changes in chemical shifts, which can be difficult to assign even for known compounds. Quantum chemical predictions can provide information that greatly facilitates the assignment of NMR signals and identification of species present. Here we explore how the prediction of paramagnetic NMR spectra may be used to gain insight into the spin crossover (SCO) properties of iron(II)-based metal organic coordination cages, specifically examining how the structure of the local metal coordination environment affects SCO. To represent the tetrahedral metal-organic cage, a model system is generated by considering an isolated metal-ion vertex: fac-ML3(2+) (M = Fe(II), Co(II); L = N-phenyl-2-pyridinaldimine). The sensitivity of the (1)H paramagnetic chemical shifts to local coordination environments is assessed and utilised to shed light on spin crossover behaviour in iron complexes. Our data indicate that expansion of the metal coordination sphere must precede any thermal SCO. An attempt to correlate experimental enthalpies of SCO with static properties of bound guests shows that no simple relationship exists, and that effects are likely due to nuanced dynamic response to encapsulation.

  5. 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.

  6. 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.

  7. Phase shift analysis of low energy $\\pi^{\\pm}p$ scattering data and a comparison with pionic hydrogen data

    CERN Document Server

    Gashi, A; Oades, G C; Rasche, G; Woolcock, W S

    2000-01-01

    Using newly calculated electromagnetic corrections, we have made a phase shift analysis of experimental data on pi+/- p elastic scattering up to 100 MeV, assuming the effective hadronic interaction to be isospin invariant. The output consists of parametrised s and p-wave hadronic phases for isospin 1/2 and 3/2. It is not possible to fit the charge exchange data satisfactorily. We give values for the s-wave scattering lengths and effective ranges and for the p-wave scattering volumes. The combinations 2a_1 + a_3 and a_1 - a_3 of s-wave scattering lengths extracted from pionic hydrogen data are compared with those obtained from our analysis.

  8. Switching from static to adaptable and dynamic building envelopes: A paradigm shift for the energy efficiency in buildings

    Directory of Open Access Journals (Sweden)

    Marco Perino

    2015-11-01

    Full Text Available The key role of the building envelope in attaining building energy efficiency and satisfactory indoor comfort has long been established. Nevertheless, until recent times, all efforts and attention have mainly been focused on increasing and optimizing the thermal insulation of the envelope components. This strategy was a winning approach for a long time, but its limitations became obvious when users and designers started to consider the overall energy demand of a building and started to aim for Zero Energy Building (ZEB or nearly ZEB goals. New and more revolutionary concepts and technologies needed to be developed to satisfy such challenging requirements. The potential benefits of this technological development are relevant since the building envelope plays a key role in controlling the energy and mass flows from outdoors to indoors (and vice versa and, moreover, the facades offer a significant opportunity for solar energy exploitation. Several researches have demonstrated that the limitation of the existing facades could be overcome only by switching from ‘static’ to ‘responsive’ and ‘dynamic’ systems, such as Multifunctional Facade Modules (MFMs and Responsive Building Elements (RBE. These components are able to continuously and pro-actively react to outdoor and indoor environment conditions and facilitate and enhance the exploitation of renewable and low exergy sources. In order to reduce the energy demand, to maximize the indoor comfort conditions and to produce energy at the site, these almost ‘self-sufficient’, or even ‘positive energy’ building skins frequently incorporate different technologies and are functionally connected to other building services and installations. An overview of the technological evolution of the building envelope that has taken place, ranging from traditional components to the innovative skins, will be given in this paper, while focusing on the different approaches that have characterized this

  9. 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.

  10. 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.)

  11. 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.

  12. 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.

  13. 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.

  14. On the Inclusion of Energy-Shifting Demand Response in Production Cost Models: Methodology and a Case Study

    DEFF Research Database (Denmark)

    O'Connell, Niamh; Hale, Elaine; Doebber, Ian

    a case study of aggregated supermarket refrigeration systems providing balancing energy reserves in real-time markets at different levels of variable generation (VG). This DR resource is implemented in a test power system that represents a subset of the U.S Western Interconnection centered on Colorado......% to 55% VG. This is attributable to the inability of DR to provide energy storage on horizons longer than 24 hours. Overall, this work is a study in methodology. The case study is included primarily to show that the model is working properly and that this line of research is worthwhile. The reported...... penetration (increasing). Future work includes extending this method and developing new methods to be able to model physically realistic DR resources at scale. Some important aspects not studied here include capturing all possible value streams for a single resource (capacity, energy, and ancillary service...

  15. 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.

  16. 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.

  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. Animism, Creativity, and a Tree: Shifting into Nature Connection through Attention to Subtle Energies and Contemplative Art Practice

    Science.gov (United States)

    Flowers, Michelle; Lipsett, Lisa; Barrett, M. J.

    2014-01-01

    What can happen when the "monkey mind" of habitual conceptual thought is awakened to the more-than-human through attention to subtle energies and artmaking? Drawing on autoethnographic methods, we demonstrate how one graduate student's creative engagement with a tree brought animist theory to life. This paper illustrates how a…

  19. 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.

  20. Peroxisome proliferator-activated receptor γ (PPARγ) mediates a Ski oncogene-induced shift from glycolysis to oxidative energy metabolism.

    Science.gov (United States)

    Ye, Fang; Lemieux, Hélène; Hoppel, Charles L; Hanson, Richard W; Hakimi, Parvin; Croniger, Colleen M; Puchowicz, Michelle; Anderson, Vernon E; Fujioka, Hisashi; Stavnezer, Ed

    2011-11-18

    Overexpression of the Ski oncogene induces oncogenic transformation of chicken embryo fibroblasts (CEFs). However, unlike most other oncogene-transformed cells, Ski-transformed CEFs (Ski-CEFs) do not display the classical Warburg effect. On the contrary, Ski transformation reduced lactate production and glucose utilization in CEFs. Compared with CEFs, Ski-CEFs exhibited enhanced TCA cycle activity, fatty acid catabolism through β-oxidation, glutamate oxidation, oxygen consumption, as well as increased numbers and mass of mitochondria. Interestingly, expression of PPARγ, a key transcription factor that regulates adipogenesis and lipid metabolism, was dramatically elevated at both the mRNA and protein levels in Ski-CEFs. Accordingly, PPARγ target genes that are involved in lipid uptake, transport, and oxidation were also markedly up-regulated by Ski. Knocking down PPARγ in Ski-CEFs by RNA interference reversed the elevated expression of these PPARγ target genes, as well as the shift to oxidative metabolism and the increased mitochondrial biogenesis. Moreover, we found that Ski co-immunoprecipitates with PPARγ and co-activates PPARγ-driven transcription.

  1. On the Inclusion of Energy-Shifting Demand Response in Production Cost Models: Methodology and a Case Study

    Energy Technology Data Exchange (ETDEWEB)

    O' Connell, Niamh [Technical Univ. of Denmark, Lyngby (Denmark); Hale, Elaine [National Renewable Energy Lab. (NREL), Golden, CO (United States); Doebber, Ian [National Renewable Energy Lab. (NREL), Golden, CO (United States); Jorgenson, Jennie [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2015-07-20

    In the context of future power system requirements for additional flexibility, demand response (DR) is an attractive potential resource. Its proponents widely laud its prospective benefits, which include enabling higher penetrations of variable renewable generation at lower cost than alternative storage technologies, and improving economic efficiency. In practice, DR from the commercial and residential sectors is largely an emerging, not a mature, resource, and its actual costs and benefits need to be studied to determine promising combinations of physical DR resource, enabling controls and communications, power system characteristics, regulatory environments, market structures, and business models. The work described in this report focuses on the enablement of such analysis from the production cost modeling perspective. In particular, we contribute a bottom-up methodology for modeling load-shifting DR in production cost models. The resulting model is sufficiently detailed to reflect the physical characteristics and constraints of the underlying flexible load, and includes the possibility of capturing diurnal and seasonal variations in the resource. Nonetheless, the model is of low complexity and thus suitable for inclusion in conventional unit commitment and market clearing algorithms. The ability to simulate DR as an operational resource on a power system over a year facilitates an assessment of its time-varying value to the power system.

  2. 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.

  3. 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

  4. Methanol/sorbitol co-feeding induction enhanced porcine interferon-α production by P. pastoris associated with energy metabolism shift.

    Science.gov (United States)

    Gao, Min-Jie; Li, Zhen; Yu, Rui-Song; Wu, Jian-Rong; Zheng, Zhi-Yong; Shi, Zhong-Ping; Zhan, Xiao-Bei; Lin, Chi-Chung

    2012-09-01

    The production of porcine interferon-α (pIFN-α) by Pichia pastoris was largely enhanced when adopting sorbitol/methanol co-feeding induction strategy at 30 °C in a 10-L fermentor. Analysis of energy regeneration pattern and carbon metabolism revealed that major energy metabolism energizing pIFN-α synthesis shifted from formaldehyde dissimilatory energy metabolism pathway to TCA cycle under the methanol/sorbitol co-feeding induction strategy. The sorbitol/methanol co-feeding induction strategy weakened formaldehyde dissimilatory pathway and repressed the accumulation of toxic metabolite-formaldehyde, reduced theoretical oxygen consumption rate and oxygen supply requirement, and increased energy/methanol utilization efficiency so that more methanol could be effectively used for pIFN-α synthesis. As a result, pIFN-α antiviral activity reached a highest level of 1.8 × 10(7) IU/mL which was about 10- to 200-folds of those obtained under pure methanol induction at 20 and 30 °C, respectively.

  5. Effect of high energy proton irradiation on InAs/GaAs quantum dots: Enhancement of photoluminescence efficiency (up to {approx}7 times) with minimum spectral signature shift

    Energy Technology Data Exchange (ETDEWEB)

    Sreekumar, R.; Mandal, A. [Centre for Nanoelectronics, Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra (India); Gupta, S.K. [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra (India); Chakrabarti, S., E-mail: subho@ee.iitb.ac.in [Centre for Nanoelectronics, Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra (India)

    2011-11-15

    Graphical abstract: Authors demonstrate enhancement in photoluminescence efficiency (7 times) in single layer InAs/GaAs quantum dots using proton irradiation without any post-annealing treatment via either varying proton energy (a) or fluence (b). The increase in PL efficiency is explained by a proposed model before (c) and after irradiation (d). Highlights: {yields} Proton irradiation improved PL efficiency in InAs/GaAs quantum dots (QDs). {yields} Proton irradiation favoured defect and strain annihilation in InAs/GaAs QDs. {yields} Reduction in defects/non-radiative recombination improved PL efficiency. {yields} Protons could be used to improve PL efficiency without spectral shift. {yields} QD based devices will be benefited by this technique to improve device performance. -- Abstract: We demonstrate 7-fold increase of photoluminescence efficiency in GaAs/(InAs/GaAs) quantum dot hetero-structure, employing high energy proton irradiation, without any post-annealing treatment. Protons of energy 3-5 MeV with fluence in the range (1.2-7.04) x 10{sup 12} ions/cm{sup 2} were used for irradiation. X-ray diffraction analysis revealed crystalline quality of the GaAs cap layer improves on proton irradiation. Photoluminescence study conducted at low temperature and low laser excitation density proved the presence of non-radiative recombination centers in the system which gets eliminated on proton irradiation. Shift in photoluminescence emission towards higher wavelength upon irradiation substantiated the reduction in strain field existed between GaAs cap layer and InAs/GaAs quantum dots. The enhancement in PL efficiency is thus attributed to the annihilation of defects/non-radiative recombination centers present in GaAs cap layer as well as in InAs/GaAs quantum dots induced by proton irradiation.

  6. Power Shift

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ "We are entering a new era of world history: the end of Western domination and the arrival of the Asian century. The question is: will Washington wake up to this reality?" This is the central premise of Kishore Mahbubani's provocative new book The New Asian Hemisphere: The Irresistible Shift of Global Power to the East.

  7. 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...

  8. 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.

  9. Stacked search for time shifted high energy neutrinos from gamma ray bursts with the \\ANTARES neutrino telescope

    CERN Document Server

    Adrian-Martínez, S; André, M; Anton, G; Ardid, M; Aubert, J -J; Baret, B; Barrios-Marti, J; Basa, S; Bertin, V; Biagi, S; Bormuth, R; Bouwhuis, M C; Bruijn, R; Brunner, J; Busto, J; Capone, A; Caramete, L; Carr, J; Chiarusi, T; Circella, M; Coniglione, R; Costantini, H; Coyle, P; Creusot, A; Dekeyser, I; Deschamps, A; De Bonis, G; Distefano, C; Donzaud, C; Dornic, D; Drouhin, D; Dumas, A; Eberl, T; Elsasser, D; Enzenhofer, A; Fehn, K; Felis, I; Fermani, P; Folger, F; Fusco, L A; Galatà, S; Gay, P; Geisselsoeder, S; Geyer, K; Giordano, V; Gleixner, A; Gracia-Ruiz, R; Graf, K; Hallmann, S; van Haren, H; Heijboer, A J; Hello, Y; Hernàndez-Rey, J J; Hoessl, J; Hofestadt, J; Hugon, C; James, C W; de Jong, M; Kadler, M; Kadler, M; Kalekin, O; Katz, U; Kiessling, D; Kooijman, P; Kouchner, A; Kreter, M; Kreykenbohm, I; Kulikovskiy, V; Lahmann, R; Lefèvre, D; Leonora, E; Marcelin, M; Margiotta, A; Marinelli, A; Martínez-Mora, J A; Mathieu, A; Michael, T; Migliozzi, P; Moussa, A; Muller, C; Nezri, E; Pavalas, G E; Pellegrino, C; Perrina, C; Piattelli, P; Popa, V; Pradier, T; Racca, C; Riccobene, G; Richter, R; Roensch, K; Saldaña, M; Samtleben, D F E; Sánchez-Losa, A; Sanguineti, M; Sapienza, P; Schmid, J; Schnabel, J; Schussler, F; Seitz, T; Sieger, C; Spurio, M; Steijger, J J M; Stolarczyk, Th; Taiuti, M; Tamburini, C; Trovato, A; Tselengidou, M; Tonnis, C; Vallage, B; Vallée, C; Van Elewyck, V; Visser, E; Vivolo, D; Wagner, S; Wilms, J; Zornoza, J D; Zúñiga, J

    2016-01-01

    A search for high-energy neutrino emission correlated with gamma-ray bursts outside the electromagnetic prompt-emission time window is presented. Using a stacking approach of the time delays between reported gamma-ray burst alerts and spatially coincident muon-neutrino signatures, data from the Antares neutrino telescope recorded between 2007 and 2012 are analysed. One year of public data from the IceCube detector between 2008 and 2009 have been also investigated. The respective timing pro?les are scanned for statistically significant accumulations within 40 days of the Gamma Ray Burst, as expected from Lorentz Invariance Violation effects and some astrophysical models. No significant excess over the expected accidental coincidence rate could be found in either of the two data sets. The average strength of the neutrino signal is found to be fainter than one detectable neutrino signal per hundred gamma-ray bursts in the Antares data at 90% confidence level.

  10. 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.

  11. Surface core-level shifts for simple metals

    DEFF Research Database (Denmark)

    Aldén, Magnus; Skriver, Hans Lomholt; Johansson, Börje

    1994-01-01

    We have performed an ab initio study of the surface core-level binding energy shift (SCLS) for 11 of the simple metals by means of a Green’s-function technique within the tight-binding linear-muffin-tin-orbitals method. Initial- and final-state effects are included within the concept of complete....... We furthermore conclude that the unexpected negative sign of the SCLS in beryllium is predominantly an initial-state effect and is caused by the high electron density in this metal....

  12. 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.

  13. 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.

  14. An Integrated Optimal Energy Management/Gear-Shifting Strategy for an Electric Continuously Variable Transmission Hybrid Powertrain Using Bacterial Foraging Algorithm

    Directory of Open Access Journals (Sweden)

    Syuan-Yi Chen

    2016-01-01

    Full Text Available This study developed an integrated energy management/gear-shifting strategy by using a bacterial foraging algorithm (BFA in an engine/motor hybrid powertrain with electric continuously variable transmission. A control-oriented vehicle model was constructed on the Matlab/Simulink platform for further integration with developed control strategies. A baseline control strategy with four modes was developed for comparison with the proposed BFA. The BFA was used with five bacterial populations to search for the optimal gear ratio and power-split ratio for minimizing the cost: the equivalent fuel consumption. Three main procedures were followed: chemotaxis, reproduction, and elimination-dispersal. After the vehicle model was integrated with the vehicle control unit with the BFA, two driving patterns, the New European Driving Cycle and the Federal Test Procedure, were used to evaluate the energy consumption improvement and equivalent fuel consumption compared with the baseline. The results show that [18.35%,21.77%] and [8.76%,13.81%] were improved for the optimal energy management and integrated optimization at the first and second driving cycles, respectively. Real-time platform designs and vehicle integration for a dynamometer test will be investigated in the future.

  15. A shift in emission time profiles of fossil fuel combustion due to energy transitions impacts source receptor matrices for air quality.

    Science.gov (United States)

    Hendriks, Carlijn; Kuenen, Jeroen; Kranenburg, Richard; Scholz, Yvonne; Schaap, Martijn

    2015-03-01

    Effective air pollution and short-lived climate forcer mitigation strategies can only be designed when the effect of emission reductions on pollutant concentrations and health and ecosystem impacts are quantified. Within integrated assessment modeling source-receptor relationships (SRRs) based on chemistry transport modeling are used to this end. Currently, these SRRs are made using invariant emission time profiles. The LOTOS-EUROS model equipped with a source attribution module was used to test this assumption for renewable energy scenarios. Renewable energy availability and thereby fossil fuel back up are strongly dependent on meteorological conditions. We have used the spatially and temporally explicit energy model REMix to derive time profiles for backup power generation. These time profiles were used in LOTOS-EUROS to investigate the effect of emission timing on air pollutant concentrations and SRRs. It is found that the effectiveness of emission reduction in the power sector is significantly lower when accounting for the shift in the way emissions are divided over the year and the correlation of emissions with synoptic situations. The source receptor relationships also changed significantly. This effect was found for both primary and secondary pollutants. Our results indicate that emission timing deserves explicit attention when assessing the impacts of system changes on air quality and climate forcing from short lived substances.

  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. 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.

  18. 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

  19. 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 ...

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. MMPBSA Decomposition of the Binding Energy throughout a Molecular Dynamics Simulation of Amyloid-Beta (Aß10−35 Aggregation

    Directory of Open Access Journals (Sweden)

    Josep M. Campanera

    2010-04-01

    Full Text Available Recent experiments with amyloid-beta (Aβ peptides indicate that the formation of toxic oligomers may be an important contribution to the onset of Alzheimer’s disease. The toxicity of Aβ oligomers depend on their structure, which is governed by assembly dynamics. However, a detailed knowledge of the structure of at the atomic level has not been achieved yet due to limitations of current experimental techniques. In this study, replica exchange molecular dynamics simulations are used to identify the expected diversity of dimer conformations of Aβ10−35 monomers. The most representative dimer conformation has been used to track the dimer formation process between both monomers. The process has been characterized by means of the evolution of the decomposition of the binding free energy, which provides an energetic profile of the interaction. Dimers undergo a process of reorganization driven basically by inter-chain hydrophobic and hydrophilic interactions and also solvation/desolvation processes.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. Fluid Shifts

    Science.gov (United States)

    Stenger, M. B.; Hargens, A. R.; Dulchavsky, S. A.; Arbeille, P.; Danielson, R. W.; Ebert, D. J.; Garcia, K. M.; Johnston, S. L.; Laurie, S. S.; Lee, S. M. C.; Liu, J.; Macias, B.; Martin, D. S.; Minkoff, L.; Ploutz-Snyder, R.; Ribeiro, L. C.; Sargsyan, A.; Smith, S. M.

    2017-01-01

    Introduction. NASA's Human Research Program is focused on addressing health risks associated with long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but now more than 50 percent of ISS astronauts have experienced more profound, chronic changes with objective structural findings such as optic disc edema, globe flattening and choroidal folds. These structural and functional changes are referred to as the visual impairment and intracranial pressure (VIIP) syndrome. Development of VIIP symptoms may be related to elevated intracranial pressure (ICP) secondary to spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight and to determine if a relation exists with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as any VIIP-related effects of those shifts, are predicted by the crewmember's pre-flight status and responses to acute hemodynamic manipulations, specifically posture changes and lower body negative pressure. Methods. We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, and calcaneus tissue thickness (by ultrasound); (3) vascular dimensions by ultrasound (jugular veins, cerebral and carotid arteries, vertebral arteries and veins, portal vein); (4) vascular dynamics by MRI (head/neck blood flow, cerebrospinal fluid

  12. 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...

  13. 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.

  14. Proteomic analysis of chloroplast-to-chromoplast transition in tomato reveals metabolic shifts coupled with disrupted thylakoid biogenesis machinery and elevated energy-production components.

    Science.gov (United States)

    Barsan, Cristina; Zouine, Mohamed; Maza, Elie; Bian, Wanping; Egea, Isabel; Rossignol, Michel; Bouyssie, David; Pichereaux, Carole; Purgatto, Eduardo; Bouzayen, Mondher; Latché, Alain; Pech, Jean-Claude

    2012-10-01

    A comparative proteomic approach was performed to identify differentially expressed proteins in plastids at three stages of tomato (Solanum lycopersicum) fruit ripening (mature-green, breaker, red). Stringent curation and processing of the data from three independent replicates identified 1,932 proteins among which 1,529 were quantified by spectral counting. The quantification procedures have been subsequently validated by immunoblot analysis of six proteins representative of distinct metabolic or regulatory pathways. Among the main features of the chloroplast-to-chromoplast transition revealed by the study, chromoplastogenesis appears to be associated with major metabolic shifts: (1) strong decrease in abundance of proteins of light reactions (photosynthesis, Calvin cycle, photorespiration) and carbohydrate metabolism (starch synthesis/degradation), mostly between breaker and red stages and (2) increase in terpenoid biosynthesis (including carotenoids) and stress-response proteins (ascorbate-glutathione cycle, abiotic stress, redox, heat shock). These metabolic shifts are preceded by the accumulation of plastid-encoded acetyl Coenzyme A carboxylase D proteins accounting for the generation of a storage matrix that will accumulate carotenoids. Of particular note is the high abundance of proteins involved in providing energy and in metabolites import. Structural differentiation of the chromoplast is characterized by a sharp and continuous decrease of thylakoid proteins whereas envelope and stroma proteins remain remarkably stable. This is coincident with the disruption of the machinery for thylakoids and photosystem biogenesis (vesicular trafficking, provision of material for thylakoid biosynthesis, photosystems assembly) and the loss of the plastid division machinery. Altogether, the data provide new insights on the chromoplast differentiation process while enriching our knowledge of the plant plastid proteome.

  15. 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.

  16. 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.

  17. Anomalous center of mass shift: gravitational dipole moment.

    Science.gov (United States)

    Jeong, Eue Jin

    1997-02-01

    The anomalous, energy dependent shift of the center of mass of an idealized, perfectly rigid, uniformly rotating hemispherical shell which is caused by the relativistic mass increase effect is investigated in detail. It is shown that a classical object on impact which has the harmonic binding force between the adjacent constituent particles has the similar effect of the energy dependent, anomalous shift of the center of mass. From these observations, the general mode of the linear acceleration is suggested to be caused by the anomalous center of mass shift whether it's due to classical or relativistic origin. The effect of the energy dependent center of mass shift perpendicular to the plane of rotation of a rotating hemisphere appears as the non zero gravitational dipole moment in general relativity. Controlled experiment for the measurement of the gravitational dipole field and its possible links to the cylindrical type line formation of a worm hole in the extreme case are suggested. The jets from the black hole accretion disc and the observed anomalous red shift from far away galaxies are considered to be the consequences of the two different aspects of the dipole gravity.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Goos-Hänchen shift.

    Science.gov (United States)

    Snyder, A W; Love, J D

    1976-01-01

    An extremely simple derivation of the Goos-Hänchen shift is presented for total internal reflection at a plane interface between two semiinfinite dielectric media, as well as for optical waveguides of plane arid circular cross section. The derivation is based on energy considerations, requires knowledge of Fresnel's equation only, and shows explicitly that the shift is due to the flow of energy across the dielectric boundary.

  3. 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.

  4. 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

  5. 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.

  6. Quantitative proteomics reveals significant changes in cell shape and an energy shift after IPTG induction via an optimized SILAC approach for Escherichia coli.

    Science.gov (United States)

    Ping, Lingyan; Zhang, Heng; Zhai, Linhui; Dammer, Eric B; Duong, Duc M; Li, Ning; Yan, Zili; Wu, Junzhu; Xu, Ping

    2013-12-01

    Stable isotope labeling by amino acids in cell culture (SILAC) has been widely used in yeast, mammalian cells, and even some multicellular organisms. However, the lack of optimized SILAC media limits its application in Escherichia coli, the most commonly used model organism. We optimized SILACE medium (SILAC medium created in this study for E. coli) for nonauxotrophic E. coli with high growth speed and complete labeling efficiency of the whole proteome in 12 generations. We applied a swapped SILAC workflow and pure null experiment with the SILACE medium using E. coli BL21 (DE3) cells hosting a recombinant plasmid coding for glutathione-S-transferase (GST) and ubiquitin binding domain before and after isopropyl thiogalactoside (IPTG) induction. Finally, we identified 1251 proteins with a significant change in abundance. Pathway analysis suggested that cell growth and fissiparism were inhibited accompanied by the down-regulation of proteins related to energy and metabolism, cell division, and the cell cycle, resulting in the size and shape change of the induced cells. Taken together, the results confirm the development of SILACE medium suitable for efficient and complete labeling of E. coli cells and a data filtering strategy for SILAC-based quantitative proteomics studies of E. coli.

  7. 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.

  8. A thermalization energy analysis of the threshold voltage shift in amorphous indium gallium zinc oxide thin film transistors under positive gate bias stress

    NARCIS (Netherlands)

    Niang, K.M.; Barquinha, P.M.C.; Martins, R.F.P.; Cobb, B.; Powell, M.J.; Flewitt, A.J.

    2016-01-01

    Thin film transistors (TFTs) employing an amorphous indium gallium zinc oxide (a-IGZO) channel layer exhibit a positive shift in the threshold voltage under the application of positive gate bias stress (PBS). The time and temperature dependence of the threshold voltage shift was measured and analyse

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. Paradigm Shift in Transboundary Water Management Policy: Linking Water Environment Energy and Food (weef) to Catchment Hydropolitics - Needs, Scope and Benefits

    Science.gov (United States)

    RAI, S.; Wolf, A.; Sharma, N.; Tiwari, H.

    2015-12-01

    The incessant use of water due to rapid growth of population, enhanced agricultural and industrial activities, degraded environment and ecology will in the coming decades constrain the socioeconomic development of humans. To add on to the precarious situation, political boundaries rarely embrace hydrological boundaries of lakes, rivers, aquifers etc. Hydropolitics relate to the ability of geopolitical institutions to manage shared water resources in a politically sustainable manner, i.e., without tensions or conflict between political entities. Riparian hydropolitics caters to differing objectives, needs and requirements of states making it difficult to administer the catchment. The diverse riparian objectives can be merged to form a holistic catchment objective of sustainable water resources development and management. It can be proposed to make a paradigm shift in the present-day transboundary water policy from riparian hydropolitics (in which the focal point of water resources use is hinged on state's need) to catchment hydropolitics (in which the interest of the basin inhabitants are accorded primacy holistically over state interests) and specifically wherein the water, environment, energy and food (WEEF) demands of the catchment are a priority and not of the states in particular. The demands of the basin pertaining to water, food and energy have to be fulfilled, keeping the environment and ecology healthy in a cooperative political framework; the need for which is overwhelming. In the present scenario, the policy for water resources development of a basin is segmented into independent uncoordinated parts controlled by various riparians; whereas in catchment hydropolitics the whole basin should be considered as a unit. The riparians should compromise a part of national interest and work in collaboration on a joint objective which works on the principle of the whole as against the part. Catchment hydropolitics may find greater interest in the more than 250

  14. 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.

  15. 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.

  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. 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.

  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. Gain Shift Corrections at Chi-Nu

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Tristan Brooks [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Univ. of Massachusetts, Lowell, MA (United States). Dept. of Physics and Applied Physics; Devlin, Matthew James [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-08-30

    Ambient conditions have the potential to cause changes in liquid scintillator detector gain that vary with time and temperature. These gain shifts can lead to poor resolution in both energy as well as pulse shape discrimination. In order to correct for these shifts in the Chi-Nu high energy array, a laser system has been developed for calibration of the pulse height signals.

  20. 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.

  1. 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.

  2. 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

  3. Global Optimization for Electric Vehicle Equipped with EMCVT Based on Shifting Energy%基于调速能量的EMCVT电动汽车全局优化

    Institute of Scientific and Technical Information of China (English)

    叶明; 任洪; 李鑫

    2016-01-01

    Integrating motor efficiency,battery state of charge (SOC)and EMCVT efficiency, the global optimization of EV equipped with EMCVT running in new Europe driving cycle (NEDC) was carried out based on dynamic programming.In this optimization,SOC and transmission ratio were state variable and decision variable respectively.Ratio shifting model was built to estimate enerG gy consumption during shifting.New optimal control strategies were achieved by taking shifting enerG gy consumption into cost function.With this control strategy,shift times and fuel consumed are both reduced.%综合考虑电机、电池、机电控制无级自动变速器效率,采用全局动态规划的方法,以电池荷电状态值为状态变量、变速器速比为决策变量,获取装备机电控制无级自动变速器的电动汽车在 NEDC工况下的全局最优控制策略。建立了机电控制无级自动变速器调速模型,获取调速过程中的能量消耗。在全局优化控制策略的基础上,将调速能量消耗纳入指标函数,进一步优化无级变速器速比和电机扭矩。优化结果表明,采取所提出的优化策略可有效减少调速次数,进一步降低系统能量消耗。

  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. 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.

  8. Paradigm Shift in Radiation Biology/Radiation Oncology-Exploitation of the "H₂O₂ Effect" for Radiotherapy Using Low-LET (Linear Energy Transfer) Radiation such as X-rays and High-Energy Electrons.

    Science.gov (United States)

    Ogawa, Yasuhiro

    2016-02-25

    Most radiation biologists/radiation oncologists have long accepted the concept that the biologic effects of radiation principally involve damage to deoxyribonucleic acid (DNA), which is the critical target, as described in "Radiobiology for the Radiologist", by E.J. Hall and A.J. Giaccia [1]. Although the concepts of direct and indirect effects of radiation are fully applicable to low-LET (linear energy transfer) radioresistant tumor cells/normal tissues such as osteosarcoma cells and chondrocytes, it is believed that radiation-associated damage to DNA does not play a major role in the mechanism of cell death in low-LET radiosensitive tumors/normal tissues such as malignant lymphoma cells and lymphocytes. Hall and Giaccia describe lymphocytes as very radiosensitive, based largely on apoptosis subsequent to irradiation. As described in this review, apoptosis of lymphocytes and lymphoma cells is actually induced by the "hydrogen peroxide (H₂O₂) effect", which I propose in this review article for the first time. The mechanism of lymphocyte death via the H₂O₂ effect represents an ideal model to develop the enhancement method of radiosensitivity for radiation therapy of malignant neoplasms. In terms of imitating the high radiosensitivity of lymphocytes, osteosarcoma cells (representative of low-LET radioresistant cells) might be the ideal model for indicating the conversion of cells from radioresistant to radiosensitive utilizing the H₂O₂ effect. External beam radiation such as X-rays and high-energy electrons for use in modern radiotherapy are generally produced using a linear accelerator. We theorized that when tumors are irradiated in the presence of H₂O₂, the activities of anti-oxidative enzymes such as peroxidases and catalase are blocked and oxygen molecules are produced at the same time via the H₂O₂ effect, resulting in oxidative damage to low-LET radioresistant tumor cells, thereby rendering them highly sensitive to irradiation. In this

  9. Paradigm Shift in Radiation Biology/Radiation Oncology—Exploitation of the “H2O2 Effect” for Radiotherapy Using Low-LET (Linear Energy Transfer Radiation such as X-rays and High-Energy Electrons

    Directory of Open Access Journals (Sweden)

    Yasuhiro Ogawa

    2016-02-01

    Full Text Available Most radiation biologists/radiation oncologists have long accepted the concept that the biologic effects of radiation principally involve damage to deoxyribonucleic acid (DNA, which is the critical target, as described in “Radiobiology for the Radiologist”, by E.J. Hall and A.J. Giaccia [1]. Although the concepts of direct and indirect effects of radiation are fully applicable to low-LET (linear energy transfer radioresistant tumor cells/normal tissues such as osteosarcoma cells and chondrocytes, it is believed that radiation-associated damage to DNA does not play a major role in the mechanism of cell death in low-LET radiosensitive tumors/normal tissues such as malignant lymphoma cells and lymphocytes. Hall and Giaccia describe lymphocytes as very radiosensitive, based largely on apoptosis subsequent to irradiation. As described in this review, apoptosis of lymphocytes and lymphoma cells is actually induced by the “hydrogen peroxide (H2O2 effect”, which I propose in this review article for the first time. The mechanism of lymphocyte death via the H2O2 effect represents an ideal model to develop the enhancement method of radiosensitivity for radiation therapy of malignant neoplasms. In terms of imitating the high radiosensitivity of lymphocytes, osteosarcoma cells (representative of low-LET radioresistant cells might be the ideal model for indicating the conversion of cells from radioresistant to radiosensitive utilizing the H2O2 effect. External beam radiation such as X-rays and high-energy electrons for use in modern radiotherapy are generally produced using a linear accelerator. We theorized that when tumors are irradiated in the presence of H2O2, the activities of anti-oxidative enzymes such as peroxidases and catalase are blocked and oxygen molecules are produced at the same time via the H2O2 effect, resulting in oxidative damage to low-LET radioresistant tumor cells, thereby rendering them highly sensitive to irradiation. In this

  10. 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.

  11. 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.

  12. 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.

  13. Wavelength-shifted Cherenkov radiators

    Science.gov (United States)

    Krider, E. P.; Jacobson, V. L.; Pifer, A. E.; Polakos, P. A.; Kurz, R. J.

    1976-01-01

    The scintillation and Cherenkov responses of plastic Cherenkov radiators containing different wavelength-shifting fluors in varying concentrations have been studied in beams of low energy protons and pions. For cosmic ray applications, where large Cherenkov to scintillation ratios are desired, the optimum fluor concentrations are 0.000025 by weight or less.

  14. 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

  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. 变换工段节能改造小结%Sum-Up of Energy-Saving Renovation of Shift Conversion Section

    Institute of Scientific and Technical Information of China (English)

    姚鹏飞

    2015-01-01

    In running of two sets of shift conversion units which adopt 2.0 MPa without saturating tower total low-temperature shift conversion process there are problems of great system resistance and high steam consumption, etc.After sum-up and consult to relative experiences, by technical transformation the gas stream is split, enabling air speed to be in controllable range, and realizing the goal of reducing system resistance and steam consumption.After the revamp, the resistance of the shift conversion system is reduced from 0.25 MPa to about 0.01 MPa, and steam consumption per ton of ammonia is lowered from 540 ~620 kg to 420 ~440 kg.%2套采用2.0 MPa 无饱和塔全低变工艺的变换装置在运行中均存在系统阻力大、蒸汽消耗高等问题。经总结和借鉴相关经验,通过技改实现气体分流,使单套变换系统空速在可控范围内,达到了降低系统阻力及蒸汽消耗的目的。改造后,变换系统阻力由0.25 MPa 降至约0.01 MPa,吨氨蒸汽耗由540~620 kg 降至420~440 kg。

  17. 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

  18. 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.

  19. 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.

  20. 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...

  1. 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.

  2. Compressive Shift Retrieval

    Science.gov (United States)

    Ohlsson, Henrik; Eldar, Yonina C.; Yang, Allen Y.; Sastry, S. Shankar

    2014-08-01

    The classical shift retrieval problem considers two signals in vector form that are related by a shift. The problem is of great importance in many applications and is typically solved by maximizing the cross-correlation between the two signals. Inspired by compressive sensing, in this paper, we seek to estimate the shift directly from compressed signals. We show that under certain conditions, the shift can be recovered using fewer samples and less computation compared to the classical setup. Of particular interest is shift estimation from Fourier coefficients. We show that under rather mild conditions only one Fourier coefficient suffices to recover the true shift.

  3. 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 .

  4. The energies of formation and mobilities of Cu surface species on Cu and ZnO in methanol and water gas shift atmospheres studied by DFT

    DEFF Research Database (Denmark)

    Rasmussen, Dominik Bjørn; Janssens, Ton V.W.; Temel, Burcin;

    2012-01-01

    ) species are investigated in relevant synthesis gas compositions. The CuCO and Cu2HCOO species are identified to be predominant for metal transport on Cu particles, which may contribute to sintering of Cu by particle migration and coalescence. Furthermore, transport of Cu on ZnO is found mostly to occur......Catalysts based on copper, such as the Cu/ZnO/Al2O3 system are widely used for industrial scale methanol synthesis and the low temperature water gas shift reaction. A common characteristic of these catalysts is that they deactivate quite rapidly during operation and therefore understanding...... through CuCO species, which indicates that CuCO is an important species for Ostwald ripening in a Cu/ZnO catalyst. These results provide atomistic perspective on the diffusion of the species that may contribute to catalyst sintering, therefore lending a valuable foundation for future investigations...

  5. Energy band‐gap shift with gamma-ray radiation and carbon n-delta-doping in GaAs/AlGaAs QWs structures

    Energy Technology Data Exchange (ETDEWEB)

    Daoudi, M., E-mail: mahmouddaoudi@ymail.com [Laboratoire de Photovoltaïque, Centre de Recherche et des Technologies de l' énergie, BP 95, Hammam-Lif 2050 (Tunisia); Hosni, F. [Laboratoire de Radio-traitement, Centre National des Sciences et Technologie Nucléaires, 2020 Sidi-Thabet (Tunisia); Khalifa, N.; Dhifallah, I. [Laboratoire de Photovoltaïque, Centre de Recherche et des Technologies de l' énergie, BP 95, Hammam-Lif 2050 (Tunisia); Farah, K. [Laboratoire de Radio-traitement, Centre National des Sciences et Technologie Nucléaires, 2020 Sidi-Thabet (Tunisia); Hamzaoui, A.H. [Centre National de Recherche en Sciences des Matériaux, Hammam-Lif 2050 (Tunisia); Ouerghi, A. [Laboratoire de Photonique et de Nanostructures, CNRS Route de Nozay, 91460 Marcoussis (France); Chtourou, R. [Laboratoire de Photovoltaïque, Centre de Recherche et des Technologies de l' énergie, BP 95, Hammam-Lif 2050 (Tunisia)

    2014-05-01

    The aim of this work is to investigate two different delta-doping (silicon and carbon) after gamma irradiation. Delta-doping GaAs/AlGaAs heterojunctions grown by molecular beam epitaxy on (1 0 0) GaAs substrates have been studied by photoluminescence (PL) spectroscopy. A theoretical study was conducted using the resolution of Schrödinger and Poisson equations written within the Hartree approximation. PL measurements as function of the power excitation at 10 K shows a red-shift due to free carriers effect on properties of GaAs/AlGaAs quantum well (QW). Its dependence on the density of the two-dimensional electron gas (2DEG) at the GaAs/AlGaAs interface has been analyzed on the basis of the quantum confined Stark, the band-gap renormalization and Burstein–Moss (BM) effects. It is noted that the gamma radiation has changed the type of the exciton recombination.

  6. Design principles for shift current photovoltaics

    Science.gov (United States)

    Cook, Ashley M.; M. Fregoso, Benjamin; de Juan, Fernando; Coh, Sinisa; Moore, Joel E.

    2017-01-01

    While the basic principles of conventional solar cells are well understood, little attention has gone towards maximizing the efficiency of photovoltaic devices based on shift currents. By analysing effective models, here we outline simple design principles for the optimization of shift currents for frequencies near the band gap. Our method allows us to express the band edge shift current in terms of a few model parameters and to show it depends explicitly on wavefunctions in addition to standard band structure. We use our approach to identify two classes of shift current photovoltaics, ferroelectric polymer films and single-layer orthorhombic monochalcogenides such as GeS, which display the largest band edge responsivities reported so far. Moreover, exploring the parameter space of the tight-binding models that describe them we find photoresponsivities that can exceed 100 mA W-1. Our results illustrate the great potential of shift current photovoltaics to compete with conventional solar cells.

  7. Design principles for shift current photovoltaics.

    Science.gov (United States)

    Cook, Ashley M; M Fregoso, Benjamin; de Juan, Fernando; Coh, Sinisa; Moore, Joel E

    2017-01-25

    While the basic principles of conventional solar cells are well understood, little attention has gone towards maximizing the efficiency of photovoltaic devices based on shift currents. By analysing effective models, here we outline simple design principles for the optimization of shift currents for frequencies near the band gap. Our method allows us to express the band edge shift current in terms of a few model parameters and to show it depends explicitly on wavefunctions in addition to standard band structure. We use our approach to identify two classes of shift current photovoltaics, ferroelectric polymer films and single-layer orthorhombic monochalcogenides such as GeS, which display the largest band edge responsivities reported so far. Moreover, exploring the parameter space of the tight-binding models that describe them we find photoresponsivities that can exceed 100 mA W(-1). Our results illustrate the great potential of shift current photovoltaics to compete with conventional solar cells.

  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

    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

  9. Fluorescence spectroscopic studies on binding of a flavonoid antioxidant quercetin to serum albumins

    Indian Academy of Sciences (India)

    Beena Mishra; Atanu Barik; K Indira Priyadarsini; Hari Mohan

    2005-11-01

    Binding of quercetin to human serum albumin (HSA) was studied and the binding constant measured by following the red-shifted absorption spectrum of quercetin in the presence of HSA and the quenching of the intrinsic protein fluorescence in the presence of different concentrations of quercetin. Fluorescence lifetime measurements of HSA showed decrease in the average lifetimes indicating binding at a location, near the tryptophan moiety, and the possibility of fluorescence energy transfer between excited tryptophan and quercetin. Critical transfer distance () was determined, from which the mean distance between tryptophan-214 in HSA and quercetin was calculated. The above studies were also carried out with bovine serum albumin (BSA).

  10. 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.

  11. Statistical Treatment of Low-Energy Nuclear Level Schemes

    Institute of Scientific and Technical Information of China (English)

    M.Gholami; M.Kildir; A.N.Behkami

    2007-01-01

    The level density parameter and the back shift energy E1 are determined for nuclei with A-values across the whole periodic table from fits to complete level schemes at low excitation energy near the neutron binding energies.We find that the energy back shift E1 shows complicated behavior and depends on the type of the nucleus,even-even,odd mass,and odd-odd.The spin cut-off factor has also been investigated for nuclei mentioned above.The results arecompared with the previous results and different experimental data on level densities.

  12. Lamb Shift in Nonrelativistic Quantum Electrodynamics.

    Science.gov (United States)

    Grotch, Howard

    1981-01-01

    The bound electron self-energy or Lamb shift is calculated in nonrelativistic quantum electrodynamics. Retardation is retained and also an interaction previously dropped in other nonrelativistic approaches is kept. Results are finite without introducing a cutoff and lead to a Lamb shift in hydrogen of 1030.9 MHz. (Author/JN)

  13. On the calculation of Mossbauer isomer shift

    NARCIS (Netherlands)

    Filatov, Michael

    2007-01-01

    A quantum chemical computational scheme for the calculation of isomer shift in Mossbauer spectroscopy is suggested. Within the described scheme, the isomer shift is treated as a derivative of the total electronic energy with respect to the radius of a finite nucleus. The explicit use of a finite nuc

  14. The invasion of non-native grasses into California grasslands has caused a shift in energy partitioning between latent and sensible heat flux, reduced albedo and higher surface temperatures

    Science.gov (United States)

    Koteen, L. E.; Harte, J.; Baldocchi, D. D.

    2012-12-01

    In California, native grasses have been largely displaced across millions of acres of grassland habitat by the invasion of non-native grasses from Mediterranean Europe. Although seemingly subtle, this shift in grass species composition has altered the water and energy cycles in these ecosystems due to a shift in life cycle strategy. Native California grasses are perennial and long-lived. To survive California's long summer drought, they possess deep roots to harvest moisture along the full depth of the soil profile. Aboveground, most California perennial grasses are bunchy and dense, covering the ground and restricting soil evaporation. Their growing season extends over most of the year, thus maintaining an unbroken interaction along the soil-plant-atmosphere continuum, and enabling the plants to draw water from deep soil layers well into the dry summer. In contrast, the now-dominant non-native grasses are annuals. They grow from seed each year when Autumn rains begin, and die with the onset of summer drought. Aboveground, non-native annuals are sparse relative to native perennials, and possess a shallow root system with the large majority of root biomass above 20 cm depth. To determine the impact of this land cover shift on ecosystem water and energy cycles, we measured the components of the surface energy balance at a grassland site in northern coastal California where remnant perennial grasses are found growing alongside regions that have undergone non-native invasion. Specifically, in locations dominated by each grass type, we measured net radiation and ground and canopy heat flux through the surface renewal method. We also measured midday PAR albedo to determine the impact of grassland invasion on energy capture. In three years of measurements, corresponding to average, wet and dry years, we found that energy partitioning during the growing season is similar between grass types. However, once non-native annual grasses senesce in mid to late spring, the ratio

  15. 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...

  16. The retarded energy shift and pair polarizabilities of interacting atoms in an external field. Application of resummed field-theoretical perturbation theory

    NARCIS (Netherlands)

    Michels, M.A.J.; Suttorp, L.G.

    1980-01-01

    The interaction energy of two atoms in the presence of an external electrostatic field is evaluated up to sixth order with the help of covariant field-theoretical perturbation theory. The divergent Feynman diagrams entering the calculation are resummed according to a systematic procedure that the au

  17. Analytic Morse/long-range potential energy surfaces and predicted infrared spectra for CO-H2 dimer and frequency shifts of CO in (para-H2)N N = 1-20 clusters

    Science.gov (United States)

    Li, Hui; Zhang, Xiao-Long; Le Roy, Robert J.; Roy, Pierre-Nicholas

    2013-10-01

    A five-dimensional ab initio potential energy surface (PES) for CO-H2 that explicitly incorporates dependence on the stretch coordinate of the CO monomer has been calculated. Analytic four-dimensional PESs are obtained by least-squares fitting vibrationally averaged interaction energies for vCO = 0 and 1 to the Morse/long-range potential function form. These fits to 30 206 points have root-mean-square (RMS) deviations of 0.087 and 0.082 cm-1, and require only 196 parameters. The resulting vibrationally averaged PESs provide good representations of the experimental infrared data: for infrared transitions of para H2-CO and ortho H2-CO, the RMS discrepancies are only 0.007 and 0.023 cm-1, which are almost in the same accuracy as those values of 0.010 and 0.018 cm-1 obtained from full six-dimensional ab initio PESs of V12 [P. Jankowski, A. R. W. McKellar, and K. Szalewicz, Science 336, 1147 (2012)]. The calculated infrared band origin shift associated with the fundamental of CO is -0.179 cm-1 for para H2-CO, which is the same value as that extrapolated experimental value, and slightly better than the value of -0.176 cm-1 obtained from V12 PESs. With these potentials, the path integral Monte Carlo algorithm and a first order perturbation theory estimate are used to simulate the CO vibrational band origin frequency shifts of CO in (para H2)N-CO clusters for N = 1-20. The predicted vibrational frequency shifts are in excellent agreement with available experimental observations. Comparisons are also made between these model potentials.

  18. Geochemically induced shifts in catabolic energy yields explain past ecological changes of diffuse vents in the East Pacific Rise 9°50'N area

    Directory of Open Access Journals (Sweden)

    Hentscher Michael

    2012-01-01

    Full Text Available Abstract The East Pacific Rise (EPR at 9°50'N hosts a hydrothermal vent field (Bio9 where the change in fluid chemistry is believed to have caused the demise of a tubeworm colony. We test this hypothesis and expand on it by providing a thermodynamic perspective in calculating free energies for a range of catabolic reactions from published compositional data. The energy calculations show that there was excess H2S in the fluids and that oxygen was the limiting reactant from 1991 to 1997. Energy levels are generally high, although they declined in that time span. In 1997, sulfide availability decreased substantially and H2S was the limiting reactant. Energy availability dropped by a factor of 10 to 20 from what it had been between 1991 and 1995. The perishing of the tubeworm colonies began in 1995 and coincided with the timing of energy decrease for sulfide oxidizers. In the same time interval, energy availability for iron oxidizers increased by a factor of 6 to 8, and, in 1997, there was 25 times more energy per transferred electron in iron oxidation than in sulfide oxidation. This change coincides with a massive spread of red staining (putative colonization by Fe-oxidizing bacteria between 1995 and 1997. For a different cluster of vents from the EPR 9°50'N area (Tube Worm Pillar, thermodynamic modeling is used to examine changes in subseafloor catabolic metabolism between 1992 and 2000. These reactions are deduced from deviations in diffuse fluid compositions from conservative behavior of redox-sensitive species. We show that hydrogen is significantly reduced relative to values expected from conservative mixing. While H2 concentrations of the hydrothermal endmember fluids were constant between 1992 and 1995, the affinities for hydrogenotrophic reactions in the diffuse fluids decreased by a factor of 15 and then remained constant between 1995 and 2000. Previously, these fluids have been shown to support subseafloor methanogenesis. Our

  19. Effect of core quantum-dot size on power-conversion-efficiency for silicon solar-cells implementing energy-down-shift using CdSe/ZnS core/shell quantum dots.

    Science.gov (United States)

    Baek, Seung-Wook; Shim, Jae-Hyoung; Seung, Hyun-Min; Lee, Gon-Sub; Hong, Jin-Pyo; Lee, Kwang-Sup; Park, Jea-Gun

    2014-11-07

    Silicon solar cells mainly absorb visible light, although the sun emits ultraviolet (UV), visible, and infrared light. Because the surface reflectance of a textured surface with SiNX film on a silicon solar cell in the UV wavelength region (250-450 nm) is higher than ∼27%, silicon solar-cells cannot effectively convert UV light into photo-voltaic power. We implemented the concept of energy-down-shift using CdSe/ZnS core/shell quantum-dots (QDs) on p-type silicon solar-cells to absorb more UV light. CdSe/ZnS core/shell QDs demonstrated clear evidence of energy-down-shift, which absorbed UV light and emitted green-light photoluminescence signals at a wavelength of 542 nm. The implementation of 0.2 wt% (8.8 nm QDs layer) green-light emitting CdSe/ZnS core/shell QDs reduced the surface reflectance of the textured surface with SiNX film on a silicon solar-cell from 27% to 15% and enhanced the external quantum efficiency (EQE) of silicon solar-cells to around 30% in the UV wavelength region, thereby enhancing the power conversion efficiency (PCE) for p-type silicon solar-cells by 5.5%.

  20. 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.

  1. 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.

  2. Influence of Chemical Effect on the Kβ/Kα Intensity Ratios and Kβ Energy Shift of Co, Ni, Cu, and Zn Complexes

    Institute of Scientific and Technical Information of China (English)

    G. Apaydma, V. Ayhkg; Z. Biyiklioglu; E. Tirasoglu; H. Kantekin

    2008-01-01

    Chemical effects on the Kβ/Kα intensity ratios and ΔE energy differences for Co, Ni, Cu, and Zn complexes were investigated. The samples were excited by 59.5 keV γ-rays from a 241 Am annular radioactive source. K X-rays emitted by samples were counted by an Ultra-LEGe detector with a resolution of 150 eV at 5.9 keV. We observed the effects of different ligands on the Kβ/Kα intensity ratios and ΔE energy differences for Co, Ni, Cu, and Zn complexes. We tried to investigate chemical effects on central atoms using the behaviors of different ligands in these complexes. The experimental values of Kβ/Kα were compared with the theoretical and other experimental values of pure Co, Ni, Cu, and Zn.

  3. 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.

  4. Goos-Hänchen shift in negatively refractive media.

    Science.gov (United States)

    Berman, P R

    2002-12-01

    The Goos-Hänchen shift is calculated when total internal reflection occurs at an interface between "normal" and negatively refractive media. The shift is negative, consistent with the direction of energy flow in the negatively refractive medium.

  5. Invasive mussels alter the littoral food web of a large lake: stable isotopes reveal drastic shifts in sources and flow of energy.

    Directory of Open Access Journals (Sweden)

    Ted Ozersky

    Full Text Available We investigated how establishment of invasive dreissenid mussels impacted the structure and energy sources of the littoral benthic food web of a large temperate lake. We combined information about pre- and postdreissenid abundance, biomass, and secondary production of the littoral benthos with results of carbon and nitrogen stable isotope analysis of archival (predreissenid and recent (postdreissenid samples of all common benthic taxa. This approach enabled us to determine the importance of benthic and sestonic carbon to the littoral food web before, and more than a decade after dreissenid establishment. Long term dreissenid presence was associated with a 32-fold increase in abundance, 6-fold increase in biomass, and 14-fold increase in secondary production of the littoral benthos. Dreissenids comprised a large portion of the post-invasion benthos, making up 13, 38, and 56% of total abundance, biomass, and secondary production, respectively. The predreissenid food web was supported primarily by benthic primary production, while sestonic material was relatively more important to the postdreissenid food web. The absolute importance of both sestonic material and benthic primary production to the littoral benthos increased considerably following dreissenid establishment. Our results show drastic alterations to food web structure and suggest that dreissenid mussels redirect energy and material from the water column to the littoral benthos both through biodeposition of sestonic material as well as stimulation of benthic primary production.

  6. 50 years anniversary of the discovery of the core level chemical shifts. The early years of photoelectron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mårtensson, Nils [Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala (Sweden); Sokolowski, Evelyn [Tvär-Ramsdal 1, 611 99 Tystberga (Sweden); Svensson, Svante, E-mail: Svante.Svensson@fysik.uu.se [Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala (Sweden)

    2014-03-01

    Highlights: • 50 years since the discovery of t the core level chemical shift. • The pioneering years of ESCA. • A critical review of the first core electron chemical shift results. - Abstract: The pioneering years of photoelectron spectroscopy in Uppsala are discussed, especially the work leading to the discovery of the core level chemical shifts. At a very early stage of the project, the pioneering group observed what they described as evidence for chemical shifts in the core level binding energies. However, it can now be seen that the initial observations to a large extent was due to charging of the samples. It is interesting to note that the decisive experiment was realized, not as a result of a systematic study, but was obtained with a large element of serendipity. Only when a chemical binding energy shift was observed between two S2p electron lines in the same molecule, the results were accepted internationally, and the fascinating expansion of modern core level photoelectron spectroscopy could start.

  7. Lamb shift of Unruh detector levels

    Energy Technology Data Exchange (ETDEWEB)

    Garbrecht, Bjoern [School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL (United Kingdom); Prokopec, Tomislav [Institute for Theoretical Physics (ITF) and Spinoza Institute, Utrecht University, Leuvenlaan 4, Postbus 80.195, 3508 TD Utrecht (Netherlands)

    2006-06-07

    We argue that the energy levels of an Unruh detector experience an effect similar to the Lamb shift in quantum electrodynamics. As a consequence, the spectrum of energy levels in a curved background is different from that in flat space. As examples, we consider a detector in an expanding universe and in Rindler space, and for the latter case we suggest a new expression for the local virtual energy density seen by an accelerated observer. In the ultraviolet domain, that is when the space between the energy levels is larger than the Hubble rate or the acceleration of the detector, the Lamb shift quantitatively dominates over the thermal response rate.

  8. Lamb Shift of Unruh Detector Levels

    CERN Document Server

    Garbrecht, B; Garbrecht, Bjorn; Prokopec, Tomislav

    2006-01-01

    We argue that the energy levels of an Unruh detector experience an effect similar to the Lamb shift in Quantum Electrodynamics. As a consequence, the spectrum of energy levels in a curved background is different from that in flat space. As examples, we consider a detector in an expanding Universe and in Rindler space, and for the latter case we suggest a new expression for the local virtual energy density seen by an accelerated observer. In the ultraviolet domain, that is when the space between the energy levels is larger than the Hubble rate or the acceleration of the detector, the Lamb shift quantitatively dominates over the thermal response rate.

  9. Atomic many-body effects and Lamb shifts in alkali metals

    Science.gov (United States)

    Ginges, J. S. M.; Berengut, J. C.

    2016-05-01

    We present a detailed study of the radiative potential method [V. V. Flambaum and J. S. M. Ginges, Phys. Rev. A 72, 052115 (2005), 10.1103/PhysRevA.72.052115], which enables the accurate inclusion of quantum electrodynamics (QED) radiative corrections in a simple manner in atoms and ions over the range 10 ≤Z ≤120 , where Z is the nuclear charge. Calculations are performed for binding energy shifts to the lowest valence s , p , and d waves over the series of alkali-metal atoms Na to E119. The high accuracy of the radiative potential method is demonstrated by comparison with rigorous QED calculations in frozen atomic potentials, with deviations on the level of 1%. The many-body effects of core relaxation and second- and higher-order perturbation theory on the interaction of the valence electron with the core are calculated. The inclusion of many-body effects tends to increase the size of the shifts, with the enhancement particularly significant for d waves; for K to E119, the self-energy shifts for d waves are only an order of magnitude smaller than the s -wave shifts. It is shown that taking into account many-body effects is essential for an accurate description of the Lamb shift.

  10. Implementing OpenShift

    CERN Document Server

    Miller, Adam

    2013-01-01

    A standard tutorial-based approach to using OpenShift and deploying custom or pre-built web applications to the OpenShift Online cloud.This book is for software developers and DevOps alike who are interested in learning how to use the OpenShift Platform-as-a-Service for developing and deploying applications, how the environment works on the back end, and how to deploy their very own open source Platform-as-a-Service based on the upstream OpenShift Origin project.

  11. Quantized beam shifts

    CERN Document Server

    Kort-Kamp, W J M; Dalvit, D A R

    2015-01-01

    We predict quantized Imbert-Fedorov, Goos-H\\"anchen, and photonic spin Hall shifts for light beams impinging on a graphene-on-substrate system in an external magnetic field. In the quantum Hall regime the Imbert-Fedorov and photonic spin Hall shifts are quantized in integer multiples of the fine structure constant $\\alpha$, while the Goos- H\\"anchen ones in multiples of $\\alpha^2$. We investigate the influence on these shifts of magnetic field, temperature, and material dispersion and dissipation. An experimental demonstration of quantized beam shifts could be achieved at terahertz frequencies for moderate values of the magnetic field.

  12. Enhancing the output current of a CdTe solar cell via a CN-free hydrocarbon luminescent down-shifting fluorophore with intramolecular energy transfer and restricted internal rotation characteristics.

    Science.gov (United States)

    Li, Yilin; Olsen, Joseph; Dong, Wen-Ji

    2015-04-01

    A CN-free hydrocarbon fluorophore (Perylene-TPE) was synthesized as a new luminescent down-shifting (LDS) material. Its photophysical properties in both the solution state and the solid state were studied. The unity fluorescence quantum yield of Perylene-TPE observed in its solid state is considered to be from the characteristics of intramolecular energy transfer (IET) and restricted internal rotation (RIR). This is supported by the results from theoretical calculations and spectroscopic measurements. For the photovoltaic application of Perylene-TPE, a theoretical modeling study suggests that using the LDS film of Perylene-TPE may increase the output short circuit current density (Jsc) of a CdTe solar cell by 2.95%, enhance the spectral response of a CdTe solar cell at 400 nm by 41%, and shift the incident solar photon distribution from short-wavelength (500 nm). Experimentally, placing a LDS film of Perylene-TPE on a CdTe solar cell can enhance its output Jsc by as high as 3.30 ± 0.31%, which is comparable to the current commercially available LDS material – Y083 (3.28% ± 0.37%).

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. Variations of nuclear binding with quark masses

    CERN Document Server

    Carrillo-Serrano, M E; Tsushima, K; Thomas, A W; Afnan, I R

    2012-01-01

    We investigate the variation with light quark mass of the mass of the nucleon as well as the masses of the mesons commonly used in a one-boson-exchange model of the nucleon-nucleon force. Care is taken to evaluate the meson mass shifts at the kinematic point relevant to that problem. Using these results, the corresponding changes in the energy of the 1 S0 anti-bound state, the binding energies of the deuteron, triton and selected finite nuclei are evaluated using a one-boson exchange model. The results are discussed in the context of possible corrections to the standard scenario for big bang nucleosynthesis in the case where, as suggested by recent observations of quasar absorption spectra, the quark masses may have changed over the age of the Universe.

  18. Making Shifts toward Proficiency

    Science.gov (United States)

    McGatha, Maggie B.; Bay-Williams, Jennifer M.

    2013-01-01

    The Leading for Mathematical Proficiency (LMP) Framework (Bay-Williams et al.) has three components: (1) The Standards for Mathematical Practice; (2) Shifts in classroom practice; and (3) Teaching skills. This article briefly describes each component of the LMP framework and then focuses more in depth on the second component, the shifts in…

  19. Shifting employment revisited

    NARCIS (Netherlands)

    Cremers, Jan; Gramuglia, Alessia

    2014-01-01

    The CLR-network examined in 2006 the phenomenon of undeclared labour, with specific regard to the construction sector. The resulting study, Shifting Employment: undeclared labour in construction (Shifting-study hereafter), gave evidence that this is an area particularly affected by undeclared activi

  20. Shifted Independent Component Analysis

    DEFF Research Database (Denmark)

    Mørup, Morten; Madsen, Kristoffer Hougaard; Hansen, Lars Kai

    2007-01-01

    Delayed mixing is a problem of theoretical interest and practical importance, e.g., in speech processing, bio-medical signal analysis and financial data modelling. Most previous analyses have been based on models with integer shifts, i.e., shifts by a number of samples, and have often been carried...

  1. OpenShift cookbook

    CERN Document Server

    Gulati, Shekhar

    2014-01-01

    If you are a web application developer who wants to use the OpenShift platform to host your next big idea but are looking for guidance on how to achieve this, then this book is the first step you need to take. This is a very accessible cookbook where no previous knowledge of OpenShift is needed.

  2. 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.

  3. 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

  4. 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.

  5. 基于偏离份额法的河北省能源终端消费结构研究%Energy End-Use Structure of Hebei Province Obtained Using Shift-Share Methods

    Institute of Scientific and Technical Information of China (English)

    吴江; 孙彤; 石磊

    2013-01-01

    Energy is one of the most important factors for human survival and development. As China' s urbanization, economy and energy requirements continue to grow, pressure will increase on resources and the environment. It is therefore necessary to address the sustainable development of energy for Hebei province, one of the largest energy-consuming provinces in China. Based on energy data for China and Hebei from 2005 to 2009, the shift-share method was used to analyze energy end-use structure for the province. We found that energy consumption growth for Hebei was a little lower than the national average. Industrial energy consumption is the most important factor influencing energy use in Hebei. In the future, the overall energy consumption of Hebei province will not increase greatly. Among all industries, the energy consumption of agriculture, forestry, husbandry and fishery are the most likely to grow, and the energy use of life consumption is the least likely to grow. The high energy-consuming industries do not have a monopoly on the overall energy end-consumption structure in Hebei, so energy terminal consumption structure was not the main factor leading to the energy crisis in Hebei during the period we studied. We suggest that energy planning be developed as soon as possible, using legal means to restrain the disorderly development of energy and reducing the waste of energy. Advanced technology to reduce current energy usage and build a buffer for future energy consumption should be introduced. The influence of energy price mechanism on energy structure is one of the most important economic factors and results in the inefficient consumption of energy, we must leverage prices to force energy consumption structure optimization. Last, multi-channel investment and financing mechanisms to solve funds shortages should be innovated. These suggestions are given to improve energy consumption structure and achieve sustainable development in Hebei.%河北省是传统能源消

  6. Looping through the Lamb Shift

    Energy Technology Data Exchange (ETDEWEB)

    Hazi, A U

    2007-02-06

    Sometimes in science, a small measurement can have big ramifications. For a team of Livermore scientists, such was the case when they measured a small shift in the spectrum of extremely ionized atoms of uranium. The measurement involves the Lamb shift, a subtle change in the energy of an electron orbiting an atom's nucleus. The precision of the Livermore result was 10 times greater than that of existing measurements, making it the best measurement to date of a complicated correction to the simplest quantum description of how atoms behave. The measurement introduces a new realm in the search for deviations between the theory of quantum electrodynamics (QED), which is an extension of quantum mechanics, and the real world. Such deviations, if discovered, would have far-reaching consequences, indicating that QED is not a fundamental theory of nature.

  7. Adding a complex shift to HVPT

    Energy Technology Data Exchange (ETDEWEB)

    Killingbeck, John P [Observatoire de Besancon-Institut UTINAM, CNRS UMR 6213, Universite de Franche-Comte, 41 bis Avenue de l' Observatoire BP1615, 25010 Besancon cedex (France) and Centre for Mathematics, Loten Building, University of Hull, Hull HU6 7RX (United Kingdom)

    2009-03-20

    A complex coordinate shift is incorporated in renormalized hypervirial perturbation theory. Test calculations on harmonic oscillators with cubic perturbations show that the resulting method produces accurate numerical results for the real energies of PT symmetric Hamiltonians with complex potentials and for the complex resonance energies of Hamiltonians with real potentials.

  8. 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.

  9. Shift Verification and Validation

    Energy Technology Data Exchange (ETDEWEB)

    Pandya, Tara M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Evans, Thomas M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Davidson, Gregory G [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Johnson, Seth R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Godfrey, Andrew T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-09-07

    This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of Light Water Reactors (CASL). Five main types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed-source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results, and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over a burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.

  10. Shift Verification and Validation

    Energy Technology Data Exchange (ETDEWEB)

    Pandya, Tara M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Evans, Thomas M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Davidson, Gregory G [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Johnson, Seth R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Godfrey, Andrew T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-09-07

    This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of LightWater Reactors (CASL). Fivemain types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over a burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.

  11. 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.

  12. Search for Higgs shifts in white dwarfs

    Energy Technology Data Exchange (ETDEWEB)

    Onofrio, Roberto [Dipartimento di Fisica e Astronomia " Galileo Galilei," Università di Padova, Via Marzolo 8, I-35131 Padova (Italy); Wegner, Gary A., E-mail: onofrior@gmail.com, E-mail: gary.a.wegner@dartmouth.edu [Department of Physics and Astronomy, Dartmouth College, 6127 Wilder Laboratory, Hanover, NH 03755 (United States)

    2014-08-20

    We report on a search for differential shifts between electronic and vibronic transitions in carbon-rich white dwarfs BPM 27606 and Procyon B. The absence of differential shifts within the spectral resolution and taking into account systematic effects such as space motion and pressure shifts allows us to set the first upper bound of astrophysical origin on the coupling between the Higgs field and the Kreschmann curvature invariant. Our analysis provides the basis for a more general methodology to derive bounds to the coupling of long-range scalar fields to curvature invariants in an astrophysical setting complementary to the ones available from high-energy physics or table-top experiments.

  13. Influences on Dietary Choices during Day versus Night Shift in Shift Workers: A Mixed Methods Study

    Directory of Open Access Journals (Sweden)

    Emily K. Bonnell

    2017-02-01

    Full Text Available Shift work is associated with diet-related chronic conditions such as obesity and cardiovascular disease. This study aimed to explore factors influencing food choice and dietary intake in shift workers. A fixed mixed method study design was undertaken on a convenience sample of firefighters who continually work a rotating roster. Six focus groups (n = 41 were conducted to establish factors affecting dietary intake whilst at work. Dietary intake was assessed using repeated 24 h dietary recalls (n = 19. Interviews were audio recorded, transcribed verbatim, and interpreted using thematic analysis. Dietary data were entered into FoodWorks and analysed using Wilcoxon signed-rank test; p < 0.05 was considered significant. Thematic analysis highlighted four key themes influencing dietary intake: shift schedule; attitudes and decisions of co-workers; time and accessibility; and knowledge of the relationship between food and health. Participants reported consuming more discretionary foods and limited availability of healthy food choices on night shift. Energy intakes (kJ/day did not differ between days that included a day or night shift but greater energy density (EDenergy, kJ/g/day of the diet was observed on night shift compared with day shift. This study has identified a number of dietary-specific shift-related factors that may contribute to an increase in unhealthy behaviours in a shift-working population. Given the increased risk of developing chronic diseases, organisational change to support workers in this environment is warranted.

  14. 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.

  15. Ligand binding to WW tandem domains of YAP2 transcriptional regulator is under negative cooperativity.

    Science.gov (United States)

    Schuchardt, Brett J; Mikles, David C; Hoang, Lawrence M; Bhat, Vikas; McDonald, Caleb B; Sudol, Marius; Farooq, Amjad

    2014-12-01

    YES-associated protein 2 (YAP2) transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of the WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules.

  16. 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

  17. Surface shift of the occupied and unoccupied 4f levels of the rare-earth metals

    DEFF Research Database (Denmark)

    Aldén, Magnus; Johansson, Börje; Skriver, Hans Lomholt

    1995-01-01

    The surface energy shifts of the occupied and unoccupied 4f levels for the lanthanide metals have been calculated from first principles by means of a Green’s-function technique within the tight-binding linear muffin-tin orbitals method. We use the concept of complete screening to identify...... as well as those found in previous initial-state model calculations. The present theory agrees well with very recent high-resolution, single-crystal film measurements for Gd, Tb, Dy, Ho, Er, Tm, and Lu. We furthermore utilize the unique possibility offered by the lanthanide metals to clarify the roles...

  18. Nuclear size correction to the Lamb shift of one-electron atoms

    CERN Document Server

    Yerokhin, Vladimir A

    2010-01-01

    The nuclear size effect on the one-loop self energy and vacuum polarization is evaluated for the 1s, 2s, 3s, 2p_{1/2}, and 2p_{3/2} states of hydrogen-like ions. The calculation is performed to all orders in the binding nuclear strength parameter Z\\alpha. Detailed comparison is made with previous all-order calculations and calculations based on the expansion in the parameter Z\\alpha. Extrapolation of the all-order numerical results obtained towards Z=1 provides results for the radiative nuclear size effect on the hydrogen Lamb shift.

  19. STUDY ON SHIFT SCHEDULE AND SIMULATION OF AUTOMATIC TRANSMISSION

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    From the point of view of saving energy, a new shift schedule and auto-controlling strategy for automatic transmission are proposed. In order to verify this shift schedule,a simulation program using a software package of Matlab/Simulink is developed. The simulation results show the shift schedule is correct. This shift schedule has enriched the theory of vehicle automatic maneuvering and will improve the efficiency of hydrodynanic drive system of the vehicle.

  20. Architecture and energy

    DEFF Research Database (Denmark)

    Marsh, Rob; Lauring, Michael

    2011-01-01

    Traditional low-energy architecture has not necessarily led to reduced energy consumption. A paradigm shift is proposed promoting pluralistic energy-saving strategies.......Traditional low-energy architecture has not necessarily led to reduced energy consumption. A paradigm shift is proposed promoting pluralistic energy-saving strategies....