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Sample records for binding energy difference

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

    Science.gov (United States)

    Qi, Chong

    2012-10-01

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

  2. Experimental electron binding energies for thulium in different matrices

    Czech Academy of Sciences Publication Activity Database

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

    2015-01-01

    Roč. 202, JUL (2015), s. 46-55 ISSN 0368-2048 R&D Projects: GA MŠk LG14004; GA ČR(CZ) GAP203/12/1896 Institutional support: RVO:61389005 Keywords : Tm-169 * (169)yb * atomic environment * electron binding energy * chemical shift * natural atomic level width Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.561, year: 2015

  3. Quarkeosynthesis Binding Energy

    Science.gov (United States)

    Webb, Bill

    2009-05-01

    Quarkeosynthesis shows that the binding energy of a nucleus is the difference between the relativistic kinetic energies of its threesome of Jumbo Quarks and that of its building block quarks from neutrons and protons. There is no involvement of a nuclear strong force or gluon material.

  4. Valence proton-neutron interaction strengths from double binding energy differences

    International Nuclear Information System (INIS)

    Brenner, D.S.; Foy, B.D.; Warner, D.D.; Zamfir, N.V.; Casten, R.F.

    1996-01-01

    Empirical p-n interaction strengths have been extracted from experimental mass data using double-difference binding energy equations. The especially strong interactions for self-conjugate nuclei will be discussed as well as microstructure found for deformed and in doubly magic regions. Valence correlation Schemes provide a basis to comment on the stability of medium mass near-drip-line nuclei and superheavy elements

  5. 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.

  6. Correlating hydrogen oxidation and evolution activity on platinum at different pH with measured hydrogen binding energy.

    Science.gov (United States)

    Sheng, Wenchao; Zhuang, Zhongbin; Gao, Minrui; Zheng, Jie; Chen, Jingguang G; Yan, Yushan

    2015-01-08

    The hydrogen oxidation/evolution reactions are two of the most fundamental reactions in distributed renewable electrochemical energy conversion and storage systems. The identification of the reaction descriptor is therefore of critical importance for the rational catalyst design and development. Here we report the correlation between hydrogen oxidation/evolution activity and experimentally measured hydrogen binding energy for polycrystalline platinum examined in several buffer solutions in a wide range of electrolyte pH from 0 to 13. The hydrogen oxidation/evolution activity obtained using the rotating disk electrode method is found to decrease with the pH, while the hydrogen binding energy, obtained from cyclic voltammograms, linearly increases with the pH. Correlating the hydrogen oxidation/evolution activity to the hydrogen binding energy renders a monotonic decreasing hydrogen oxidation/evolution activity with the hydrogen binding energy, strongly supporting the hypothesis that hydrogen binding energy is the sole reaction descriptor for the hydrogen oxidation/evolution activity on monometallic platinum.

  7. Binding energies and energy differences for p-shell nuclei from ab initio calculations with natural orbitals

    Science.gov (United States)

    Fasano, Patrick J.; Caprio, Mark A.; Constantinou, Chrysovalantis; Maris, Pieter; Vary, James P.

    2017-09-01

    Ab initio methods in nuclear theory strive to make quantitative predictions of nuclear observables, starting with the internucleon interaction. In the no-core configuration interaction (NCCI) approach, the nuclear many-body problem is solved in a basis of Slater determinants constructed from single-particle states. NCCI calculations are computationally limited by combinatorial explosion of the many-body basis size; as such, choice of basis greatly influences convergence. Natural orbitals, constructed by diagonalizing the one-body density matrix from an initial many-body calculation, maximize occupation of the lowest single-particle states and thereby reduce the importance of higher-lying many-body basis states. We use natural orbitals to explore energies and energy differences in p-shell nuclei. Supported by the US DOE under Award Nos. DE-FG02-95ER-40934, DE-FG02-91ER-40608, DESC0008485 (SciDAC/NUCLEI), and DE-FG02-87ER40371 and the US NSF under Award No. NSF-PHY05-52843. Computational resources provided by NERSC (DOE Contract DE-AC02-05CH11231).

  8. A Correlation between the Activity of Candida antarctica Lipase B and Differences in Binding Free Energies of Organic Solvent and Substrate

    DEFF Research Database (Denmark)

    Banik, Sindrila Dutta; Nordblad, Mathias; Woodley, John

    2016-01-01

    in an inhibitory effect which is also confirmed by the binding free energies for the solvent and substrate molecules estimated from the simulations. Consequently, the catalytic activity of CALB decreases in polar solvents. This effect is significant, and CALB is over 10 orders of magnitude more active in nonpolar...... of the enzyme may be ascribed to binding of solvent molecules to the enzyme active site region and the solvation energy of substrate molecules in the different solvents. Polar solvent molecules interact strongly with CALB and compete with the substrate to bind to the active site region, resulting...

  9. Molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis on selectivity difference between FKBP51 and FKBP52: Insight into the molecular mechanism of isoform selectivity.

    Science.gov (United States)

    Shi, Danfeng; Bai, Qifeng; Zhou, Shuangyan; Liu, Xuewei; Liu, Huanxiang; Yao, Xiaojun

    2018-01-01

    As co-chaperones of the 90-kDa heat shock protein(HSP90), FK506 binding protein 51 (FKBP51) and FK506 binding protein 52 (FKBP52) modulate the maturation of steroid hormone receptor through their specific FK1 domains (FKBP12-like domain 1). The inhibitors targeting FK1 domains are potential therapies for endocrine-related physiological disorders. However, the structural conservation of the FK1 domains between FKBP51 and FKBP52 make it difficult to obtain satisfactory selectivity in FK506-based drug design. Fortunately, a series of iFit ligands synthesized by Hausch et al exhibited excellent selectivity for FKBP51, providing new opportunity for design selective inhibitors. We performed molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis to reveal selective mechanism for the inhibitor iFit4 binding with FKBP51 and FKBP52. The conformational stability evaluation of the "Phe67-in" and "Phe67-out" states implies that FKBP51 and FKBP52 have different preferences for "Phe67-in" and "Phe67-out" states, which we suggest as the determinant factor for the selectivity for FKBP51. The binding free energy calculations demonstrate that nonpolar interaction is favorable for the inhibitors binding, while the polar interaction and entropy contribution are adverse for the inhibitors binding. According to the results from binding free energy decomposition, the electrostatic difference of residue 85 causes the most significant thermodynamics effects on the binding of iFit4 to FKBP51 and FKBP52. Furthermore, the importance of substructure units on iFit4 were further evaluated by unbinding pathway analysis and residue-residue contact analysis between iFit4 and the proteins. The results will provide new clues for the design of selective inhibitors for FKBP51. © 2017 Wiley Periodicals, Inc.

  10. Binding energy of protonium ions

    Science.gov (United States)

    Assad Abdel-Raouf, Mohamed

    2009-11-01

    The goal of the present work is to calculate the binding energy of the protonium ions bar PPe+ and bar PPe- using Rayleigh- Ritz variational method. It is indicated that an employment of 21 components of the trial wavefunction yields -0.08793 eV as the ground state energy of these ions. Our result agrees quite well with recently obtained results based on elaborate Monte Carlo approximations. It confirms the possible formation of these ions in laboratory.

  11. New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces.

    Science.gov (United States)

    Simões, Inês C M; Costa, Inês P D; Coimbra, João T S; Ramos, Maria J; Fernandes, Pedro A

    2017-01-23

    Knowing how proteins make stable complexes enables the development of inhibitors to preclude protein-protein (P:P) binding. The identification of the specific interfacial residues that mostly contribute to protein binding, denominated as hot spots, is thus critical. Here, we refine an in silico alanine scanning mutagenesis protocol, based on a residue-dependent dielectric constant version of the Molecular Mechanics/Poisson-Boltzmann Surface Area method. We have used a large data set of structurally diverse P:P complexes to redefine the residue-dependent dielectric constants used in the determination of binding free energies. The accuracy of the method was validated through comparison with experimental data, considering the per-residue P:P binding free energy (ΔΔG binding ) differences upon alanine mutation. Different protocols were tested, i.e., a geometry optimization protocol and three molecular dynamics (MD) protocols: (1) one using explicit water molecules, (2) another with an implicit solvation model, and (3) a third where we have carried out an accelerated MD with explicit water molecules. Using a set of protein dielectric constants (within the range from 1 to 20) we showed that the dielectric constants of 7 for nonpolar and polar residues and 11 for charged residues (and histidine) provide optimal ΔΔG binding predictions. An overall mean unsigned error (MUE) of 1.4 kcal mol -1 relative to the experiment was achieved in 210 mutations only with geometry optimization, which was further reduced with MD simulations (MUE of 1.1 kcal mol -1 for the MD employing explicit solvent). This recalibrated method allows for a better computational identification of hot spots, avoiding expensive and time-consuming experiments or thermodynamic integration/ free energy perturbation/ uBAR calculations, and will hopefully help new drug discovery campaigns in their quest of searching spots of interest for binding small drug-like molecules at P:P interfaces.

  12. Ce3+ 5d-centroid shift and vacuum referred 4f-electron binding energies of all lanthanide impurities in 150 different compounds

    International Nuclear Information System (INIS)

    Dorenbos, Pieter

    2013-01-01

    A review on the wavelengths of all five 4f–5d transitions for Ce 3+ in about 150 different inorganic compounds (fluorides, chlorides, bromides, iodides, oxides, sulfides, selenides, nitrides) is presented. It provides data on the centroid shift and the crystal field splitting of the 5d-configuration which are then used to estimate the Eu 2+ inter 4f-electron Coulomb repulsion energy U(6,A) in compound A. The four semi-empirical models (the redshift model, the centroid shift model, the charge transfer model, and the chemical shift model) on lanthanide levels that were developed past 12 years are briefly reviewed. It will be demonstrated how those models together with the collected data of this work and elsewhere can be united to construct schemes that contain the binding energy of electrons in the 4f and 5d states for each divalent and each trivalent lanthanide ion relative to the vacuum energy. As example the vacuum referred binding energy schemes for LaF 3 and La 2 O 3 will be constructed. - Highlights: ► An compilation on all five Ce 3+ 4f–5d energies in 150 inorganic compounds is presented. ► The relationship between the 5d centroid shift and host cation electronegativity id demonstrated. ► The electronic structure scheme of the lanthanides in La 2 O 3 and LaF 3 is presented.

  13. Binding energy of the barbell exciton

    Science.gov (United States)

    Peeters, F. M.; Golub, J. E.

    1991-02-01

    The exciton binding energy in asymmetric coupled double quantum wells is calculated. As the system is electrically tuned from type I to type II, the exciton binding energy decreases from that of a two-dimensional exciton to the binding energy of a spatially separated electron-hole pair, i.e., the barbell exciton.$-- We compare our theoretical results with a recent experiment and find good agreement.

  14. Exciton Binding Energy of Monolayer WS2

    Science.gov (United States)

    Zhu, Bairen; Chen, Xi; Cui, Xiaodong

    2015-03-01

    The optical properties of monolayer transition metal dichalcogenides (TMDC) feature prominent excitonic natures. Here we report an experimental approach to measuring the exciton binding energy of monolayer WS2 with linear differential transmission spectroscopy and two-photon photoluminescence excitation spectroscopy (TP-PLE). TP-PLE measurements show the exciton binding energy of 0.71 +/- 0.01 eV around K valley in the Brillouin zone.

  15. 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....

  16. 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.

  17. Binding energies of hypernuclei and hypernuclear interactions

    International Nuclear Information System (INIS)

    Bodmer, A.R.; Univ. of Illinois, Chicago, IL; Murali, S.; Usmani, Q.N.

    1996-01-01

    In part 1 the effect of nuclear core dynamics on the binding energies of Λ 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 Λ single-particle energy in terms of basic Λ-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 ΛNN forces are required. Also in this framework they discuss core polarization for medium and heavier hypernuclei

  18. Li+-ligand binding energies and the effect of ligand fluorination on the binding energies

    Science.gov (United States)

    Bauschlicher, Charles W.

    2018-02-01

    The Li+-ligand binding energies are computed for seven ligands and their perfluoro analogs using Density Functional Theory. The bonding is mostly electrostatic in origin. Thus the size of the binding energy tends to correlate with the ligand dipole moment, however, the charge-induced dipole contribution can be sufficiently large to affect the dipole-binding energy correlation. The perfluoro species are significantly less strongly bound than their parents, because the electron withdrawing power of the fluorine reduces the ligand dipole moment.

  19. Ubiquitin-binding proteins: similar, but different

    DEFF Research Database (Denmark)

    Andersen, Katrine M; Hofmann, Kay; Hartmann-Petersen, Rasmus

    2005-01-01

    and phosphatases, specific sets of ubiquitinating/deubiquitinating enzymes control the degree of ubiquitination. A large number of ubiquitin-binding proteins act at different steps in the downstream pathways, followed by the ubiquitinated protein. Different families of ubiquitin-binding proteins have been...... described. UBA (ubiquitin-associated) domain-containing proteins is the largest family and includes members involved in different cell processes. The smaller groups of UIM (ubiquitin-interacting motif), GAT [GGA (Golgi-associated gamma-adaptin homologous) and Tom1 (target of Myb 1)], CUE (coupling...

  20. 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.

  1. Different Thermodynamic Signatures for DNA Minor Groove Binding with Changes in Salt Concentration and Temperature

    OpenAIRE

    Wang, Shuo; Kumar, Arvind; Aston, Karl; Nguyen, Binh; Bashkin, James K.; Boykin, David W.; Wilson, W. David

    2013-01-01

    The effects of salt concentration and temperature on the thermodynamics of DNA minor groove binding have quite different signatures: binding enthalpy is salt concentration independent but temperature dependent. Conversely, binding free energy is salt dependent but essentially temperature independent through enthalpy-entropy compensation.

  2. Binding-energy distribution and dephasing of localized biexcitons

    DEFF Research Database (Denmark)

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

    1997-01-01

    We report on the binding energy and dephasing of localized biexciton states in narrow ZnSe multiple quantum wells. The measured binding-energy distribution of the localized biexcitons shows a width of 2.2 meV centered at 8.5 meV, and is fairly independent of the exciton localization energy. In four...

  3. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

    Science.gov (United States)

    Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

    2011-01-01

    The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

  4. Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways.

    Directory of Open Access Journals (Sweden)

    Yu-Ru Zhang

    Full Text Available BACKGROUND: Retinoids are a class of compounds that are chemically related to vitamin A, which is an essential nutrient that plays a key role in vision, cell growth and differentiation. In vivo, retinoids must bind with specific proteins to perform their necessary functions. Plasma retinol-binding protein (RBP and epididymal retinoic acid binding protein (ERABP carry retinoids in bodily fluids, while cellular retinol-binding proteins (CRBPs and cellular retinoic acid-binding proteins (CRABPs carry retinoids within cells. Interestingly, although all of these transport proteins possess similar structures, the modes of binding for the different retinoid ligands with their carrier proteins are different. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we analyzed the various retinoid transport mechanisms using structure and sequence comparisons, binding site analyses and molecular dynamics simulations. Our results show that in the same family of proteins and subcellular location, the orientation of a retinoid molecule within a binding protein is same, whereas when different families of proteins are considered, the orientation of the bound retinoid is completely different. In addition, none of the amino acid residues involved in ligand binding is conserved between the transport proteins. However, for each specific binding protein, the amino acids involved in the ligand binding are conserved. The results of this study allow us to propose a possible transport model for retinoids. CONCLUSIONS/SIGNIFICANCE: Our results reveal the differences in the binding modes between the different retinoid-binding proteins.

  5. Perturbation method for calculating impurity binding energy in an ...

    Indian Academy of Sciences (India)

    Perturbation method is used to calculate the binding energy within the framework of effective mass approximation and taking into account the effect of dielectric mismatch between the dot and the barrier material. The ground-state binding energy of the donor is computed as a function of dot size for finite confinement.

  6. 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...

  7. Perturbation method for calculating impurity binding energy in an ...

    Indian Academy of Sciences (India)

    Nilanjan Sil

    2017-12-18

    Dec 18, 2017 ... Abstract. In the present paper, we have studied the binding energy of the shallow donor hydrogenic impurity, which is confined in an inhomogeneous cylindrical quantum dot (CQD) of GaAs-AlxGa1−xAs. Perturbation method is used to calculate the binding energy within the framework of effective mass ...

  8. Computation of pH-Dependent Binding Free Energies

    Science.gov (United States)

    Kim, M. Olivia; McCammon, J. Andrew

    2015-01-01

    Protein-ligand binding accompanies changes in the surrounding electrostatic environments of the two binding partners and may lead to changes in protonation upon binding. In cases where the complex formation results in a net transfer of protons, the binding process is pH-dependent. However, conventional free energy computations or molecular docking protocols typically employ fixed protonation states for the titratable groups in both binding partners set a priori, which are identical for the free and bound states. In this review, we draw attention to these important yet largely ignored binding-induced protonation changes in protein-ligand association by outlining physical origins and prevalence of the protonation changes upon binding. Following a summary of various theoretical methods for pKa prediction, we discuss the theoretical framework to examine the pH dependence of protein-ligand binding processes. PMID:26202905

  9. Atomic Mass and Nuclear Binding Energy for Y-90 (Yttrium)

    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 Y-90 (Yttrium, atomic number Z = 39, mass number A = 90).

  10. 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.

  11. Binding Studies of Lamotrigine with Sera of Different Animal Species

    African Journals Online (AJOL)

    Erah

    into the mechanism of interaction, evaluate the effect of dielectric constant on binding affinity, and to determine the effect of ..... Physico-chemical aspects of protein binding of nimesulide, Ind J. Pharm Sci, 2005; 2: 243-246. 10. Dutta, SK, Basu, SK, Sen KK. Binding of diclofenac sodium with bovine serum albumin at different ...

  12. Protein Binding Capacity of Different Forages Tannin

    Science.gov (United States)

    Yusiati, L. M.; Kurniawati, A.; Hanim, C.; Anas, M. A.

    2018-02-01

    Eight forages of tannin sources(Leucaena leucocephala, Arachis hypogaea, Mimosa pudica, Morus alba L, Swietenia mahagoni, Manihot esculenta, Gliricidia sepium, and Bauhinia purpurea)were evaluated their tannin content and protein binding capacity. The protein binding capacity of tannin were determined using precipitation of bovine serum albumin (BSA). Swietenia mahagonihas higest total tannin level and condensed tannin (CT) compared with other forages (Ptannin (HT) level (Ptannin content of Swietenia mahagoni were 11.928±0.04 mg/100 mg and 9.241±0.02mg/100mg dry matter (DM) of leaves. The hydrolysable tannin content of Leucaena leucocephala was 5.338±0.03 mg/100 mg DM of leaves. Binding capacity was highest in Swietenia mahagoni and Leucaena leucocephala compared to the other forages (Ptannin in Leucaena leucocephala and Swietenia mahagoniwere1.181±0.44 and 1.217±0.60mg/mg dry matter of leaves. The present study reports that Swietenia mahagoni has highest of tannin content and Leucaena leucocephala and Swietenia mahagoni capacity of protein binding.

  13. Structure-function relationships of Na+, K+, ATP, or Mg2+ binding and energy transduction in Na,K-ATPase

    DEFF Research Database (Denmark)

    Jorgensen, Peter L.; Pedersen, Per Amstrup

    2000-01-01

    Na,K-ATPase; Mutagenesis; Na+ binding; K+ binding; Tl+ binding; Mg2+ binding; ATP binding; Cation binding site; Energy transduction......Na,K-ATPase; Mutagenesis; Na+ binding; K+ binding; Tl+ binding; Mg2+ binding; ATP binding; Cation binding site; Energy transduction...

  14. Theoretical insight into the binding energy and detonation performance of ε-, γ-, β-CL-20 cocrystals with β-HMX, FOX-7, and DMF in different molar ratios, as well as electrostatic potential.

    Science.gov (United States)

    Feng, Rui-Zhi; Zhang, Shu-Hai; Ren, Fu-de; Gou, Rui-Jun; Gao, Li

    2016-06-01

    Molecular dynamics method was employed to study the binding energies on the selected crystal planes of the ε-, γ-, β-conformation 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (ε-, γ-, β-CL-20) cocrystal explosives with 1,1-diamino-2,2-dinitroethylene (FOX-7), 1,3,5,7-tetranitro- 1,3,5,7-tetrazacyclooctane with β-conformation (β-HMX) and N,N-dimethylformamide (DMF) in different molar ratios. The oxygen balance, density, detonation velocity, detonation pressure, and surface electrostatic potential were analyzed. The results indicate that the binding energies E b (*) and stabilities are in the order of 1:1 > 2:1 > 3:1 > 5:1 > 8:1 (CL-20:FOX-7/β-HMX/DMF). The values of E b (*) and stabilities of the energetic-nonenergetic CL-20/DMF cocrystals are far larger than those of the energetic-energetic CL-20/FOX-7 and CL-20/β-HMX, and those of CL-20/β-HMX are the smallest. For CL-20/FOX-7 and CL-20/β-HMX, the largest E b (*) appears in the cocrystals with the 1:1, 1:2 or 1:3 molar ratio, and the stabilities of the cocrystals with the excess ratio of CL-20 are weaker than those in the cocrystals with the excess ratio of FOX-7 or β-HMX. In CL-20/FOX-7, CL-20 prefers adopting the γ-form, and ε-CL-20 is the preference in CL-20/β-HMX, and ε-CL-20 and β-CL-20 can be found in CL-20/DMF. The CL-20/FOX-7 and CL-20/β-HMX cocrystals with low molar ratios can meet the requirements of low sensitive high energetic materials. Surface electrostatic potential reveals the nature of the sensitivity change upon the cocrystal formation. Graphical Abstract MD method was employed to study the binding energies on the selected crystal planes in the ε-, γ-, β-CL-20 cocrystals with FOX-7, β-HMX and DMF in different molar ratios. Surface electrostatic potential reveals the nature of the sensitivity change in cocrystals.

  15. An energy conservation approach to adsorbate-induced surface stress and the extraction of binding energy using nanomechanics

    Science.gov (United States)

    Pinnaduwage, Lal A.; Boiadjiev, Vassil I.; Hawk, John E.; Gehl, Anthony C.; Fernando, Gayanath W.; Rohana Wijewardhana, L. C.

    2008-03-01

    Surface stress induced by molecular adsorption in three different binding processes has been studied experimentally using a microcantilever sensor. A comprehensive free-energy analysis based on an energy conservation approach is proposed to explain the experimental observations. We show that when guest molecules bind to atoms/molecules on a microcantilever surface, the released binding energy is retained in the host surface, leading to a metastable state where the excess energy on the surface is manifested as an increase in surface stress leading to the bending of the microcantilever. The released binding energy appears to be almost exclusively channeled to the surface energy, and energy distribution to other channels, including heat, appears to be inactive for this micromechanical system. When this excess surface energy is released, the microcantilever relaxes back to the original state, and the relaxation time depends on the particular binding process involved. Such vapor phase experiments were conducted for three binding processes: physisorption, hydrogen bonding, and chemisorption. Binding energies for these three processes were also estimated.

  16. An energy conservation approach to adsorbate-induced surface stress and the extraction of binding energy using nanomechanics

    Energy Technology Data Exchange (ETDEWEB)

    Pinnaduwage, Lal A; Boiadjiev, Vassil I; Hawk, John E; Gehl, Anthony C [Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6122 (United States); Fernando, Gayanath W [Physics Department, University of Connecticut, Storrs, CT 06269 (United States); Wijewardhana, L C Rohana [Physics Department, University of Cincinnati, Cincinnati, OH 45221 (United States)

    2008-03-12

    Surface stress induced by molecular adsorption in three different binding processes has been studied experimentally using a microcantilever sensor. A comprehensive free-energy analysis based on an energy conservation approach is proposed to explain the experimental observations. We show that when guest molecules bind to atoms/molecules on a microcantilever surface, the released binding energy is retained in the host surface, leading to a metastable state where the excess energy on the surface is manifested as an increase in surface stress leading to the bending of the microcantilever. The released binding energy appears to be almost exclusively channeled to the surface energy, and energy distribution to other channels, including heat, appears to be inactive for this micromechanical system. When this excess surface energy is released, the microcantilever relaxes back to the original state, and the relaxation time depends on the particular binding process involved. Such vapor phase experiments were conducted for three binding processes: physisorption, hydrogen bonding, and chemisorption. Binding energies for these three processes were also estimated.

  17. Using the fast fourier transform in binding free energy calculations.

    Science.gov (United States)

    Nguyen, Trung Hai; Zhou, Huan-Xiang; Minh, David D L

    2018-04-30

    According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the unbound ligand ensemble and a rigid receptor. Here, we use the fast Fourier transform (FFT) to efficiently evaluate BPMFs by calculating interaction energies when rigid ligand configurations from the unbound ensemble are discretely translated across rigid receptor conformations. Results for standard binding free energies between T4 lysozyme and 141 small organic molecules are in good agreement with previous alchemical calculations based on (1) a flexible complex ( R≈0.9 for 24 systems) and (2) flexible ligand with multiple rigid receptor configurations ( R≈0.8 for 141 systems). While the FFT is routinely used for molecular docking, to our knowledge this is the first time that the algorithm has been used for rigorous binding free energy calculations. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  18. Sampling and energy evaluation challenges in ligand binding protein design.

    Science.gov (United States)

    Dou, Jiayi; Doyle, Lindsey; Jr Greisen, Per; Schena, Alberto; Park, Hahnbeom; Johnsson, Kai; Stoddard, Barry L; Baker, David

    2017-12-01

    The steroid hormone 17α-hydroxylprogesterone (17-OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in development of sensors for this compound. We used computational protein design to generate protein models with binding sites for 17-OHP containing an extended, nonpolar, shape-complementary binding pocket for the four-ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand. Eight of 16 designed proteins experimentally tested bind 17-OHP with micromolar affinity. A co-crystal structure of one of the designs revealed that 17-OHP is rotated 180° around a pseudo-two-fold axis in the compound and displays multiple binding modes within the pocket, while still interacting with all of the designed residues in the engineered site. Subsequent rounds of mutagenesis and binding selection improved the ligand affinity to nanomolar range, while appearing to constrain the ligand to a single bound conformation that maintains the same "flipped" orientation relative to the original design. We trace the discrepancy in the design calculations to two sources: first, a failure to model subtle backbone changes which alter the distribution of sidechain rotameric states and second, an underestimation of the energetic cost of desolvating the carbonyl and hydroxyl groups of the ligand. The difference between design model and crystal structure thus arises from both sampling limitations and energy function inaccuracies that are exacerbated by the near two-fold symmetry of the molecule. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  19. Measurement of Exciton Binding Energy of Monolayer WS2

    Science.gov (United States)

    Chen, Xi; Zhu, Bairen; Cui, Xiaodong

    Excitonic effects are prominent in monolayer crystal of transition metal dichalcogenides (TMDCs) because of spatial confinement and reduced Coulomb screening. Here we use linear differential transmission spectroscopy and two-photon photoluminescence excitation spectroscopy (TP-PLE) to measure the exciton binding energy of monolayer WS2. Peaks for excitonic absorptions of the direct gap located at K valley of the Brillouin zone and transitions from multiple points near Γ point of the Brillouin zone, as well as trion side band are shown in the linear absorption spectra of WS2. But there is no gap between distinct excitons and the continuum of the interband transitions. Strong electron-phonon scattering, overlap of excitons around Γ point and the transfer of the oscillator strength from interband continuum to exciton states make it difficult to resolve the electronic interband transition edge even down to 10K. The gap between excited states of the band-edge exciton and the single-particle band is probed by TP-PLE measurements. And the energy difference between 1s exciton and the single-particle gap gives the exciton binding energy of monolayer WS2 to be about 0.71eV. The work is supported by Area of excellency (AoE/P-04/08), CRF of Hong Kong Research Grant Council (HKU9/CRF/13G) and SRT on New Materials of The University of Hong Kong.

  20. 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}-...

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

    Directory of Open Access Journals (Sweden)

    Manuela Maurer

    2016-04-01

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

  2. Enzyme activation through the utilization of intrinsic dianion binding energy.

    Science.gov (United States)

    Amyes, T L; Malabanan, M M; Zhai, X; Reyes, A C; Richard, J P

    2017-03-01

    We consider 'the proposition that the intrinsic binding energy that results from the noncovalent interaction of a specific substrate with the active site of the enzyme is considerably larger than is generally believed. An important part of this binding energy may be utilized to provide the driving force for catalysis, so that the observed binding energy represents only what is left over after this utilization' [Jencks,W.P. (1975) Adv. Enzymol. Relat. Areas. Mol. Biol. , , 219-410]. The large ~12 kcal/mol intrinsic substrate phosphodianion binding energy for reactions catalyzed by triosephosphate isomerase (TIM), orotidine 5'-monophosphate decarboxylase and glycerol-3-phosphate dehydrogenase is divided into 4-6 kcal/mol binding energy that is expressed on the formation of the Michaelis complex in anchoring substrates to the respective enzyme, and 6-8 kcal/mol binding energy that is specifically expressed at the transition state in activating the respective enzymes for catalysis. A structure-based mechanism is described where the dianion binding energy drives a conformational change that activates these enzymes for catalysis. Phosphite dianion plays the active role of holding TIM in a high-energy closed active form, but acts as passive spectator in showing no effect on transition-state structure. The result of studies on mutant enzymes is presented, which support the proposal that the dianion-driven enzyme conformational change plays a role in enhancing the basicity of side chain of E167, the catalytic base, by clamping the base between a pair of hydrophobic side chains. The insight these results provide into the architecture of enzyme active sites and the development of strategies for the de novo design of protein catalysts is discussed.

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

    Science.gov (United States)

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

    2017-05-01

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

  4. Funnel metadynamics as accurate binding free-energy method

    Science.gov (United States)

    Limongelli, Vittorio; Bonomi, Massimiliano; Parrinello, Michele

    2013-01-01

    A detailed description of the events ruling ligand/protein interaction and an accurate estimation of the drug affinity to its target is of great help in speeding drug discovery strategies. We have developed a metadynamics-based approach, named funnel metadynamics, that allows the ligand to enhance the sampling of the target binding sites and its solvated states. This method leads to an efficient characterization of the binding free-energy surface and an accurate calculation of the absolute protein–ligand binding free energy. We illustrate our protocol in two systems, benzamidine/trypsin and SC-558/cyclooxygenase 2. In both cases, the X-ray conformation has been found as the lowest free-energy pose, and the computed protein–ligand binding free energy in good agreement with experiments. Furthermore, funnel metadynamics unveils important information about the binding process, such as the presence of alternative binding modes and the role of waters. The results achieved at an affordable computational cost make funnel metadynamics a valuable method for drug discovery and for dealing with a variety of problems in chemistry, physics, and material science. PMID:23553839

  5. Atomic Mass and Nuclear Binding Energy for Cf-252 (Californium)

    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 Cf-252 (Californium, atomic number Z = 98, mass number A = 252).

  6. Analysis of experimental positron-molecule binding energies

    International Nuclear Information System (INIS)

    Danielson, J R; Surko, C M; Young, J A

    2010-01-01

    Experiments show that positron annihilation on molecules frequently occurs via capture into vibrational Feshbach resonances. In these cases, the downshifts in the annihilation spectra from the vibrational mode spectra provide measures of the positron-molecule binding energies. An analysis of these binding energy data is presented in terms of the molecular dipole polarizability, the permanent dipole moment, and the number of π bonds in aromatic molecules. The results of this analysis are in reasonably good agreement with other information about positron-molecule bound states. Predictions for other targets and promising candidate molecules for further investigation are discussed.

  7. Binding energy and formation heat of UO2

    International Nuclear Information System (INIS)

    Almeida, M.R. de; Veado, J.T.; Siqueira, M.L. de

    The Born-Haber cycle is utilized for the calculation of the heat of formation of UO 2 , on the assumption that the binding energy is predominantly ionic in character. The ionization potentials of U and the repulsion energy are two critical values that influence calculations. Calculations of the ionization potentials with non-relativistic Hartree-Fock-Gaspar-Kohn-Sham approximation are presented [pt

  8. 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...

  9. Nuclear Cartography: Patterns in Binding Energies and Subatomic Structure

    Science.gov (United States)

    Simpson, E. C.; Shelley, M.

    2017-01-01

    Nuclear masses and binding energies are some of the first nuclear properties met in high school physics, and can be used to introduce radioactive decays, fusion, and fission. With relatively little extension, they can also illustrate fundamental concepts in nuclear physics, such as shell structure and pairing, and to discuss how the elements…

  10. Binding energy of impurity states in an inverse parabolic quantum well under magnetic field

    International Nuclear Information System (INIS)

    Kasapoglu, E.; Sari, H.; Soekmen, I.

    2007-01-01

    We have investigated the effects of the magnetic field which is directed perpendicular to the well on the binding energy of the hydrogenic impurities in an inverse parabolic quantum well (IPQW) with different widths as well as different Al concentrations at the well center. The Al concentration at the barriers was always x max =0.3. The calculations were performed within the effective mass approximation, using a variational method. We observe that IPQW structure turns into parabolic quantum well with the inversion effect of the magnetic field and donor impurity binding energy in IPQW strongly depends on the magnetic field, Al concentration at the well center and well dimensions

  11. Magnetic properties and core electron binding energies of liquid water

    Science.gov (United States)

    Galamba, N.; Cabral, Benedito J. C.

    2018-01-01

    The magnetic properties and the core and inner valence electron binding energies of liquid water are investigated. The adopted methodology relies on the combination of molecular dynamics and electronic structure calculations. Born-Oppenheimer molecular dynamics with the Becke and Lee-Yang-Parr functionals for exchange and correlation, respectively, and includes an empirical correction (BLYP-D3) functional and classical molecular dynamics with the TIP4P/2005-F model were carried out. The Keal-Tozer functional was applied for predicting magnetic shielding and spin-spin coupling constants. Core and inner valence electron binding energies in liquid water were calculated with symmetry adapted cluster-configuration interaction. The relationship between the magnetic shielding constant σ(17O), the role played by the oxygen atom as a proton acceptor and donor, and the tetrahedral organisation of liquid water are investigated. The results indicate that the deshielding of the oxygen atom in water is very dependent on the order parameter (q) describing the tetrahedral organisation of the hydrogen bond network. The strong sensitivity of magnetic properties on changes of the electronic density in the nuclei environment is illustrated by a correlation between σ(17O) and the energy gap between the 1a1[O1s] (core) and the 2a1 (inner valence) orbitals of water. Although several studies discussed the eventual connection between magnetic properties and core electron binding energies, such a correlation could not be clearly established. Here, we demonstrate that for liquid water this correlation exists although involving the gap between electron binding energies of core and inner valence orbitals.

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

    Science.gov (United States)

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

    2015-03-01

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

  13. Effect of valence nucleons on nuclear binding energy

    Energy Technology Data Exchange (ETDEWEB)

    Angeli, I. (Kossuth Lajos Tudomanyegyetem, Debrecen (HU))

    1991-10-01

    The nucleonic promiscuity factor P = N{sub p}N{sub n}/(N{sub p} + N{sub n}), where N{sub p}(N{sub n}) is the number of valence protons (neutrons) or holes, is shown to be a useful parameter in the description of the mass number dependence of nuclear binding energies. This means that most of the deviation from a smooth mass number dependence is caused by the isoscalar interaction between valence protons and neutrons.

  14. Impurity binding energy for δ-doped quantum well structures

    Indian Academy of Sciences (India)

    Administrator

    Abstract. 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 n-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.

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

    International Nuclear Information System (INIS)

    Dorenbos, Pieter

    2013-01-01

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

  16. Calculation of the Relative Change in Binding Free Energy of a Protein-Inhibitor Complex

    Science.gov (United States)

    Bash, Paul A.; Singh, U. Chandra; Brown, Frank K.; Langridge, Robert; Kollman, Peter A.

    1987-01-01

    By means of a thermodynamic perturbation method implemented with molecular dynamics, the relative free energy of binding was calculated for the enzyme thermolysin complexed with a pair of phosphonamidate and phosphonate ester inhibitors. The calculated difference in free energy of binding was 4.21 ± 0.54 kilocalories per mole. This compares well with the experimental value of 4.1 kilocalories per mole. The method is general and can be used to determine a change or ``mutation'' in any system that can be suitably represented. It is likely to prove useful for protein and drug design.

  17. 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. © 2015 The Protein Society.

  18. Incremental binding free energies of aluminum (III) vs. magnesium (II) complexes

    International Nuclear Information System (INIS)

    Mercero, Jose M.; Mujika, Jon I.; Matxain, Jon M.; Lopez, Xabier; Ugalde, Jesus M.

    2003-01-01

    A sequential ligand addition to the aluminum (III) cation has been studied using the B3LYP functional and a combined all-electron/pseudopotentials basis set. The aluminum complexes are compared with analogous magnesium (II) complexes. Different thermodynamical data, such as incremental binding energies, enthalpies, entropies and free energies, are presented for these addition reactions. While the magnesium (II) cation can only accommodate three negatively charged ligands, aluminum (III) accommodates four even after including bulk solvent effects. The main differences between both cations complexing with the neutral ligands, is that aluminum (III) is not able to form complexes with methanol until the number of methanol ligands is equal to 3. Magnesium (II) prefers to bind methanol and formamide when the number of ligands is small, while aluminum prefers formamide. For the largest complexes both cations prefer to bind water

  19. Binding energy and single–particle Energies in the 16 0 region ...

    African Journals Online (AJOL)

    ... single-particle energies in the oxygen region by folding together a Hamiltonian in the rest-frame of the nucleus with two-body correlation functions based on the Njimegen potential. We have found that the binding energies are very sensitive to the core radius rc and that the effects of tensor correlations are non-negligible.

  20. Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations.

    Science.gov (United States)

    Zhang, Yuxin; Huang, Xiaoqin; Han, Keli; Zheng, Fang; Zhan, Chang-Guo

    2016-11-25

    The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profile of the CocE)-(+)-cocaine binding process in comparison with that of the corresponding CocE-(-)-cocaine binding process. According to the MD simulations, the equilibrium CocE-(+)-cocaine binding mode is similar to the CocE-(-)-cocaine binding mode. However, based on the simulated free energy profiles, a significant free energy barrier (∼5 kcal/mol) exists in the CocE-(+)-cocaine binding process whereas no obvious free energy barrier exists in the CocE-(-)-cocaine binding process, although the free energy barrier of ∼5 kcal/mol is not high enough to really slow down the CocE-(+)-cocaine binding process. In addition, the obtained free energy profiles also demonstrate that (+)-cocaine and (-)-cocaine have very close binding free energies with CocE, with a negligible difference (∼0.2 kcal/mol), which is qualitatively consistent with the nearly same experimental K M values of the CocE enzyme for (+)-cocaine and (-)-cocaine. The consistency between the computational results and available experimental data suggests that the mechanistic insights obtained from this study are reasonable. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  1. 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.

  2. How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

    Science.gov (United States)

    2016-01-01

    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

  3. 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

  4. Exciton binding energy in a pyramidal quantum dot

    Science.gov (United States)

    Anitha, A.; Arulmozhi, M.

    2018-05-01

    The effects of spatially dependent effective mass, non-parabolicity of the conduction band and dielectric screening function on exciton binding energy in a pyramid-shaped quantum dot of GaAs have been investigated by variational method as a function of base width of the pyramid. We have assumed that the pyramid has a square base with area a× a and height of the pyramid H=a/2. The trial wave function of the exciton has been chosen according to the even mirror boundary condition, i.e. the wave function of the exciton at the boundary could be non-zero. The results show that (i) the non-parabolicity of the conduction band affects the light hole (lh) and heavy hole (hh) excitons to be more bound than that with parabolicity of the conduction band, (ii) the dielectric screening function (DSF) affects the lh and hh excitons to be more bound than that without the DSF and (iii) the spatially dependent effective mass (SDEM) affects the lh and hh excitons to be less bound than that without the SDEM. The combined effects of DSF and SDEM on exciton binding energy have also been calculated. The results are compared with those available in the literature.

  5. Human PD-1 binds differently to its human ligands: a comprehensive modeling study.

    Science.gov (United States)

    Viricel, Clement; Ahmed, Marawan; Barakat, Khaled

    2015-04-01

    Programmed death-1 (PD-1) is a potent inhibitory receptor of T cells which binds to two different ligands, namely PD-L1 and PD-L2, and upon binding, it inhibits T cell activation, differentiation, and proliferation, leading to a state of immune tolerance. Blocking these interactions recently emerged as a 'game changer' approach in immunotherapy. Despite the significant therapeutic potential of targeting the PD-1 pathway, the interaction between human PD-1 and its two human ligands is not fully understood. Current crystal structures describe the interactions of mouse PD-1 with human PD-L1 or mouse PD-L2. However, recent mutational and nuclear magnetic resonance (NMR) analyses suggest that human PD-1 binds its human ligands differently compared to their mouse counterparts. No detailed model is currently available to consistently fit these data. The lack of these accurate structures constitutes a high barrier against rationally developing more effective and safer agents targeting these interactions. Here we describe for the first time two accurate models for human PD-1 bound to its two human ligands. Our methodology involved combining molecular dynamics (MD) simulations with protein-protein docking and binding energy analysis to predict the most probable binding conformations for PD1 to its ligands. Our results confirm the available experimental NMR and mutational data and reveal the most accurate atomistic details so far of how human PD-1 binds to human PD-Ls and why the two ligands bind with different affinities to the same receptor. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Can the energy gap in the protein-ligand binding energy landscape be used as a descriptor in virtual ligand screening?

    Directory of Open Access Journals (Sweden)

    Arsen V Grigoryan

    Full Text Available The ranking of scores of individual chemicals within a large screening library is a crucial step in virtual screening (VS for drug discovery. Previous studies showed that the quality of protein-ligand recognition can be improved using spectrum properties and the shape of the binding energy landscape. Here, we investigate whether the energy gap, defined as the difference between the lowest energy pose generated by a docking experiment and the average energy of all other generated poses and inferred to be a measure of the binding energy landscape sharpness, can improve the separation power between true binders and decoys with respect to the use of the best docking score. We performed retrospective single- and multiple-receptor conformation VS experiments in a diverse benchmark of 40 domains from 38 therapeutically relevant protein targets. Also, we tested the performance of the energy gap on 36 protein targets from the Directory of Useful Decoys (DUD. The results indicate that the energy gap outperforms the best docking score in its ability to discriminate between true binders and decoys, and true binders tend to have larger energy gaps than decoys. Furthermore, we used the energy gap as a descriptor to measure the height of the native binding phase and obtained a significant increase in the success rate of near native binding pose identification when the ligand binding conformations within the boundaries of the native binding phase were considered. The performance of the energy gap was also evaluated on an independent test case of VS-identified PKR-like ER-localized eIF2α kinase (PERK inhibitors. We found that the energy gap was superior to the best docking score in its ability to more highly rank active compounds from inactive ones. These results suggest that the energy gap of the protein-ligand binding energy landscape is a valuable descriptor for use in VS.

  7. Species differences in [11C]clorgyline binding in brain

    International Nuclear Information System (INIS)

    Fowler, Joanna S.; Ding, Yu-Shin; Logan, Jean; MacGregor, Robert R.; Shea, Colleen; Garza, Victor; Gimi, Raomond; Volkow, Nora D.; Wang, Gene-Jack; Schlyer, David; Ferrieri, Richard; Gatley, S. John; Alexoff, David; Carter, Pauline; King, Payton; Pappas, Naomi; Arnett, Carroll D.

    2001-01-01

    [ 11 C]Clorgyline selectively binds to MAO A in the human brain. This contrasts with a recent report that [ 11 C]clorgyline (in contrast to other labeled MAO A inhibitors) is not retained in the rhesus monkey brain . To explore this difference, we compared [ 11 C]clorgyline in the baboon brain before and after clorgyline pretreatment and we also synthesized deuterium substituted [ 11 C]clorgyline (and its nor-precursor) for comparison. [ 11 C]Clorgyline was not retained in the baboon brain nor was it influenced by clorgyline pretreatment or by deuterium substitution, contrasting to results in humans. This suggests a species difference in the susceptibility of MAO A to inhibition by clorgyline and represents an unusual example of where the behavior of a radiotracer in the baboon brain does not predict its behavior in the human brain

  8. An exploration of possible design options for a binding energy savings target in Europe

    NARCIS (Netherlands)

    Harmsen, Robert; Eichhammer, Wolfgang; Wesselink, Bart

    2014-01-01

    As Europe is not on track in meeting its 2020 energy savings target, there has been quite some debate to make the energy savings target binding instead of indicative. Although the final draft text of the Energy Efficiency Directive left the option of a binding target explicitly open for the period

  9. Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase.

    Science.gov (United States)

    Nascimento, Érica C M; Oliva, Mónica; Andrés, Juan

    2018-03-26

    In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

  10. Is the Binding Pattern of Zinc(II) Equal in Different Bryophyte Species?

    Science.gov (United States)

    Sabovljević, Marko S; Weidinger, Marieluise; Sabovljević, Aneta D; Adlassnig, Wolfram; Lang, Ingeborg

    2018-02-01

    Bryophytes are usually taken as good bioindicators. However, they represent a large group of terrestrial plants and they express an enormous range of peculiarities within the plant kingdom. With the aim to search for a common pattern of zinc binding, we established axenical in vitro cultures of a dozen bryophyte species that include hornworts, thallose, and leafy liverworts, as well as acrocarp and pleurocarp mosses. The species were grown free of contaminants for many years prior to the application of different treatments, i.e. offering Zn(II) from solid and liquid media and in combination with different anions. The localization and binding of zinc was detected by confocal microscopy using the zinc-specific dye FluoZin™-3. In one of the species, Hypnum cupressiforme (which is widely used for atmospheric heavy metal deposition studies in biomonitoring), semi-quantitative analyses of zinc were performed by energy dispersive X-ray microspectrometry (EDX) in a scanning electron microscope. The results suggest no common pattern of Zn(II) binding in different bryophyte species. Instead, the binding pattern seems to be species specific. Zinc is located in certain areas or cellular compartments, as clearly shown by the EDX measurements in H. cupressiforme.

  11. Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA

    Directory of Open Access Journals (Sweden)

    Hong Zhang

    2018-01-01

    Full Text Available DNA is the target of chemical compounds (drugs, pollutants, photosensitizers, etc., which bind through non-covalent interactions. Depending on their structure and their chemical properties, DNA binders can associate to the minor or to the major groove of double-stranded DNA. They can also intercalate between two adjacent base pairs, or even replace one or two base pairs within the DNA double helix. The subsequent biological effects are strongly dependent on the architecture of the binding motif. Discriminating between the different binding patterns is of paramount importance to predict and rationalize the effect of a given compound on DNA. The structural characterization of DNA complexes remains, however, cumbersome at the experimental level. In this contribution, we employed all-atom molecular dynamics simulations to determine the standard binding free energy of DNA with netropsin, a well-characterized antiviral and antimicrobial drug, which associates to the minor groove of double-stranded DNA. To overcome the sampling limitations of classical molecular dynamics simulations, which cannot capture the large change in configurational entropy that accompanies binding, we resort to a series of potentials of mean force calculations involving a set of geometrical restraints acting on collective variables.

  12. Binding affinity of a small molecule to an amorphous polymer in a solvent. Part 1: free energy of binding to a binding site.

    Science.gov (United States)

    Chunsrivirot, Surasak; Diao, Ying; Trout, Bernhardt L

    2011-10-18

    Crystallization is commonly used in a separation and purification process in the production of a wide range of materials in various industries. In industry, crystallization usually starts with heterogeneous nucleation on a foreign surface. The complicated mechanism of heterogeneous nucleation is not well understood; however, we hypothesize that there might be a possible correlation between binding affinity to a surface and enhancement of nucleation. Recent studies show that amorphous polymers can be used to control crystallization, selectively produce pharmaceutical polymorphs, and discover novel pharmaceutical polymorphs. To investigate the possible correlation between the binding affinity of one molecule to key binding sites (local binding) and heterogeneous nucleation activity as well as the possibility of using this binding affinity to help guide the selection of polymers that promote heterogeneous nucleation, we computed the free energy of binding of aspirin to four nonporous cross-linked polymers in an ethanol-water 38 v% mixture. These cross-linked polymers are poly(4-acryloylmorpholine) (PAM), poly(2-carboxyethyl acrylate) (PCEA), poly(4-hydroxylbutyl acrylate) (PHBA), and polystyrene (PS); all of them were cross-linked with divinylbenzene (DVB). These systems were used because their heterogeneous nucleation activities are available in literature, and the ranking is PAM > PCEA > PHBA ≈ PS. We generated three independent surfaces for each polymer and computed the free energy of binding of aspirin to the best binding site that we found on each surface. The average free energies of binding to the best sites of PAM, PCEA, PHBA, and PS are -20.4 ± 1.0, -16.7 ± 1.0, -14.4 ± 1.1, and -13.6 ± 1.1 kcal/mol, respectively. We found that the trend of the magnitudes of the average free energies of binding to the best sites is PAM > PCEA > PHBA ≈ PS. This trend is very similar to that of heterogeneous nucleation activity. Our results suggest the importance of the

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

  14. An Energy Conservation Approach to Adsorbate-Induced Surface Stress and the Extraction of Binding Energy Using Nanomechanics

    Energy Technology Data Exchange (ETDEWEB)

    Pinnaduwage, Lal A [ORNL; Boiadjiev, Vassil I [ORNL; Fernando, G. W. [University of Connecticut, Storrs; Hawk, J. E. [Oak Ridge National Laboratory (ORNL); Wijewardhana, L.C. R. [University of Cincinnati; Gehl, Anthony C [ORNL

    2008-01-01

    Microcantilevers are ideally-suited for the study of surface phenomena due to their large surface-to-volume ratios, which amplify surface effects. We show that when guest molecules bind to atoms/molecules on a microcantilever surface, the released binding energy is retained in the host surface, leading to a metastable state where the excess energy on the surface is manifested as an increase in surface stress leading to the bending of the microcantilever. When the excess energy is released, the microcantilever relaxes back to the original state, and the relaxation time depends on the particular binding process involved. Such experiments were conducted for three binding processes in vapor phase experiments: physisorption, hydrogen bonding, and chemisorption. To our knowledge, such an energy conservation approach has not been taken into account in adsorbate-induced surface effect investigations. Furthermore, these experiments illustrate that detailed molecular-level information on binding energies can be extracted from this simple micromechanical sensor.

  15. 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.

  16. 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.

  17. Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores

    Science.gov (United States)

    Benson, Mark L.; Faver, John C.; Ucisik, Melek N.; Dashti, Danial S.; Zheng, Zheng; Merz, Kenneth M.

    2012-05-01

    Two families of binding affinity estimation methodologies are described which were utilized in the SAMPL3 trypsin/fragment binding affinity challenge. The first is a free energy decomposition scheme based on a thermodynamic cycle, which included separate contributions from enthalpy and entropy of binding as well as a solvent contribution. Enthalpic contributions were estimated with PM6-DH2 semiempirical quantum mechanical interaction energies, which were modified with a statistical error correction procedure. Entropic contributions were estimated with the rigid-rotor harmonic approximation, and solvent contributions to the free energy were estimated with several different methods. The second general methodology is the empirical score LISA, which contains several physics-based terms trained with the large PDBBind database of protein/ligand complexes. Here we also introduce LISA+, an updated version of LISA which, prior to scoring, classifies systems into one of four classes based on a ligand's hydrophobicity and molecular weight. Each version of the two methodologies (a total of 11 methods) was trained against a compiled set of known trypsin binders available in the Protein Data Bank to yield scaling parameters for linear regression models. Both raw and scaled scores were submitted to SAMPL3. Variants of LISA showed relatively low absolute errors but also low correlation with experiment, while the free energy decomposition methods had modest success when scaling factors were included. Nonetheless, re-scaled LISA yielded the best predictions in the challenge in terms of RMS error, and six of these models placed in the top ten best predictions by RMS error. This work highlights some of the difficulties of predicting binding affinities of small molecular fragments to protein receptors as well as the benefit of using training data.

  18. 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.

  19. 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 fo...

  20. Enzymes in Commercial Cellulase Preparations Bind Differently to Dioxane Extracted Lignins

    Energy Technology Data Exchange (ETDEWEB)

    Yarbrough, John M.; Mittal, Ashutosh; Katahira, Rui; Mansfield, Elisabeth; Taylor, Larry E.; Decker, Stephen R.; Himmel, Michael E.; Vinzant, Todd

    2017-04-24

    Commercial fungal cellulases used in biomass-to-biofuels processes can be grouped into three general classes: native, augmented, and engineered. To evaluate lignin binding affinities of different enzyme activities in various commercial cellulase formulations in order to determine if enzyme losses due to lignin binding can be modulated by using different enzymes of the same activity We used water:dioxane (1:9) to extract lignin from pretreated corn stover. Commercial cellulases were incubated with lignin and the unbound supernatants were evaluated for individual enzyme loss by SDS=PAGE and these were correlated with activity loss using various pNP-sugar substrates. Colorimetric assays for general glycosyl hydrolase activities showed distinct differences in enzyme binding to lignin for each enzyme activity. Native systems demonstrated low binding of endo- and exo-cellulases, high binding of xylanase, and moderate ..beta..-glucosidase binding. Engineered cellulase mixtures exhibited low binding of exo-cellulases, very strong binding of endocellulases and ..beta..- glucosidase, and mixed binding of xylanase activity. The augmented cellulase had low binding of exocellulase, high binding of endocellulase and xylanase, and moderate binding of ..beta..-glucosidase activities. Bound and unbound activities were correlated with general molecular weight ranges of proteins as measured by loss of proteins bands in bound fractions on SDS-PAGE gels. Lignin-bound high molecular weight bands correlated with binding of ..beta..-glucosidase activity. While ..beta..-glucosidases demonstrated high binding in many cases, they have been shown to remain active. Bound low molecular weight bands correlated with xylanase activity binding. Contrary to other literature, exocellulase activity did not show strong lignin binding. The variation in enzyme activity binding between the three classes of cellulases preparations indicate that it is certainly possible to alter the binding of specific

  1. Different characteristics and nucleotide binding properties of inosine monophosphate dehydrogenase (IMPDH isoforms.

    Directory of Open Access Journals (Sweden)

    Elaine C Thomas

    Full Text Available We recently reported that Inosine Monophosphate Dehydrogenase (IMPDH, a rate-limiting enzyme in de novo guanine nucleotide biosynthesis, clustered into macrostructures in response to decreased nucleotide levels and that there were differences between the IMPDH isoforms, IMPDH1 and IMPDH2. We hypothesised that the Bateman domains, which are present in both isoforms and serve as energy-sensing/allosteric modules in unrelated proteins, would contribute to isoform-specific differences and that mutations situated in and around this domain in IMPDH1 which give rise to retinitis pigmentosa (RP would compromise regulation. We employed immuno-electron microscopy to investigate the ultrastructure of IMPDH macrostructures and live-cell imaging to follow clustering of an IMPDH2-GFP chimera in real-time. Using a series of IMPDH1/IMPDH2 chimera we demonstrated that the propensity to cluster was conferred by the N-terminal 244 amino acids, which includes the Bateman domain. A protease protection assay suggested isoform-specific purine nucleotide binding characteristics, with ATP protecting IMPDH1 and AMP protecting IMPDH2, via a mechanism involving conformational changes upon nucleotide binding to the Bateman domain without affecting IMPDH catalytic activity. ATP binding to IMPDH1 was confirmed in a nucleotide binding assay. The RP-causing mutation, R224P, abolished ATP binding and nucleotide protection and this correlated with an altered propensity to cluster. Collectively these data demonstrate that (i the isoforms are differentially regulated by AMP and ATP by a mechanism involving the Bateman domain, (ii communication occurs between the Bateman and catalytic domains and (iii the RP-causing mutations compromise such regulation. These findings support the idea that the IMPDH isoforms are subject to distinct regulation and that regulatory defects contribute to human disease.

  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. Health impacts of different energy sources

    International Nuclear Information System (INIS)

    1982-01-01

    Energy is needed to sustain the economy, health and welfare of nations. As a consequence of this, energy consumption figures are frequently used as an index of a nation's advancement. As a result of the global energy crisis, almost every nation has had to develop all its available energy resources and plan its future use of energy. The planners of national and international energy policies are however often faced with a problem of 'public acceptance' arising from the potential health and environmental impacts of developing energy resources. The public's desire to preserve the quality of man's health and his environment frequently results in opposition to many industrial innovations, including the generation and use of energy. Reliable, quantitative data and information are needed on the risks to health and the environment of different contemporary energy systems, to improve public understanding, and to serve as the basis from which national planners can choose between different energy supply options. With the exception of nuclear energy, even in technologically advanced countries little systematic research and development has been done on the quantitative assessment of the effects on health and the environment of the conventional energy sources. The need for this information has only been realized over the past decade as the climate and environment in many regions of the world has deteriorated with the unabated release of pollutants from factories and energy generating plants in particular. A number of countries have started national environmental health research programmes to monitor and regulate toxic emissions from industry and energy plants. Energy-related environmental health research has been supported and co-ordinated by various international organizations such as the International Atomic Energy Agency (IAEA), World Health Organization (WHO) and United Nations Environment Programme (UNEP). WHO has supported expert reviews on the potential health risks posed

  4. Interdependence of different symmetry energy elements

    Science.gov (United States)

    Mondal, C.; Agrawal, B. K.; De, J. N.; Samaddar, S. K.; Centelles, M.; Viñas, X.

    2017-08-01

    Relations between the nuclear symmetry energy coefficient and its density derivatives are derived. The relations hold for a class of interactions with quadratic momentum dependence and a power-law density dependence. The structural connection between the different symmetry energy elements as obtained seems to be followed by almost all reasonable nuclear energy density functionals, both relativistic and nonrelativistic, suggesting a universality in the correlation structure. This, coupled with known values of some well-accepted constants related to nuclear matter, helps in constraining values of different density derivatives of the nuclear symmetry energy, shedding light on the isovector part of the nuclear interaction.

  5. 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.

  6. How to shape a binding energy savings target for Europe that allows for effective evaluation

    NARCIS (Netherlands)

    Harmsen, R.; Wesselink, B.; Eichhammer, W.

    2012-01-01

    This paper considers which design of a binding energy savings target for the EU is the most feasible to both make it work and to ensure it can be evaluated in an efficient and transparent manner. We look at four possible design options. We conclude that a binding target at Member State level

  7. Binding free energy analysis of protein-protein docking model structures by evERdock.

    Science.gov (United States)

    Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

    2018-03-14

    To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures. In our current work, we applied this method (evERdock) to 100 or 300 model structures of four protein-protein complexes. The crystal structures and the near-native decoys showed the lowest binding free energy of all the examined structures, indicating that evERdock can successfully evaluate decoys. Several decoys that show low interface root-mean-square distance but relatively high binding free energy were also identified. Analysis of the fraction of native contacts, hydrogen bonds, and salt bridges at the protein-protein interface indicated that these decoys were insufficiently optimized at the interface. After optimizing the interactions around the interface by including interfacial water molecules, the binding free energies of these decoys were improved. We also investigated the effect of solute entropy on binding free energy and found that consideration of the entropy term does not necessarily improve the evaluations of decoys using the normal model analysis for entropy calculation.

  8. Binding free energy analysis of protein-protein docking model structures by evERdock

    Science.gov (United States)

    Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

    2018-03-01

    To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures. In our current work, we applied this method (evERdock) to 100 or 300 model structures of four protein-protein complexes. The crystal structures and the near-native decoys showed the lowest binding free energy of all the examined structures, indicating that evERdock can successfully evaluate decoys. Several decoys that show low interface root-mean-square distance but relatively high binding free energy were also identified. Analysis of the fraction of native contacts, hydrogen bonds, and salt bridges at the protein-protein interface indicated that these decoys were insufficiently optimized at the interface. After optimizing the interactions around the interface by including interfacial water molecules, the binding free energies of these decoys were improved. We also investigated the effect of solute entropy on binding free energy and found that consideration of the entropy term does not necessarily improve the evaluations of decoys using the normal model analysis for entropy calculation.

  9. Effect of magnetic field on the impurity binding energy of the excited ...

    Indian Academy of Sciences (India)

    Abstract. The effect of external magnetic field on the excited state energies in a spher- ical 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 ...

  10. Effect of magnetic field on the impurity binding energy of the excited ...

    Indian Academy of Sciences (India)

    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 ...

  11. 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

  12. Partitioning of metals in different binding phases of tropical estuarine sediments: importance of metal chemistry.

    Science.gov (United States)

    Chakraborty, Parthasarathi; Chakraborty, Sucharita; Vudamala, Krushna; Sarkar, Arindam; Nath, B Nagender

    2016-02-01

    Distribution of metals in different binding phases of estuarine sediments provides chemically significant description of metal-sediment interactions. This study describes the influences of ligand field stabilization energy (LFSE), Jahn-Teller effect, and water exchange rate (k-w) on metal distribution in different binding phases of estuarine sediments. It was found that Cu had highest affinity for organic binding phases in the studied sediments followed by Ni and Pb. However, Pb showed strong association with Fe/Mn oxide phases followed by Ni and Cu. Faster k-w of Cu (II) (1 × 10(9) s(-1)) increased the rate of complex formation of Cu(2+) ion with ligand in the organic phases. The Cu-ligand (from organic phase) complexes gained extra stability by the Jahn-Teller effect. The combined effects of these two phenomena and high ionic potential increased the association of Cu with the organic phases of the sediments than Ni and Pb. The smaller ionic radii of Ni(2+) (0.72 Å) than Pb(2+) (1.20 Å) increase the stability of Ni-ligand complexes in the organic phase of the sediments. High LFSE of Ni(II) (compared with Pb(2+) ions) also make Ni-organic complexes increasingly stable than Pb. High k-w (7 × 10(9) s(-1)) of Pb did not help it to associate with organic phases in the sediments. The high concentration of Pb in the Fe/Mn oxyhydroxide binding phase was probably due to co-precipitation of Pb(2+) and Fe(3+). High surface area or site availability for Pb(2+) ion on Fe oxyhydroxide phase was probably responsible for the high concentration of Pb in Fe/Mn oxyhydroxide phase. Increasing concentrations of Cu in organic phases with the increasing Cu loading suggest that enough binding sites were available for Cu in the organic binding phases of the sediments. This study also describes the influence of nature of sedimentary organic carbon (terrestrial and marine derived OC) in controlling these metal distribution and speciation in marine sediment.

  13. Dependence of single-walled carbon nanotube adsorption kinetics on temperature and binding energy.

    Science.gov (United States)

    Rawat, D S; Krungleviciute, V; Heroux, L; Bulut, M; Calbi, M M; Migone, A D

    2008-12-02

    We present results for the isothermal adsorption kinetics of methane, hydrogen, and tetrafluoromethane on closed-ended single-walled carbon nanotubes. In these experiments, we monitor the pressure decrease as a function of time as equilibrium is approached, after a dose of gas is added to the cell containing the nanotubes. The measurements were performed at different fractional coverages limited to the first layer. The results indicate that, for a given coverage and temperature, the equilibration time is an increasing function of E/(k(B)T), where E is the binding energy of the adsorbate and k(B)T is the thermal energy. These findings are consistent with recent theoretical predictions and computer simulations results that we use to interpret the experimental measurements.

  14. Similar serotonin-2A receptor binding in rats with different coping styles or levels of aggression

    DEFF Research Database (Denmark)

    Visser, Anniek Kd; Ettrup, Anders; Klein, Anders Bue

    2015-01-01

    Individual differences in coping style emerge as a function of underlying variability in the activation of a mesocorticolimbic brain circuitry. Particularly serotonin seems to play an important role. For this reason, we assessed serotonin-2A receptor (5-HT2A R) binding in the brain of rats...... with different coping styles. We compared proactive and reactive males of two rat strains, Wild-type Groningen (WTG) and Roman high- and low avoidance (RHA, RLA). 5-HT2A R binding in (pre)frontal cortex (FC) and hippocampus was investigated using a radiolabeled antagonist ([(3) H]MDL-100907) and agonist ([(3) H......]Cimbi-36) in binding assays. No differences in 5-HT2A R binding were observed in male animals with different coping styles. [(3) H]MDL-100907 displayed a higher specific-to-nonspecific binding ratio than [(3) H]Cimbi-36. Our findings suggest that in these particular rat strains, 5-HT2A R binding...

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

    Science.gov (United States)

    Zhao, Yan-Ping; Li, Ping; Gou, Qing-Quan; Liu, Wei-Na

    2008-12-01

    The formation mechanism for the regular octahedral structure of Li6cluster is proposed. The curve of the total energy versus the separation R between any two neighboring nuclei has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of -44.736 89 a.u. at R = 5.07a0. When R approaches infinity, the total energy of six lithium atoms has the value of -44.568 17 a.u. So the binding energy of Li6 with respect to six lithium atoms is 0.1687 a.u. Therefore, the binding energy per atom for Li6 is 0.028 12 a.u., or 0.7637 eV, which is greater than the binding energy per atom of 0.453 eV for Li2 and the binding energy per atom of 0.494 eV for Li3 calculated in our previous work. This means that the Li6 cluster may be formed in a regular octahedral structure with a greater binding energy.

  16. 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/.

  17. An accurate redetermination of the sup 1 sup 1 sup 8 Sn binding energy

    CERN Document Server

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

    2002-01-01

    The energy of well-known strong gamma line from sup 1 sup 9 sup 8 Au, the 'gold standard', has been modified in the light of new adjustments in the fundamental constants and the value of 411.80176(12) keV was determined, which is 0.29 eV lower than the latest 1999 value. An energy calibration procedure for determining the neutron binding energy, B sub n , from complicated (n, gamma) spectra has been developed. A mathematically simple minimization function consisting only of terms having as parameters the coefficients of the energy calibration curve (polynomial) is used. A priori information about the relationships among the energies of different peaks on the spectrum is taken into account by a Monte-Carlo simulation. The procedure was used in obtaining B sub n for sup 1 sup 1 sup 8 Sn. The gamma-ray spectrum from thermal neutron radiative capture by sup 1 sup 1 sup 7 Sn has been measured on the IBR-2 pulsed reactor. gamma-rays were detected by a 72 cm sup 3 HPGe detector. For a better determination of B sub n...

  18. Perturbation method for calculating impurity binding energy in an ...

    Indian Academy of Sciences (India)

    Nilanjan Sil

    2017-12-18

    Dec 18, 2017 ... the physical properties in them. As a result, the energy of the electrons in the confined directions become quan- tized and forms a discrete energy spectrum. For such size-quantized electrons, the scattering probability is drastically suppressed [15]. The donor impurity in semiconductor nanoheterostru-.

  19. Distinct phosphotyrosines on a growth factor receptor bind to specific molecules that mediate different signaling pathways.

    Science.gov (United States)

    Fantl, W J; Escobedo, J A; Martin, G A; Turck, C W; del Rosario, M; McCormick, F; Williams, L T

    1992-05-01

    The receptor for platelet-derived growth factor (PDGF) binds two proteins containing SH2 domains, GTPase activating protein (GAP) and phosphatidylinositol 3-kinase (PI3-kinase). The sites on the receptor that mediate this interaction were identified by using phosphotyrosine-containing peptides representing receptor sequences to block specifically binding of either PI3-kinase or GAP. These results suggested that PI3-kinase binds two phosphotyrosine residues, each located in a 5 aa motif with an essential methionine at the fourth position C-terminal to the tyrosine. Point mutations at these sites caused a selective elimination of PI3-kinase binding and loss of PDGF-stimulated DNA synthesis. Mutation of the binding site for GAP prevented the receptor from associating with or phosphorylating GAP, but had no effect on PI3-kinase binding and little effect on DNA synthesis. Therefore, GAP and PI3-kinase interact with the receptor by binding to different phosphotyrosine-containing sequence motifs.

  20. Interband absorption and exciton binding energy in an inverse parabolic quantum well under the magnetic field

    International Nuclear Information System (INIS)

    Kasapoglu, E.; Soekmen, I.

    2007-01-01

    We have investigated the effects of the magnetic field which is applied perpendicular to the growth direction of the well on the interband absorption and on the binding energy of the excitons in an GaAs/Ga 1-x Al x As inverse parabolic quantum well (IPQW) with different widths as well as different Al concentrations at the well center. The calculations were performed within the effective mass approximation, using a variational method. We observe that IPQW structure turns into parabolic quantum well with the inversion effect of the magnetic field and the effective band gap of the system can be modified by changing Al concentration at the well center, the strength of the magnetic field and well dimensions. This case directly influences the nature of electronic and optical properties in this structure

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

    Science.gov (United States)

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

    2017-07-01

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

  2. Competitive association binding kinetic assays: a new tool to detect two different binding orientations of a ligand to its target protein under distinct conditions?

    Science.gov (United States)

    Wittmann, Hans-Joachim; Strasser, Andrea

    2017-06-01

    Within the last years, for several ligands, binding to G protein-coupled receptors or other target proteins, a binding of the ligand in two different orientations is described. One appropriate experimental technique to detect two different binding orientations is the crystallization of the ligand-protein-complex, but crystallization and subsequent X-ray analysis do not belong to the routine methods. By traditional competitive radioligand equilibrium binding assays, it is not possible to detect or to distinguish between two different binding orientations, but there is a possibility to identify two different binding orientations by performing kinetic competitive radioligand-binding assays. To study the limitations of this new technique, the related differential equations were defined and solved numerically for 8 different sets of rate constants, also considering an experimental error up to ~10%. In principal, the kinetic competitive radioligand binding assay is a suitable technique to detect two different ligand binding orientations. However, the present study shows that this is only possible under distinct conditions: (1) the rate constants of dissociation for both binding orientations of the cold ligand should at least be > 10-fold different to each other and (2) the experimental error should be as small as possible. Although there are some limitations for the experimental usability of this method, it is worthwhile to perform kinetic competitive binding assays, especially if there are hints for two binding orientations of a ligand, e.g. based on molecular modelling studies.

  3. Effect of magnetic field on the impurity binding energy of the excited ...

    Indian Academy of Sciences (India)

    Keywords. Impurity energy; turning point; binding energy. PACS Nos 73.20.Dx; 73.20.Hb; 71.55.-i; 71.55.Eq. 1. Introduction. Because of the recent advances in nanofabrication technology, it is possible to pro- duce quantum dots whose characteristic dimensions are comparable with the elec- tronic de Broglie wavelengths.

  4. Analysis of binding energy activity of TIBO and HIV-RT based on ...

    African Journals Online (AJOL)

    KEN

    2007-02-05

    Feb 5, 2007 ... the structure of TIBO-HIV-RT complex (Ren et al., 1995,. 1999). In this theoretical research, the energy change corresponding to the conformational change within TIBO was investigated. It was observed that change in the beta dihedral angle conformation critically affects the binding energy. Decreased ...

  5. 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.

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

    International Nuclear Information System (INIS)

    Liu Weina; Li Ping; Gou Qingquan; Zhao Yanping

    2008-01-01

    The formation mechanism for the body-centred regular icosahedral structure of Li 13 cluster is proposed. The curve of the total energy versus the separation R between the nucleus at the centre and nuclei at the apexes for this structure of Li 13 has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of -96.951 39 a.u. at R = 5.46a 0 . When R approaches to infinity, the total energy of thirteen lithium atoms has the value of -96.564 38 a.u. So the binding energy of Li 13 with respect to thirteen lithium atoms is 0.387 01 a.u. Therefore the binding energy per atom for Li 13 is 0.029 77 a.u. or 0.810 eV, which is greater than the binding energy per atom of 0.453 eV for Li 2 , 0.494 eV for Li 3 , 0.7878 eV for Li 4 , 0.632 eV for Li 5 , and 0.674 eV for Li 7 calculated by us previously. This means that the Li 13 cluster may be formed stably in a body-centred regular icosahedral structure with a greater binding energy

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

    Science.gov (United States)

    Liu, Wei-Na; Li, Ping; Gou, Qing-Quan; Zhao, Yan-Ping

    2008-11-01

    The formation mechanism for the body-centred regular icosahedral structure of Li13 cluster is proposed. The curve of the total energy versus the separation R between the nucleus at the centre and nuclei at the apexes for this structure of Li13 has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of 96.951 39 a.u. at R = 5.46a0. When R approaches to infinity, the total energy of thirteen lithium atoms has the value of 96.564 38 a.u. So the binding energy of Li13 with respect to thirteen lithium atoms is 0.387 01 a.u. Therefore the binding energy per atom for Li13 is 0.029 77 a.u. or 0.810 eV, which is greater than the binding energy per atom of 0.453 eV for Li2, 0.494 eV for Li3, 0.7878 eV for Li4, 0.632 eV for Li5, and 0.674 eV for Li7 calculated by us previously. This means that the Li13 cluster may be formed stably in a body-centred regular icosahedral structure with a greater binding energy.

  8. Different mechanisms are involved in the antibody mediated inhibition of ligand binding to the urokinase receptor

    DEFF Research Database (Denmark)

    List, K; Høyer-Hansen, G; Rønne, E

    1999-01-01

    Certain monoclonal antibodies are capable of inhibiting the biological binding reactions of their target proteins. At the molecular level, this type of effect may be brought about by completely different mechanisms, such as competition for common binding determinants, steric hindrance or interfer...

  9. Binding energies: New values and impact on the efficiency of chemical desorption

    Science.gov (United States)

    Wakelam, V.; Loison, J.-C.; Mereau, R.; Ruaud, M.

    2017-03-01

    Recent laboratory measurements have confirmed that chemical desorption (desorption of products due to exothermic surface reactions) can be an efficient process. The impact of including this process into gas-grain chemical models entirely depends on the formalism used and the associated parameters. Among these parameters, binding energies are probably the most uncertain ones for the moment. We propose a new model to compute binding energy of species to water ice surfaces. We have also compared the model results using either the new chemical desorption model proposed by Minissale et al. (2016) or the one of Garrod et al. (2007). The new binding energies have a strong impact on the formation of complex organic molecules. In addition, the new chemical desorption model from Minissale produces a much smaller desorption of these species and also of methanol. Combining the two effects, the abundances of CH3OH and COMs observed in cold cores cannot be reproduced by astrochemical models anymore.

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

    DEFF Research Database (Denmark)

    Greeley, Jeffrey Philip; Nørskov, Jens Kehlet

    2005-01-01

    A simple scheme for the estimation of oxygen binding energies on transition metal surface alloys is presented. It is shown that a d-band center model of the alloy surfaces is a convenient and appropriate basis for this scheme; variations in chemical composition, strain effects, and ligand effects...... are all incorporated into the binding energy analysis through this parameter. With few exceptions, the agreement of the results from the simple model with full DFT calculations on hundreds of binary surface alloys is remarkable. The scheme should therefore provide a fast and effective method...... for the estimation of oxygen binding energies on a wide variety of transition metal alloys. (c) 2005 Elsevier B.V. All rights reserved....

  11. 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.

  12. A comparison of binding energy and metastable zone width for adipic acid with various additives

    Science.gov (United States)

    Myerson, Allan S.; Jang, Shyh M.

    1995-12-01

    The binding energy of nine alkanoic acids to the major crystal faces of adipic acid were calculated employing molecular modelling techniques. The results indicate that the alkanoic acids bind strongly to the surface when compared to solvents and to adipic acid itself indicating that the alkanoic acids could be potential growth and nucleation inhibitors. The binding energies were found to increase with increasing carbon number to C 14 to decrease from C 14 to C 16 and then to increase again. The effect of the alkanoic acids on the metastable zone width of adipic acid in ethanol solution were measured employing a differential scanning calorimeter. The results showed that each of the nine alkanoic acids increased the metastable zone width. The metastable zone widths were found to increase with increasing carbon number to C 14 to decrease from C 14 to C 16 and to then increase again thus correlating well with the results obtained from binding energies. These results indicate that binding energy calculations appear to provide a valid method to screen impurities as potential nucleation inhibitors.

  13. Shedding Light on the EOS-Gravity Degeneracy and Constraining the Nuclear Symmetry Energy from the Gravitational Binding Energy of Neutron Stars

    Directory of Open Access Journals (Sweden)

    He Xiao-Tao

    2016-01-01

    Full Text Available A thorough understanding of properties of neutron stars requires both a reliable knowledge of the equation of state (EOS of super-dense nuclear matter and the strong-field gravity theories simultaneously. To provide information that may help break this EOS-gravity degeneracy, we investigate effects of nuclear symmetry energy on the gravitational binding energy of neutron stars within GR and the scalar-tensor subset of alternative gravity models. We focus on effects of the slope L of nuclear symmetry energy at saturation density and the high-density behavior of nuclear symmetry energy. We find that the variation of either the density slope L or the high-density behavior of nuclear symmetry energy leads to large changes in the binding energy of neutron stars. The difference in predictions using the GR and the scalar-tensor theory appears only for massive neutron stars, and even then is significantly smaller than the difference resulting from variations in the symmetry energy.

  14. Binding energies of hypernuclei and Λ-nuclear interactions

    International Nuclear Information System (INIS)

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

    1985-01-01

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

  15. 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.

  16. The influence of gravitational binding energy on cosmic expansion dynamics: new perspectives for cosmology

    Science.gov (United States)

    Fahr, Hans-Jörg; Sokaliwska, Michael

    2012-06-01

    Confronted with microwave background observations by WMAP and with consternating supernova locations in the magnitude-redshift diagram modern cosmology feels enforced to call for cosmic vacuum energy as a necessary cosmological ingredient. Most often this vacuum energy is associated with Einstein's cosmological constant Λ or with so-called "dark energy". A positive value of Λ describes an inflationary action on cosmic dynamics which in view of recent cosmological data appears as an absolute need. In this article, however, we question the hypothesis of a constant vacuum energy density since not justifiable on physical grounds. Instead we show that gravitational binding energy of cosmic matter, connected with ongoing structure formation during cosmic expansion, acts similar to vacuum energy, since it reduces the effective gravitating proper mass density. Thus one may be encouraged to believe that actions of cosmic vacuum energy and gravitational binding energy concerning their cosmological effects are closely related to each other, perhaps in some respects even have identical phenomenologies. Based on results presented in this article we propose that the generally wanted action of vacuum energy on cosmic spacetime dynamics inevitably leads to a decay of vacuum energy density. Connected with this decay is a decrease of cosmic binding energy and the generation of new effective gravitating mass in the universe. If this all is adequately taken into account by the energy-momentum tensor of the GR field equations, one is then led to non-standard cosmologies which for the first time can guarantee the conservation of the total energy both in static and expanding universes. We describe the structuring of cosmic matter by a change in time of the 2-point correlation-function. We do show here that cosmic structure formation drives accelerated cosmic expansion and feigns the action of vacuum energy density.

  17. Pressure-dependent shallow donor binding energy in InGaN/GaN square QWWs

    International Nuclear Information System (INIS)

    Ghazi, Haddou El; Jorio, Anouar; Zorkani, Izeddine

    2013-01-01

    Using a variational approach, we perform a theoretical study of hydrostatic pressure effect on the ground-state of axial hydrogenic shallow-donor impurity binding energy in InGaN/GaN square quantum well wire (SQWWs) as a function of the side length within the effective-mass scheme and finite potential barrier. The pressure dependence of wire length, effective mass, dielectric constant and potential barrier are taken into account. Numerical results show that: (i) the binding energy is strongly affected by the wire length and the external applied pressure and (ii) its maximum moves to the narrow wire in particular for height pressure.

  18. Experimental Support for Desolvation Energy Term in Governing Equations for Binding Equilibria

    OpenAIRE

    Castellano, Brian M.; Eggers, Daryl K.

    2013-01-01

    This study introduces a new thermodynamic framework for aqueous reaction equilibria that treats water as a co-reactant in the development of a general binding equation. The approach features an explicit consideration for the change in hydration that occurs when two solvated surfaces come into contact. As an outcome of this framework, the standard state free energy of binding is defined by the summation of two terms, the traditional term (−RTlnKi) plus a desolvation free energy term that is we...

  19. 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.

  20. Lowest excited-state impurity binding energy in InGaN/GaN parabolic QWW: magnetic field effect

    International Nuclear Information System (INIS)

    Haddou El Ghazi; Anouar Jorio; Izeddine Zorkani

    2013-01-01

    In this paper, we have investigated the magnetic field effect on the lowest excited-state binding energy of hydrogenic shallow-donor impurity in wurtzite (In,Ga)N/GaN parabolic transversal-section quantum-well wire (PQWW) using the finite-difference method within the quasi-one-dimensional effective potential model. The calculations are performed within the framework of the effective mass approximation. A cylindrical QWW effective radius is taken into account to describe the lateral confinement strength. The numerical results show that: (i) the probability density is the largest on a circularity whose radius is the effective radius and (ii) the lowest excited-state binding energy is the largest when an impurity is located on this circularity while it starts to decrease as the impurity is away from the circularity. (author)

  1. Analysis of binding energy activity of TIBO and HIV-RT based on ...

    African Journals Online (AJOL)

    Tetrahydro-imidazo[4,5,l-jk][1,4]-benzodiazepin-2 (1 H)one (TIBO) is a noncompetitive non nucleotide antiretroviral drug with a specific allosteric binding site of HIV-1 RT. The conformational analysis shows that the effect of the drug depends on the potential energy which varied due to the beta rotatable dihedral angles (N6 ...

  2. Binding of Hydrophobic Guests in a Coordination Cage Cavity is Driven by Liberation of "High-Energy" Water.

    Science.gov (United States)

    Metherell, Alexander J; Cullen, William; Williams, Nicholas H; Ward, Michael D

    2018-02-01

    The cavity of an M 8 L 12 cubic coordination cage can accommodate a cluster of ten water molecules in which the average number of hydrogen bonds per water molecule is 0.5 H-bonds less than it would be in the bulk solution. The presence of these "hydrogen-bond frustrated" or "high-energy" water molecules in the cavity results in the hydrophobic effect associated with guest binding being predominantly enthalpy-based, as these water molecules can improve their hydrogen-bonding environment on release. This contrasts with the classical form of the hydrophobic effect in which the favourable entropy change associated with release of ordered molecules from hydrophobic surfaces dominates. For several guests Van't Hoff plots showed that the free energy of binding in water is primarily enthalpy driven. For five homologous pairs of guests related by the presence or absence of a CH 2 group, the incremental changes to ΔH and TΔS for guest binding-that is, ΔΔH and TΔΔS, the difference in contributions arising from the CH 2 group-are consistently 5(±1) kJ mol -1 for ΔΔH and 0(±1) kJ mol -1 for TΔΔS. This systematic dominance of ΔH in the binding of hydrophobic guests is consistent with the view that guest binding is dominated by release of "high energy" water molecules into a more favourable solvation environment, as has been demonstrated recently for some members of the cucurbituril family. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  3. Measurement of specific [3H]-ouabain binding to different types of human leucocytes

    DEFF Research Database (Denmark)

    Boon, Arnold; Oh, V M; Taylor, John E.

    1984-01-01

    We have studied the specific binding of [3H]-ouabain to intact mononuclear leucocytes (82% lymphocytes) and polymorphonuclear leucocytes. In both types of cells [3H]-ouabain binding was saturable, confined to a single site of high affinity, slow to reach equilibrium, slow to reverse, temperature......-dependent, competitively antagonized by potassium, and facilitated by the presence of divalent cations. The equilibrium dissociation constants were 2.4 +/- 0.7 nmol/l (polymorphs) and 2.4 +/- 0.4 nmol/l (mononuclear cells) (NS). The values of maximal specific ouabain binding, measured by Scatchard analysis...... were expressed per square micron of cell surface area the difference between the two cell types was proportionately greater (83 and 186 sites per micron 2 respectively). We conclude that the [3H]-ouabain binding sites on mononuclear and polymorphonuclear leucocytes are similar in nature, but different...

  4. 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

  5. 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. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  6. Molecular dynamics study of binding energies, mechanical properties, and detonation performances of bicyclo-HMX-based PBXs.

    Science.gov (United States)

    Qiu, Ling; Xiao, Heming

    2009-05-15

    To investigate the effect of polymer binders on the monoexplosive, molecular dynamics simulations were performed to study the binding energies, mechanical properties, and detonation performances of the bicyclo-HMX-based polymer-bonded explosives (PBXs). The results show that the binding energies on different crystalline surfaces of bicyclo-HMX decrease in the order of (010)>(100)>(001). On each crystalline surface, binding properties of different polymers with the same chain segment are different from each other, while those of the polymers in the same content decrease in the sequence of PVDF>F(2311)>F(2314) approximately PCTFE. The mechanical properties of a dozen of model systems (elastic coefficients, various moduli, Cauchy pressure, and Poisson's ratio) have been obtained. It is found that mechanical properties are effectively improved by adding small amounts of fluorine polymers, and the overall effect of fluorine polymers on three crystalline surfaces of bicyclo-HMX changes in the order of (010)>(001) approximately (100). In comparison with the base explosive, detonation performances of the PBXs decrease slightly, but they are still superior to TNT. These suggestions may be useful for the formulation design of bicyclo-HMX-based PBXs.

  7. Binding Energy and Dissociation Barrier: Experimental Determination of the Key Parameters of the Potential Energy Curve of Diethyl Ether on Si(001).

    Science.gov (United States)

    Reutzel, Marcel; Lipponer, Marcus; Dürr, Michael; Höfer, Ulrich

    2015-10-01

    The key parameters of the potential energy curve of organic molecules on semiconductor surfaces, binding energy of the intermediate state and dissociation barrier, were experimentally investigated for the model system of diethyl ether (Et2O) on Si(001). Et2O adsorbs via a datively bonded intermediate from which it converts via ether cleavage into a covalently attached final state. This thermally activated conversion into the final state was followed in real-time by means of optical second-harmonic generation (SHG) at different temperatures and the associated energy barrier ϵa = 0.38 ± 0.05 eV and pre-exponential factor νa = 10(4±1) s(-1) were determined. From molecular beam experiments on the initial sticking probability, the difference between the desorption energy ϵd and ϵa was extracted and thus the binding energy of the intermediate state was determined (0.62 ± 0.08 eV). The results are discussed in terms of general chemical trends as well as with respect to a wider applicability on adsorbate reactions on semiconductor surfaces.

  8. Differences in Binding and Monitoring Mechanisms Contribute to Lifespan Age Differences in False Memory

    Science.gov (United States)

    Fandakova, Yana; Shing, Yee Lee; Lindenberger, Ulman

    2013-01-01

    Based on a 2-component framework of episodic memory development across the lifespan (Shing & Lindenberger, 2011), we examined the contribution of memory-related binding and monitoring processes to false memory susceptibility in childhood and old age. We administered a repeated continuous recognition task to children (N = 20, 10-12 years),…

  9. Computation of the binding affinities of catechol-O-methyltransferase inhibitors: multisubstate relative free energy calculations.

    Science.gov (United States)

    Palma, P Nuno; Bonifácio, Maria João; Loureiro, Ana Isabel; Soares-da-Silva, Patrício

    2012-04-05

    Alchemical free energy simulations are amongst the most accurate techniques for the computation of the free energy changes associated with noncovalent protein-ligand interactions. A procedure is presented to estimate the relative binding free energies of several ligands to the same protein target where multiple, low-energy configurational substates might coexist, as opposed to one unique structure. The contributions of all individual substates were estimated, explicitly, with the free energy perturbation method, and combined in a rigorous fashion to compute the overall relative binding free energies and dissociation constants. It is shown that, unless the most stable bound forms are known a priori, inaccurate results may be obtained if the contributions of multiple substates are ignored. The method was applied to study the complex formed between human catechol-O-methyltransferase and BIA 9-1067, a newly developed tight-binding inhibitor that is currently under clinical evaluation for the therapy of Parkinson's disease. Our results reveal an exceptionally high-binding affinity (K(d) in subpicomolar range) and provide insightful clues on the interactions and mechanism of inhibition. The inhibitor is, itself, a slowly reacting substrate of the target enzyme and is released from the complex in the form of O-methylated product. By comparing the experimental catalytic rate (k(cat)) and the estimated dissociation rate (k(off)) constants of the enzyme-inhibitor complex, one can conclude that the observed inhibition potency (K(i)) is primarily dependent on the catalytic rate constant of the inhibitor's O-methylation, rather than the rate constant of dissociation of the complex. Copyright © 2012 Wiley Periodicals, Inc.

  10. Reshaping the Energy Landscape Transforms the Mechanism and Binding Kinetics of DNA Threading Intercalation.

    Science.gov (United States)

    Clark, Andrew G; Naufer, M Nabuan; Westerlund, Fredrik; Lincoln, Per; Rouzina, Ioulia; Paramanathan, Thayaparan; Williams, Mark C

    2018-02-06

    Molecules that bind DNA via threading intercalation show high binding affinity as well as slow dissociation kinetics, properties ideal for the development of anticancer drugs. To this end, it is critical to identify the specific molecular characteristics of threading intercalators that result in optimal DNA interactions. Using single-molecule techniques, we quantify the binding of a small metal-organic ruthenium threading intercalator (Δ,Δ-B) and compare its binding characteristics to a similar molecule with significantly larger threading moieties (Δ,Δ-P). The binding affinities of the two molecules are the same, while comparison of the binding kinetics reveals significantly faster kinetics for Δ,Δ-B. However, the kinetics is still much slower than that observed for conventional intercalators. Comparison of the two threading intercalators shows that the binding affinity is modulated independently by the intercalating section and the binding kinetics is modulated by the threading moiety. In order to thread DNA, Δ,Δ-P requires a "lock mechanism", in which a large length increase of the DNA duplex is required for both association and dissociation. In contrast, measurements of the force-dependent binding kinetics show that Δ,Δ-B requires a large DNA length increase for association but no length increase for dissociation from DNA. This contrasts strongly with conventional intercalators, for which almost no DNA length change is required for association but a large DNA length change must occur for dissociation. This result illustrates the fundamentally different mechanism of threading intercalation compared with conventional intercalation and will pave the way for the rational design of therapeutic drugs based on DNA threading intercalation.

  11. 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. © 2011 American Chemical Society

  12. Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

    Science.gov (United States)

    Tofoleanu, Florentina; Pickard, Frank C.; König, Gerhard; Huang, Jing; Damjanović, Ana; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.

    2016-01-01

    Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett’s acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments. PMID:27677749

  13. Experimental support for a desolvation energy term in governing equations for binding equilibria.

    Science.gov (United States)

    Castellano, Brian M; Eggers, Daryl K

    2013-07-11

    This study introduces a new thermodynamic framework for aqueous reaction equilibria that treats water as a coreactant in the development of a general binding equation. The approach features an explicit consideration for the change in hydration that occurs when two solvated surfaces come into contact. As an outcome of this framework, the standard-state free energy of binding is defined by the summation of two terms: the traditional term (-RT ln Ki) plus a desolvation free-energy term that is weighted by the number of complexes formed at equilibrium. The new formalism suggests that the equilibrium ratio, Ki, is not a constant and that the observed concentration dependence of Ki may be used to obtain the molar desolvation energy and the standard-state free energy at infinite dilution. The governing equation is supported by results from isothermal titration calorimetry using the chelation of calcium(II) by EDTA as a model binding reaction. This work may have far-reaching implications for solution thermodynamics, including an explanation for the oft-noted discrepancy between the enthalpy values obtained by calorimetry and those from the van't Hoff approach.

  14. Experimental Support for Desolvation Energy Term in Governing Equations for Binding Equilibria

    Science.gov (United States)

    Castellano, Brian M.; Eggers, Daryl K.

    2013-01-01

    This study introduces a new thermodynamic framework for aqueous reaction equilibria that treats water as a co-reactant in the development of a general binding equation. The approach features an explicit consideration for the change in hydration that occurs when two solvated surfaces come into contact. As an outcome of this framework, the standard state free energy of binding is defined by the summation of two terms, the traditional term (−RTlnKi) plus a desolvation free energy term that is weighted by the number of complexes formed at equilibrium. The new formalism suggests that the equilibrium ratio, Ki, is not a constant and that the observed concentration dependence of Ki may be used to obtain the molar desolvation energy and the standard state free energy at infinite dilution. The governing equation is supported by results from isothermal titration calorimetry using the chelation of calcium(II) by EDTA as a model binding reaction. This work may have far-reaching implications for solution thermodynamics, including an explanation for the oft-noted discrepancy between enthalpy values obtained by calorimetry and the van’t Hoff approach. PMID:23773139

  15. Binding Thermodynamics of Ferredoxin:NADP+ Reductase: Two Different Protein Substrates and One Energetics

    Science.gov (United States)

    Martínez-Júlvez, Marta; Medina, Milagros; Velázquez-Campoy, Adrián

    2009-01-01

    Abstract The thermodynamics of the formation of binary and ternary complexes between Anabaena PCC 7119 FNR and its substrates, NADP+ and Fd, or Fld, has been studied by ITC. Despite structural dissimilarities, the main difference between Fd and Fld binding to FNR relates to hydrophobicity, reflected in different binding heat capacity and number of water molecules released from the interface. At pH 8, the formation of the binary complexes is both enthalpically and entropically driven, accompanied by the protonation of at least one ionizable group. His299 FNR has been identified as the main responsible for the proton exchange observed. However, at pH 10, where no protonation occurs and intrinsic binding parameters can be obtained, the formation of the binary complexes is entropically driven, with negligible enthalpic contribution. Absence of the FMN cofactor in Fld does not alter significantly the strength of the interaction, but considerably modifies the enthalpic and entropic contributions, suggesting a different binding mode. Ternary complexes show negative cooperativity (6-fold and 11-fold reduction in binding affinity, respectively), and an increase in the enthalpic contribution (more favorable) and a decrease in the entropic contribution (less favorable), with regard to the binary complexes energetics. PMID:19527656

  16. Precision measurements of high-energy conversion electron lines and determination of neutron binding energies

    International Nuclear Information System (INIS)

    Braumandl, F.

    1979-01-01

    The paper first discusses the energy accuracy of the BILL conversion electron spectrometer at the Grenoble high flux reactor. With an improved temperature stabilisation of the magnets, an energy accuracy of ΔE/E -5 can be reached. After this, highly exact measurements of high-energy conversion electron lines of the 200 Hg, 114 Cd, 165 Dy, 168 Er, 239 U nuclei and the 13 C, 28 Al 3 H and 92 Zr photoelectron lines were carried out. Energy calibration of the spectrometer was carried out in the 1.5 MeV to 6.5 MeV range with intensive high-energy transitions of the 200 Hg nucleus. Systematic calibration errors could be investigated by means of combinations between the calibration lines. A calibration for absolute energies was obtained by comparing low-energy gamma transitions of 200 Hg with the 411.8 keV gold standard. (orig.) [de

  17. Hole burning study of cyanobacterial Photosystem II complexes differing in the content of small putative chlorophyll-binding proteins

    Energy Technology Data Exchange (ETDEWEB)

    Dedic, R. E-mail: roman@kchf-43.karlov.mff.cuni.cz; Promnares, K.; Psencik, J.; Svoboda, A.; Korinek, M.; Tichy, M.; Komenda, J.; Funk, C.; Hala, J

    2004-05-01

    This contribution presents low-temperature absorption, both broad-band and site-selective excited fluorescence, and persistent hole burning spectra of Photosystem II complexes from the Photosystem I-lacking strains of the cyanobacterium Synechocystis sp. PCC 6803 differing in the content of small putative chlorophyll-binding proteins (Scps). These proteins are homologous to light-harvesting complex of higher plants and may bind pigments. The excited state lifetimes of the complexes were determined from zero-phonon hole widths extrapolated to zero-burning dose. The area and spectral position of a phonon side-band with respect to the zero-phonon hole provided additional information concerning chlorophyll-protein coupling and the Stokes shift. Decrease of three absorption subbands at (670.0, 672.9, and 675.7 nm) in the Photosystem II isolated from the strain lacking ScpC and ScpD is in agreement with a hypothesis about the role of Scps in the chlorophyll binding. In addition, narrowing of the zero-phonon hole in Photosystem II without both Scps indicates slowering of the excitation energy transfer which may be explained by the absence of a protective excitation energy quenching related to the presence of Scps.

  18. Isothermal titration calorimetry and surface plasmon resonance allow quantifying substrate binding to different binding sites of Bacillus subtilis xylanase

    DEFF Research Database (Denmark)

    Cuyvers, Sven; Dornez, Emmie; Abou Hachem, Maher

    2012-01-01

    Isothermal titration calorimetry and surface plasmon resonance were tested for their ability to study substrate binding to the active site (AS) and to the secondary binding site (SBS) of Bacillus subtilis xylanase A separately. To this end, three enzyme variants were compared. The first was a cat......Isothermal titration calorimetry and surface plasmon resonance were tested for their ability to study substrate binding to the active site (AS) and to the secondary binding site (SBS) of Bacillus subtilis xylanase A separately. To this end, three enzyme variants were compared. The first...

  19. Quantum confinement effect and exciton binding energy of layered perovskite nanoplatelets

    Directory of Open Access Journals (Sweden)

    Qiang Wang

    2018-02-01

    Full Text Available We report the preparation of monolayer (n = 1, few-layer (n = 2–5 and 3D (n = ∞ organic lead bromide perovskite nanoplatelets (NPLs by tuning the molar ratio of methylammonium bromide (MABr and hexadecammonium bromide (HABr. The absorption spectrum of the monolayer (HA2PbBr4 perovskite NPLs shows about 138 nm blue shift from that of 3D MAPbBr3 perovskites, which is attributed to strong quantum confinement effect. We further investigate the two-photon photoluminescence (PL of the NPLs and measure the exciton binding energy of monolayer perovskite NPLs using linear absorption and two-photon PL excitation spectroscopy. The exciton binding energy of monolayer perovskite NPLs is about 218 meV, which is far larger than tens of meV in 3D lead halide perovskites.

  20. Neuroticism Associates with Cerebral in Vivo Serotonin Transporter Binding Differently in Males and Females

    DEFF Research Database (Denmark)

    Tuominen, Lauri; Miettunen, Jouko; Cannon, Dara M

    2017-01-01

    scores from 91 healthy males and 56 healthy females. We specifically tested if the association between neuroticism and serotonin transporter is different in females and males. Results: We found that neuroticism and thalamic serotonin transporter binding potentials were associated in both males...... and females, but with opposite directionality. Higher neuroticism associated with higher serotonin transporter binding potential in males (standardized beta 0.292, P=.008), whereas in females, higher neuroticism associated with lower serotonin transporter binding potential (standardized beta -0.288, P=.014......). Conclusions: The finding is in agreement with recent studies showing that the serotonergic system is involved in affective disorders differently in males and females and suggests that contribution of thalamic serotonin transporter to the risk of affective disorders depends on sex....

  1. Binding energy of a hydrogenic impurity in a coaxial quantum wire with an insulator layer

    Science.gov (United States)

    Kes, H.; Bilekkaya, A.; Aktas, S.; Okan, S. E.

    2017-11-01

    The electronic properties of a coaxial cylindrical quantum well-barrier system constituted about an central insulating wire were determined under an external electric field. The model wire, inside to outside, was considered to be layered as AlAs / GaAs / Alx1 Ga1 -x1 As / GaAs / Alx2 Ga1 -x2 As. Within the framework of the effective mass-approximation, the binding energy of a hydrogenic impurity is calculated by using the combination of the fourth-order Runge-Kutta method and variational approaches. The binding energy exhibits sharp changes depending on the impurity position and the geometrical parameters of the structure such as the well widths of the GaAs wires and the height and thickness of the barrier constituted by Alx1 Ga1 -x1 As . The binding energy of the electron was found to be independent from the impurity position for the specific widths of the well wires. Also, the barrier properties appeared as very effective parameters in controlling the probability distribution of the electron.

  2. The structure and binding energy of K+endash ether complexes: A comparison of MP2, RI-MP2, and density functional methods

    International Nuclear Information System (INIS)

    Feller, D.; Apra, E.; Nichols, J.A.; Bernholdt, D.E.

    1996-01-01

    The structures and binding energies of several cation:ether complexes (K + :dimethyl ether, K + :dimethoxyethane, K + :12-crown-4 and K + :18-crown-6) were determined with second and fourth order perturbation theory using correlation consistent basis sets. Several of these are the largest correlated calculations yet attempted on crown ethers. The observed systematic convergence to the complete basis set limit provides a standard by which the accuracy of previous studies can be measured and facilitates the calibration of density functional methods. Recent Fouier transform ion cyclotron resonance experiments predicted K + :18-crown-6 binding energies which were significantly smaller than ab initio calculations. None of the potential sources of error examined in the present study were large enough to explain this difference. Although the 6-31+G* basis set used in an earlier theoretical study was smaller than the smallest of the correlation consistent basis sets, with suitable correction for basis set superposition error, it appears capable of yielding binding energies within several kcal/mol of the basis set limit. Perturbation theory calculations exploiting the open-quote open-quote resolution of the identity close-quote close-quote approximation were found to faithfully reproduce binding energies and conformational differences. Although the cation endash ether interaction is dominated by classical electrostatics, the accuracy of density functional techniques was found to be quite sensitive to the choice of functionals. The local density SVWN procedure performed well for binding energies and conformational differences, while underestimating K + O distances by up to 0.08 A. The gradient-corrected Becke endash Lee endash Yang endash Parr functional underestimated the K + :12c4 binding energy by 4 endash 7 kcal/mol or 15%. copyright 1996 American Institute of Physics

  3. 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. © 2015 The Protein Society.

  4. Ail proteins of Yersinia pestis and Y. pseudotuberculosis have different cell binding and invasion activities.

    Science.gov (United States)

    Tsang, Tiffany M; Wiese, Jeffrey S; Felek, Suleyman; Kronshage, Malte; Krukonis, Eric S

    2013-01-01

    The Yersinia pestis adhesin Ail mediates host cell binding and facilitates delivery of cytotoxic Yop proteins. Ail from Y. pestis and Y. pseudotuberculosis is identical except for one or two amino acids at positions 43 and 126 depending on the Y. pseudotuberculosis strain. Ail from Y. pseudotuberculosis strain YPIII has been reported to lack host cell binding ability, thus we sought to determine which amino acid difference(s) are responsible for the difference in cell adhesion. Y. pseudotuberculosis YPIII Ail expressed in Escherichia coli bound host cells, albeit at ~50% the capacity of Y. pestis Ail. Y. pestis Ail single mutants, Ail-E43D and Ail-F126V, both have decreased adhesion and invasion in E. coli when compared to wild-type Y. pestis Ail. Y. pseudotuberculosis YPIII Ail also had decreased binding to the Ail substrate fibronectin, relative to Y. pestis Ail in E. coli. When expressed in Y. pestis, there was a 30-50% decrease in adhesion and invasion depending on the substitution. Ail-mediated Yop delivery by both Y. pestis Ail and Y. pseudotuberculosis Ail were similar when expressed in Y. pestis, with only Ail-F126V giving a statistically significant reduction in Yop delivery of 25%. In contrast to results in E. coli and Y. pestis, expression of Ail in Y. pseudotuberculosis led to no measurable adhesion or invasion, suggesting the longer LPS of Y. pseudotuberculosis interferes with Ail cell-binding activity. Thus, host context affects the binding activities of Ail and both Y. pestis and Y. pseudotuberculosis Ail can mediate cell binding, cell invasion and facilitate Yop delivery.

  5. Similar serotonin-2A receptor binding in rats with different coping styles or levels of aggression

    NARCIS (Netherlands)

    Visser, Anniek K. D.; Ettrup, Anders; Klein, Anders B.; van Waarde, Aren; Bosker, Fokko J.; Meerlo, Peter; Knudsen, Gitte M.; De Boer, Sietse F.

    2015-01-01

    Individual differences in coping style emerge as a function of underlying variability in the activation of a mesocorticolimbic brain circuitry. Particularly serotonin seems to play an important role. For this reason, we assessed serotonin-2A receptor (5-HT2AR) binding in the brain of rats with

  6. Ligand-receptor binding affinities from saturation transfer difference (STD) NMR spectroscopy: the binding isotherm of STD initial growth rates.

    Science.gov (United States)

    Angulo, Jesús; Enríquez-Navas, Pedro M; Nieto, Pedro M

    2010-07-12

    The direct evaluation of dissociation constants (K(D)) from the variation of saturation transfer difference (STD) NMR spectroscopy values with the receptor-ligand ratio is not feasible due to the complex dependence of STD intensities on the spectral properties of the observed signals. Indirect evaluation, by competition experiments, allows the determination of K(D), as long as a ligand of known affinity is available for the protein under study. Herein, we present a novel protocol based on STD NMR spectroscopy for the direct measurements of receptor-ligand dissociation constants (K(D)) from single-ligand titration experiments. The influence of several experimental factors on STD values has been studied in detail, confirming the marked impact on standard determinations of protein-ligand affinities by STD NMR spectroscopy. These factors, namely, STD saturation time, ligand residence time in the complex, and the intensity of the signal, affect the accumulation of saturation in the free ligand by processes closely related to fast protein-ligand rebinding and longitudinal relaxation of the ligand signals. The proposed method avoids the dependence of the magnitudes of ligand STD signals at a given saturation time on spurious factors by constructing the binding isotherms using the initial growth rates of the STD amplification factors, in a similar way to the use of NOE growing rates to estimate cross relaxation rates for distance evaluations. Herein, it is demonstrated that the effects of these factors are cancelled out by analyzing the protein-ligand association curve using STD values at the limit of zero saturation time, when virtually no ligand rebinding or relaxation takes place. The approach is validated for two well-studied protein-ligand systems: the binding of the saccharides GlcNAc and GlcNAcbeta1,4GlcNAc (chitobiose) to the wheat germ agglutinin (WGA) lectin, and the interaction of the amino acid L-tryptophan to bovine serum albumin (BSA). In all cases, the

  7. Binding of plasma proteins to titanium dioxide nanotubes with different diameters

    Science.gov (United States)

    Kulkarni, Mukta; Flašker, Ajda; Lokar, Maruša; Mrak-Poljšak, Katjuša; Mazare, Anca; Artenjak, Andrej; Čučnik, Saša; Kralj, Slavko; Velikonja, Aljaž; Schmuki, Patrik; Kralj-Iglič, Veronika; Sodin-Semrl, Snezna; Iglič, Aleš

    2015-01-01

    Titanium and titanium alloys are considered to be one of the most applicable materials in medical devices because of their suitable properties, most importantly high corrosion resistance and the specific combination of strength with biocompatibility. In order to improve the biocompatibility of titanium surfaces, the current report initially focuses on specifying the topography of titanium dioxide (TiO2) nanotubes (NTs) by electrochemical anodization. The zeta potential (ζ-potential) of NTs showed a negative value and confirmed the agreement between the measured and theoretically predicted dependence of ζ-potential on salt concentration, whereby the absolute value of ζ-potential diminished with increasing salt concentrations. We investigated binding of various plasma proteins with different sizes and charges using the bicinchoninic acid assay and immunofluorescence microscopy. Results showed effective and comparatively higher protein binding to NTs with 100 nm diameters (compared to 50 or 15 nm). We also showed a dose-dependent effect of serum amyloid A protein binding to NTs. These results and theoretical calculations of total available surface area for binding of proteins indicate that the largest surface area (also considering the NT lengths) is available for 100 nm NTs, with decreasing surface area for 50 and 15 nm NTs. These current investigations will have an impact on increasing the binding ability of biomedical devices in the body leading to increased durability of biomedical devices. PMID:25733829

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-12-15

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

  9. Seasonal difference in brain serotonin transporter binding predicts symptom severity in patients with seasonal affective disorder

    DEFF Research Database (Denmark)

    Mc Mahon, Brenda; Andersen, Sofie B.; Madsen, Martin K.

    2016-01-01

    from the first longitudinal investigation of seasonal serotonin transporter fluctuations in both patients with seasonal affective disorder and in healthy individuals. Eighty 11 C-DASB positron emission tomography scans were conducted to quantify cerebral serotonin transporter binding; 23 healthy...... controls with low seasonality scores and 17 patients diagnosed with seasonal affective disorder were scanned in both summer and winter to investigate differences in cerebral serotonin transporter binding across groups and across seasons. The two groups had similar cerebral serotonin transporter binding...... in the summer but in their symptomatic phase during winter, patients with seasonal affective disorder had higher serotonin transporter than the healthy control subjects (P = 0.01). Compared to the healthy controls, patients with seasonal affective disorder changed their serotonin transporter significantly less...

  10. Differences in both glycosylation and binding properties between rat and mouse liver prolactin receptors.

    Science.gov (United States)

    Lascols, O; Cherqui, G; Munier, A; Picard, J; Capeau, J

    1994-05-01

    To investigate whether glycanic chains of prolactin receptors (PRL-R) play a role in hormone binding activity, comparison was made of rat and mouse liver solubilized receptors with respect to both their affinity for the hormone and their glycosylation properties. As compared with rat receptors, mouse receptors exhibited a 2-fold higher affinity for human growth hormone (hGH), the hormone being bound by both tissues with a lactogenic specificity. Along with this increased affinity, mouse receptors had a 2 lower M(r) relative to rat receptors (62 kDa versus 64 kDa as measured on hGH cross-linked receptors). These differences could be ascribed to different glycosylation properties of the receptors from the two species, as supported by the followings. 1) After treatment with endoglycosidase F (endo F), rat and mouse PRL-R no longer exhibited any difference in their M(r) (54 kDa for both cross-linked receptors). 2) Neuraminidase treatment increased by 37% the binding of hGH to mouse receptors, but was ineffective on the hormone-binding to rat receptors. Conversely, wheat germ agglutinin (WGA), another sialic acid specific probe, decreased hGH binding to rat receptors by 25%, but had no effect on this process for mouse ones. 3) Marked differences were observed in the recoveries of rat and mouse hormone-receptor (HR) complexes from ricin-1- (RCA1-), concanavalin A- (ConA-) and WGA-immobilized lectins. These differences were reduced (RCA1 and ConA) or abolished (WGA) after rat and mouse receptor desialylation by neuraminidase, a treatment which decreased the M(r) of both receptors by 2 kDa. Taken together, these results strongly suggest that the PRL-R from rat and mouse liver contain biantennary N-linked oligosaccharidic chains with distinct type of sialylation, which may account for their differential hormone-binding affinities.

  11. Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies.

    Science.gov (United States)

    Genheden, Samuel; Ryde, Ulf

    2011-11-08

    We have evaluated the efficiency of two popular end-point methods to calculate ligand-binding free energies, LIE (linear interaction energy) and MM/GBSA (molecular mechanics with generalized Born surface-area solvation), i.e. the computational effort needed to obtain estimates of a similar precision. As a test case, we use the binding of seven biotin analogues to avidin. The energy terms used by MM/GBSA and LIE exhibit a similar correlation time (∼5 ps), and the equilibration time seems also to be similar, although it varies much between the various ligands. The results show that the LIE method is more effective than MM/GBSA, by a factor of 2-7 for a truncated spherical system with a radius of 26 Å and by a factor of 1.0-2.4 for the full avidin tetramer (radius 47 Å). The reason for this is the cost for the MM/GBSA entropy calculations, which more than compensates for the extra simulation of the free ligand in LIE. On the other hand, LIE requires that the protein is neutralized, whereas MM/GBSA has no such requirements. Our results indicate that both the truncation and neutralization of the proteins may slow the convergence and emphasize small differences in the calculations, e.g., differences between the four subunits in avidin. Moreover, LIE cannot take advantage of the fact that avidin is a tetramer. For this test case, LIE gives poor results with the standard parametrization, but after optimizing the scaling factor of the van der Waals terms, reasonable binding affinities can be obtained, although MM/GBSA still gives a significantly better predictive index and correlation to the experimental affinities.

  12. Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module.

    Science.gov (United States)

    Wojciechowski, Michał; Różycki, Bartosz; Huy, Pham Dinh Quoc; Li, Mai Suan; Bayer, Edward A; Cieplak, Marek

    2018-03-22

    The assembly of the polysaccharide degradating cellulosome machinery is mediated by tight binding between cohesin and dockerin domains. We have used an empirical model known as FoldX as well as molecular mechanics methods to determine the free energy of binding between a cohesin and a dockerin from Clostridium thermocellum in two possible modes that differ by an approximately 180° rotation. Our studies suggest that the full-length wild-type complex exhibits dual binding at room temperature, i.e., the two modes of binding have comparable probabilities at equilibrium. The ability to bind in the two modes persists at elevated temperatures. However, single-point mutations or truncations of terminal segments in the dockerin result in shifting the equilibrium towards one of the binding modes. Our molecular dynamics simulations of mechanical stretching of the full-length wild-type cohesin-dockerin complex indicate that each mode of binding leads to two kinds of stretching pathways, which may be mistakenly taken as evidence of dual binding.

  13. The effects of electron binding energy corrections on Monte Carlo models in the diagnostic x-ray energy range

    International Nuclear Information System (INIS)

    Sim, L.H.; Van Doorn, T.; Michael, G.J.

    1996-01-01

    Full text: The effects of incorporating electron binding energy corrections for incoherent scatter (BEC) into Monte Carlo models of X-ray transport in the diagnostic energy range have been examined. The inclusion of BEC can significantly increase computing overhead both in terms of data storage and execution time. In a modern PC application, data storage is unlikely to be a significant problem. However, execution time is a major consideration when assessing the relative usefulness of Monte Carlo systems. If the effectiveness of including BEC is barely more than equivocal, as is the case in some of the studies reported here, then a decision to include them requires consideration of the photon energy being modelled and the data being sought. This work seeks to clarify the real significance of inclusion of BEC by examining their effects without the confounding influence of coherent scattering effects. A Monte Carlo computer code has been developed to study a variety of X-ray transport phenomena. Models of radiation dose deposition in a semi-infinite medium, a similar model in tissue using a realistic source spectrum and diverging beam geometry, a simulation of pencil beam bone densitometry measurements, models of barrier penetration by X-rays and models of the angular distribution of scattered radiation have been undertaken. Results of previous studies have been confirmed. Models of radiation dose deposition for 10 keV, 30 keV and 100 keV photons have shown that inclusion of BEC has only a small effect upon values of total depth dose. Differences are of the same order of magnitude as the standard deviation of the results. A larger effect was noted for the values of dose due to scattered photons. This effect reached a maximum of 7% at 30 keV. Similar results were obtained from a model using a realistic source spectrum and diverging beam geometry. In the simulation of bone densitometry measurements the effects are significant (i.e. of the order of 10%). The angular

  14. Sialic Acid Binding Properties of Soluble Coronavirus Spike (S1) Proteins: Differences between Infectious Bronchitis Virus and Transmissible Gastroenteritis Virus

    Science.gov (United States)

    Shahwan, Katarina; Hesse, Martina; Mork, Ann-Kathrin; Herrler, Georg; Winter, Christine

    2013-01-01

    The spike proteins of a number of coronaviruses are able to bind to sialic acids present on the cell surface. The importance of this sialic acid binding ability during infection is, however, quite different. We compared the spike protein of transmissible gastroenteritis virus (TGEV) and the spike protein of infectious bronchitis virus (IBV). Whereas sialic acid is the only receptor determinant known so far for IBV, TGEV requires interaction with its receptor aminopeptidase N to initiate infection of cells. Binding tests with soluble spike proteins carrying an IgG Fc-tag revealed pronounced differences between these two viral proteins. Binding of the IBV spike protein to host cells was in all experiments sialic acid dependent, whereas the soluble TGEV spike showed binding to APN but had no detectable sialic acid binding activity. Our results underline the different ways in which binding to sialoglycoconjugates is mediated by coronavirus spike proteins. PMID:23896748

  15. Sialic Acid Binding Properties of Soluble Coronavirus Spike (S1 Proteins: Differences between Infectious Bronchitis Virus and Transmissible Gastroenteritis Virus

    Directory of Open Access Journals (Sweden)

    Christine Winter

    2013-07-01

    Full Text Available The spike proteins of a number of coronaviruses are able to bind to sialic acids present on the cell surface. The importance of this sialic acid binding ability during infection is, however, quite different. We compared the spike protein of transmissible gastroenteritis virus (TGEV and the spike protein of infectious bronchitis virus (IBV. Whereas sialic acid is the only receptor determinant known so far for IBV, TGEV requires interaction with its receptor aminopeptidase N to initiate infection of cells. Binding tests with soluble spike proteins carrying an IgG Fc-tag revealed pronounced differences between these two viral proteins. Binding of the IBV spike protein to host cells was in all experiments sialic acid dependent, whereas the soluble TGEV spike showed binding to APN but had no detectable sialic acid binding activity. Our results underline the different ways in which binding to sialoglycoconjugates is mediated by coronavirus spike proteins.

  16. Human Ku70 protein binds hairpin RNA and double stranded DNA through two different sites.

    Science.gov (United States)

    Anisenko, Andrey N; Knyazhanskaya, Ekaterina S; Zatsepin, Timofey S; Gottikh, Marina B

    2017-01-01

    Human protein Ku usually functions in the cell as a complex of two subunits, Ku70 and Ku80. The Ku heterodimer plays a key role in the non-homologous end joining DNA repair pathway by specifically recognizing the DNA ends at the site of the lesion. The binding of the Ku heterodimer to DNA has been well-studied, and its interactions with RNA have been also described. However, Ku70 subunit is known to have independent DNA binding capability, which is less characterized. RNA binding properties of Ku70 have not been yet specially studied. We have prepared recombinant full-length Ku70 and a set of its truncated mutants in E. coli, and studied their interactions with nucleic acids of various structures: linear single- and double-stranded DNA and RNA, as well as closed circular DNA and hairpin RNA. Ku70 has demonstrated a high affinity binding to double stranded DNA and hairpin RNA with a certain structure only. Interestingly, in contrast to the Ku heterodimer, Ku70 is found to interact with closed circular DNA. We also show for the first time that Ku70 employs two different sites for DNA and RNA binding. The double-stranded DNA is recognized by the C-terminal part of Ku70 including SAP domain as it has been earlier demonstrated, whereas hairpin RNA binding is provided by amino acids 251-438. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  17. Constraining the gravitational binding energy of PSR J0737-3039B using terrestrial nuclear data

    International Nuclear Information System (INIS)

    Newton, W. G.; Li Baoan

    2009-01-01

    We show that the gravitational binding energy of a neutron star of a given mass is correlated with the slope of the nuclear symmetry energy at 1-2 times nuclear saturation density for equations of state without significant softening (i.e., those that predict maximum masses M max >1.44M · in line with the largest accurately measured neutron star mass). Applying recent laboratory constraints on the slope of the symmetry energy to this correlation we extract a constraint on the baryon mass of the lower mass member of the double pulsar binary system, PSR J0737-3039B. We compare with independent constraints derived from modeling the progenitor star of J0737-3039B up to and through its collapse under the assumption that it formed in an electron capture supernova. The two sets of constraints are consistent only if L < or approx. 70 MeV.

  18. 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.

  19. Substitutional disorder, random dipoles and the binding energy of orthorhombic La2-xSrxCuO4

    International Nuclear Information System (INIS)

    Birkholz, M.; Rudert, R.

    1995-01-01

    This study investigates the effect of heterovalent, substitutional disorder on the binding energy of La 2-x Sr x CuO 4 . First, disorder has been found to create crystal electric fields that fluctuate over different lattice sites and induce ionic dipole moments of varying strength and orientation. The strength of these random dipoles will be presented for increasing x. Second, disorder may slightly displace the ions from their average lattice sites. The large thermal parameters obtained from diffraction experiments are discussed in this context. Finally, the polarization energy related to random dipoles was calculated to be on the order of eV and favourizes the positive charge carriers introduced by Sr doping to be associated with the copper ions. It is concluded that the solid exists in a state containing mixed copper valencies (Cu 2+ /Cu 3+ ). (orig.)

  20. The Duffy binding protein (PkDBPαII) of Plasmodium knowlesi from Peninsular Malaysia and Malaysian Borneo show different binding activity level to human erythrocytes.

    Science.gov (United States)

    Lim, Khai Lone; Amir, Amirah; Lau, Yee Ling; Fong, Mun Yik

    2017-08-11

    The zoonotic Plasmodium knowlesi is a major cause of human malaria in Malaysia. This parasite uses the Duffy binding protein (PkDBPαII) to interact with the Duffy antigen receptor for chemokines (DARC) receptor on human and macaque erythrocytes to initiate invasion. Previous studies on P. knowlesi have reported distinct Peninsular Malaysia and Malaysian Borneo PkDBPαII haplotypes. In the present study, the differential binding activity of these haplotypes with human and macaque (Macaca fascicularis) erythrocytes was investigated. The PkDBPαII of Peninsular Malaysia and Malaysian Borneo were expressed on the surface of COS-7 cells and tested with human and monkey erythrocytes, with and without anti-Fy6 (anti-Duffy) monoclonal antibody treatment. Binding activity level was determined by counting the number of rosettes formed between the transfected COS-7 cells and the erythrocytes. Anti-Fy6 treatment was shown to completely block the binding of human erythrocytes with the transfected COS-7 cells, thus verifying the specific binding of human DARC with PkDBPαII. Interestingly, the PkDBPαII of Peninsular Malaysia displayed a higher binding activity with human erythrocytes when compared with the Malaysian Borneo PkDBPαII haplotype (mean number of rosettes formed = 156.89 ± 6.62 and 46.00 ± 3.57, respectively; P < 0.0001). However, no difference in binding activity level was seen in the binding assay using M. fascicularis erythrocytes. This study is the first report of phenotypic difference between PkDBPαII haplotypes. The biological implication of this finding is yet to be determined. Therefore, further studies need to be carried out to determine whether this differential binding level can be associated with severity of knowlesi malaria in human.

  1. Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding.

    Science.gov (United States)

    Higuchi, Mariko; Fujii, Jumpei; Yonetani, Yoshiteru; Kitao, Akio; Go, Nobuhiro

    2011-01-01

    MutT distinguishes substrate 8-oxo-dGTP from dGTP and also 8-oxo-dGMP from dGMP despite small differences of chemical structures between them. In this paper we show by the method of molecular dynamics simulation that the transition between conformational substates of MutT is a key mechanism for a high-resolution molecular recognition of the differences between the very similar chemical compounds. (1) The native state MutT has two conformational substates with similar free energies, each characterized by either open or closed of two loops surrounding the substrate binding active site. Between the two substates, the open substate is more stable in free MutT and in dGMP-MutT complex, and the closed substate is more stable in 8-oxo-dGMP-MutT complex. (2) Conformational fluctuation of the open substate is much larger than that of the closed substate. An estimate of associated entropy difference was found to be consistent with the experimentally found difference of entropy contribution to the binding free energies of the two molecules. (3) A hydrogen bond between H7 atom of 8-oxo-dGMP and the sidechain of Asn119 plays a crucial role for maintaining the closed substate in 8-oxo-dGMP-MutT complex. When this hydrogen bond is absent in the H7-deficient dGMP-MutT complex, the closed substate is no more maintained and transition to the more entropically-favored open substate is induced. (4) Thus, this mechanism of the hydrogen bond controlling the relative stabilities of the drastically different two conformational substates enhances the resolution to recognize the small difference of the chemical structures between the two molecules, dGMP and 8-oxo-dGMP. Copyright © 2010 Elsevier Inc. All rights reserved.

  2. 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.

  3. Neuroticism Associates with Cerebral in Vivo Serotonin Transporter Binding Differently in Males and Females

    DEFF Research Database (Denmark)

    Tuominen, Lauri; Miettunen, Jouko; Cannon, Dara M

    2017-01-01

    Background: Neuroticism is a major risk factor for affective disorders. This personality trait has been hypothesized to associate with synaptic availability of the serotonin transporter, which critically controls serotonergic tone in the brain. However, earlier studies linking neuroticism...... studies. Methods: Here, we combined data from 4 different positron emission tomography imaging centers to address whether neuroticism is related to serotonin transporter binding in vivo. The data set included serotonin transporter binding potential values from the thalamus and striatum and personality......). Conclusions: The finding is in agreement with recent studies showing that the serotonergic system is involved in affective disorders differently in males and females and suggests that contribution of thalamic serotonin transporter to the risk of affective disorders depends on sex....

  4. Computation of binding energies including their enthalpy and entropy components for protein-ligand complexes using support vector machines.

    Science.gov (United States)

    Koppisetty, Chaitanya A K; Frank, Martin; Kemp, Graham J L; Nyholm, Per-Georg

    2013-10-28

    Computing binding energies of protein-ligand complexes including their enthalpy and entropy terms by means of computational methods is an appealing approach for selecting initial hits and for further optimization in early stages of drug discovery. Despite the importance, computational predictions of thermodynamic components have evaded attention and reasonable solutions. In this study, support vector machines are used for developing scoring functions to compute binding energies and their enthalpy and entropy components of protein-ligand complexes. The binding energies computed from our newly derived scoring functions have better Pearson's correlation coefficients with experimental data than previously reported scoring functions in benchmarks for protein-ligand complexes from the PDBBind database. The protein-ligand complexes with binding energies dominated by enthalpy or entropy term could be qualitatively classified by the newly derived scoring functions with high accuracy. Furthermore, it is found that the inclusion of comprehensive descriptors based on ligand properties in the scoring functions improved the accuracy of classification as well as the prediction of binding energies including their thermodynamic components. The prediction of binding energies including the enthalpy and entropy components using the support vector machine based scoring functions should be of value in the drug discovery process.

  5. Different methods for waste to energy transformation

    NARCIS (Netherlands)

    Koning, J. de

    1998-01-01

    In the past 25 years, many technological developments have taken place in the thermal treatment of Municipal Solid Waste (MSW). Apart from the initials goal of the technology (i.e., volume reduction and inertisation), flue gas emissions, solid residues, energy efficiency and economics became

  6. Theoretical analysis of the time-resolved binary (e, 2e) binding energy spectra on three-body photodissociation of acetone at 195 nm

    Science.gov (United States)

    Yamazaki, M.; Nakayama, S.; Zhu, C. Y.; Takahashi, M.

    2017-11-01

    We report on theoretical progress in time-resolved (e, 2e) electron momentum spectroscopy of photodissociation dynamics of the deuterated acetone molecule at 195 nm. We have examined the predicted minimum energy reaction path to investigate whether associated (e, 2e) calculations meet the experimental results. A noticeable difference between the experiment and calculations has been found at around binding energy of 10 eV, suggesting that the observed difference may originate, at least partly, in ever-unconsidered non-minimum energy paths.

  7. 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.

  8. Binding energy and optical properties of an off-center hydrogenic donor impurity in a spherical quantum dot placed at the center of a cylindrical nano-wire

    International Nuclear Information System (INIS)

    Safarpour, Gh.; Barati, M.; Zamani, A.; Niknam, E.

    2014-01-01

    The binding energy as well as the linear, third-order nonlinear and total optical absorption coefficient and refractive index changes of an off-center hydrogenic donor impurity in an InAs spherical quantum dot placed at the center of a GaAs cylindrical nano-wire have been investigated. In this regard, the effective-mass approximation approach is considered and eigenvalues and corresponding eigenfunctions are calculated via the finite element method. The binding energy is plotted as a function of the dot size and impurity position along with optical properties as a function of photon energy. In this study two different directions have been considered for impurity position, along the nano-wire axis and perpendicular to it. It has been found that the binding energy, absorption coefficient and refractive index changes are impressively affected not only by the dot radius but also by the position of the impurity and its direction. Additionally, the optical saturation can be tuned by the direction of the impurity and incident optical intensity. -- Highlights: • We consider spherical quantum dot located at the center of a cylindrical nano-wire. • An off-center hydrogenic donor impurity is considered in the system. • Binding energy is affected by orientation of impurity and its distance from center. • Saturation depends on the orientation of impurity position. • By shifting impurity position, orientation and dot radius blue- and red-shifts appear

  9. RECOGNITION DYNAMICS OF ESCHERICHIA COLI THIOREDOXIN PROBED USING MOLECULAR DYNAMICS AND BINDING FREE ENERGY CALCULATIONS

    Directory of Open Access Journals (Sweden)

    M. S. Shahul Hameed

    2016-03-01

    Full Text Available E. coli thioredoxin has been regarded as a hub protein as it interacts with, and regulates, numerous target proteins involved in a wide variety of cellular processes. Thioredoxin can form complexes with a variety of target proteins with a wide range of affinity, using a consensus binding surface. In this study an attempt to deduce the molecular basis for the observed multispecificity of E. coli thioredoxin has been made. In this manuscript it has been shown that structural plasticity, adaptable and exposed hydrophobic binding surface, surface electrostatics, closely clustered multiple hot spot residues and conformational changes brought about by the redox status of the protein have been shown to account for the observed multispecificity and molecular recognition of thioredoxin. Dynamical differences between the two redox forms of the enzyme have also been studied to account for their differing interactions with some target proteins.

  10. Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region

    Directory of Open Access Journals (Sweden)

    Alonso Ángel

    2006-03-01

    Full Text Available Abstract Background Papillomaviruses (PVs infect stratified squamous epithelia in warm-blooded vertebrates and have undergone a complex evolutionary process. The control of the expression of the early ORFs in PVs depends on the binding of cellular and viral transcription factors to the upstream regulatory region (URR of the virus. It is believed that there is a core of transcription factor binding sites (TFBS common to all PVs, with additional individual differences, although most of the available information focuses only on a handful of viruses. Results We have studied the URR of sixty-one PVs, covering twenty different hosts. We have predicted the TFBS present in the URR and analysed these results by principal component analysis and genetic algorithms. The number and nature of TFBS in the URR might be much broader than thus far described, and different PVs have different repertoires of TFBS. Conclusion There are common fingerprints in the URR in PVs that infect primates, although the ancestors of these viruses diverged a long time ago. Additionally, there are obvious differences between the URR of alpha and beta PVs, despite these PVs infect similar histological cell types in the same host, i.e. human. A thorough analysis of the TFBS in the URR might provide crucial information about the differential biology of cancer-associated PVs.

  11. First principle prediction of shallow defect level binding energies and deep level nonradiative recombination rates

    Science.gov (United States)

    Wang, Linwang

    2014-03-01

    Accurate calculation of defect level energies in semiconductors and their carrier capturing rate is an important issue in ab initio prediction of semiconductor properties. In this talk, I will present our result work in ab initio shallow level calculation and deep level caused nonradiative recombination rate calculation. In the shallow acceptor level calculation, a large system up to 64,000 atoms needs to be used to properly describe the weakly bounded hole wave functions. The single particle Hamiltonian of that system is patched from bulk potential and central potential. Furthermore, GW calculation is used to correct the one site potential of the impurity atom. The resulting binding energy agrees excellently with the experiments within 10 meV. To calculate the nonradiative decay rate, the electron-phonon coupling constants in the defect system are calculated all at once using a new variational algorithm. Multiphonon process formalism is used to calculate the nonradiative decay rate. It is found that the transition is induced by the electron and the optical phonon coupling, but the energy conservation is mostly satisfied by the acoustic phonons. The new algorithm allows fast calculation of such nonradiative decay rate for any defect levels, as well as other multiphonon processes in nanostructures. This work was supported by the Director, Office of Science (SC), Basic Energy Science (BES)/Materials Science and Engineering Division (MSED) of the U.S. Department of Energy (DOE) under the contract No. DE-AC02-05CH11231.

  12. 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. © 2015 John Wiley & Sons A/S.

  13. Energy spectrum of two-dimensional tight-binding electrons in a spatially varying magnetic field

    International Nuclear Information System (INIS)

    Oh, G.Y.; Lee, M.H.

    1996-01-01

    The electronic energy spectrum of a two-dimensional lattice in a spatially varying magnetic field is studied within the framework of the tight-binding model by using the scheme of the transfer matrix. It is found that, in comparison with the case of a uniform magnetic field, the energy spectrum exhibits more complicated behavior; band broadening (or gap closing) and band splitting (or gap opening) occur depending on characteristic parameters of the lattice. The origin of these phenomena lies in the existence of direct touching and indirect overlapping between neighboring subbands. Dependence of direct touching and indirect overlapping, and thus the electronic band structure together with the density of states, on characteristic parameters of the lattice is elucidated in detail. copyright 1996 The American Physical Society

  14. Hybrid density functional-molecular mechanics calculations for core-electron binding energies of glycine in water solution.

    Science.gov (United States)

    Niskanen, Johannes; Arul Murugan, N; Rinkevicius, Zilvinas; Vahtras, Olav; Li, Cui; Monti, Susanna; Carravetta, Vincenzo; Agren, Hans

    2013-01-07

    We report hybrid density functional theory-molecular mechanics (DFT/MM) calculations performed for glycine in water solution at different pH values. In this paper, we discuss several aspects of the quantum mechanics-molecular mechanics (QM/MM) simulations where the dynamics and spectral binding energy shifts are computed sequentially, and where the latter are evaluated over a set of configurations generated by molecular or Car-Parrinello dynamics simulations. In the used model, core ionization takes place in glycine as a quantum mechanical (QM) system modeled with DFT, and the solution is described with expedient force fields in a large molecular mechanical (MM) volume of water molecules. The contribution to the core electronic binding energy from all interactions within and between the two (DFT and MM) parts is accounted for, except charge transfer and dispersion. While the obtained results were found to be in qualitative agreement with experiment, their precision must be qualified with respect to the problem of counter ions, charge transfer and optimal division of QM and MM parts of the system. Results are compared to those of a recent study [Ottoson et al., J. Am. Chem. Soc., 2011, 133, 3120].

  15. Photoelectron binding energy shifts observed during oxidation of group IIA, IIIA and IVA elemental surfaces

    International Nuclear Information System (INIS)

    Heide, P.A.W. van der

    2006-01-01

    An extensive re-evaluation of XPS binding energies (BE's) and binding energy shifts (ΔBE's) from metals, oxides and the carbonates of the group II, III and IVA elements (exceptions are Be, Mg and Hf) has been carried out using a substrate specific BE referencing approach. From this, O-1s BE's are found to fall into surface oxide, bulk oxide and carbonate groupings, with bulk oxides showing the lowest BE's followed by surface oxides (+∼1.5 eV) and then carbonates (+∼3.0 eV). The O-1s BE's from the bulk oxides also appear to scale with 1/d, where d is inter-atomic distance. The same is noted in the ΔBE's observed from the metallic counterparts during oxidation of the elemental surfaces. This, and the decreasing BE exhibited by Ca, Sr and Ba on oxidation is explained within the charge potential model as resulting from competing inter- and intra-atomic effects, and is shown to be consistent with partial covalency arguments utilizing Madulung potentials. The ΔBE's also fall into groups according to the elements location in the periodic table, i.e. s, p or d block. These trends open up the possibility of approximating ΔBE's arising from initial and final state effects, and bond distances

  16. Differing lectin-binding patterns of malignant melanoma and nevocellular and Spitz nevi.

    Science.gov (United States)

    Kohchiyama, A; Oka, D; Ueki, H

    1987-01-01

    The lectin-binding patterns of primary malignant melanoma, nevocellular nevus, and Spitz nevus were studied on formalin-fixed, paraffin-embedded sections using a series of biotinylated lectins--concanavalin A (ConA), Ricinus communis agglutinin-1 (RCA1), dolichos biflorus agglutinin (DBA), soybean agglutinin (SBA), maclura pomifera agglutinin (MPA), peanut agglutinin (PNA), wheat germ agglutinin (WGA), and Ulex europeus agglutinin-1(UEA1)--and employing the avidin-biotin-peroxidase complex method. In nevocellular and Spitz nevi, all of the nevus cells were positively stained with ConA and RCA1. No positive staining was observed, however, with the other lectins and no change in binding patterns occurred following neuraminidase pretreatment. In malignant melanoma, all of the melanoma cells were positively stained with ConA and RCA1, and some were also stained with MPA, PNA, and WGA. In addition, DBA, SBA, MPA, PNA, and WGA labeled all of the melanoma cells after neuraminidase pretreatment. No positive staining was observed with UEA1 despite neuraminidase pretreatment. The present results showed that malignant melanoma and nevocellular and Spitz nevi have different lectin-binding patterns and different responses to neuraminidase pretreatment. We, therefore, believe that the lectin staining on paraffin-embedded sections can be a useful probe for the differentiation of these diseases.

  17. The tumorigenic diversity of the three PLAG family members is associated with different DNA binding capacities.

    Science.gov (United States)

    Hensen, Karen; Van Valckenborgh, Isabelle C C; Kas, Koen; Van de Ven, Wim J M; Voz, Marianne L

    2002-03-01

    Pleomorphic adenoma gene (PLAG) 1, the main translocation target in pleomorphic adenomas of the salivary glands, is a member of a new subfamily of zinc finger proteins comprising the tumor suppressor candidate PLAG-like1 (also called ZAC1 or lost on transformation 1) and PLAGL2. In this report, we show that NIH3T3 cells overexpressing PLAG1 or PLAGL2 display the typical markers of neoplastic transformation: (a) the cells lose cell-cell contact inhibition; (b) show anchorage-independent growth; and (c) are able to induce tumors in nude mice. In contrast, PLAGL1 has been shown to prevent the proliferation of tumor cells by inducing cell cycle arrest and apoptosis. This difference in function is also reflected in their DNA binding, as we show here that the three PLAG proteins, although highly homologous in their DNA-binding domain, bind different DNA sequences in a distinct fashion. Interestingly, the PLAG1- and PLAGL2-induced transformation is accompanied by a drastic up-regulation of insulin-like growth factor-II, which we prove is a target of PLAG1 and PLAGL2. This strongly suggests that the oncogenic capacity of PLAG1 and PLAGL2 is mediated at least partly by activating the insulin-like growth factor-II mitogenic pathway.

  18. Differences in serotonin transporter binding affinity in patients with major depressive disorder and night eating syndrome.

    Science.gov (United States)

    Lundgren, J D; Amsterdam, J; Newberg, A; Allison, K C; Wintering, N; Stunkard, A J

    2009-03-01

    We examined serotonin transporter (SERT) binding affinity using single photon emission computed tomography (SPECT) in patients with major depressive disorder (MDD) and night eating syndrome (NES). There are similarities between MDD and NES in affective symptoms, appetite disturbance, nighttime awakenings, and, particularly, response to selective serotonin reuptake inhibitors (SSRIs). Six non-depressed patients with NES and seven patients with MDD underwent SPECT brain imaging with 123I-ADAM, a radiopharmaceutical agent selective for SERT sites. Uptake ratios of 123I-ADAM SERT binding were obtained for the midbrain, basal ganglia, and temporal lobe regions compared to the cerebellum reference region. Patients with NES had significantly greater SERT uptake ratios (effect size range 0.64-0.84) in the midbrain, right temporal lobe, and left temporal lobe regions than those with MDD whom we had previously studied. Pathophysiological differences in SERT uptake between patients with NES and MDD suggest these are distinct clinical syndromes.

  19. Evolutionary Implications of Metal Binding Features in Different Species’ Prion Protein: An Inorganic Point of View

    Directory of Open Access Journals (Sweden)

    Diego La Mendola

    2014-05-01

    Full Text Available Prion disorders are a group of fatal neurodegenerative conditions of mammals. The key molecular event in the pathogenesis of such diseases is the conformational conversion of prion protein, PrPC, into a misfolded form rich in β-sheet structure, PrPSc, but the detailed mechanistic aspects of prion protein conversion remain enigmatic. There is uncertainty on the precise physiological function of PrPC in healthy individuals. Several evidences support the notion of its role in copper homeostasis. PrPC binds Cu2+ mainly through a domain composed by four to five repeats of eight amino acids. In addition to mammals, PrP homologues have also been identified in birds, reptiles, amphibians and fish. The globular domain of protein is retained in the different species, suggesting that the protein carries out an essential common function. However, the comparison of amino acid sequences indicates that prion protein has evolved differently in each vertebrate class. The primary sequences are strongly conserved in each group, but these exhibit a low similarity with those of mammals. The N-terminal domain of different prions shows tandem amino acid repeats with an increasing amount of histidine residues going from amphibians to mammals. The difference in the sequence affects the number of copper binding sites, the affinity and the coordination environment of metal ions, suggesting that the involvement of prion in metal homeostasis may be a specific characteristic of mammalian prion protein. In this review, we describe the similarities and the differences in the metal binding of different species’ prion protein, as revealed by studies carried out on the entire protein and related peptide fragments.

  20. Investigating structural changes induced by nucleotide binding to RecA using difference FTIR.

    OpenAIRE

    Butler, Blaine C; Hanchett, Ross H; Rafailov, Helena; MacDonald, Gina

    2002-01-01

    Nucleotide binding to RecA results in either the high-DNA affinity form (Adenosine 5'-triphosphate (ATP)-bound) or the more inactive protein conformation associated with a lower affinity for DNA (Adenosine 5'-diphosphate (ADP)-bound). Many of the key structural differences between the RecA-ATP and RecA-ADP bound forms have yet to be elucidated. We have used caged-nucleotides and difference FTIR in efforts to obtain a comprehensive understanding of the molecular changes induced by nucleotide b...

  1. Resonance energy transfer study on the proximity relationship between the GTP binding site and the rifampicin binding site of Escherichia coli RNA polymerase

    International Nuclear Information System (INIS)

    Kumar, K.P.; Chatterji, D.

    1990-01-01

    Terbium(III) upon complexation with guanosine 5'-triphosphate showed remarkable enhancement of fluorescence emission at 488 and 545 nm when excited at 295 nm. Analysis of the binding data yielded a value for the mean K d between Tb(III) and GTP of 0.2 μM, with three binding sites for TB(III) on GTP. 31 P and 1 H NMR measurements revealed that Tb(III) mainly binds the phosphate moiety of GTP. Fluorescence titration of the emission signals of the TbGTP complex with varying concentrations of Escherichia coli RNA polymerase resulted in a K d values of 4 μM between the TbGTP and the enzyme. It was observed that TbGTP can be incorporated in the place of GTP during E. coli RNA polymerase catalyzed abortive synthesis of dinucleotide tetraphosphate at T7A2 promoter. Both the substrate TbGTP and the inhibitor of the initiation of transcription rifampicin bind to the β-subunit of E. coli RNA polymerase. This allows the measurement of the fluorescence excited-state energy transfer from the donor TbGTP-RNA polymerase to the acceptor rifampicin. Both emission bands of Tb(III) overlap with the rifampicin absorption, and the distances at 50% efficiency of energy transfer were calculated to be 28 and 24 angstrom for the 488- and 545-nm emission bands, respectively. The distance between the substrate binding site and the rifampicin binding site on the β-subunit of E. coli RNA polymerase was measured to be around 30 angstrom. This suggest that the nature of inhibition of transcription by rifampicin is essentially noncompetitive with the substrate

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

    Science.gov (United States)

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

    2016-09-01

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

  3. Binding of plasma proteins to titanium dioxide nanotubes with different diameters

    Directory of Open Access Journals (Sweden)

    Kulkarni M

    2015-02-01

    Full Text Available Mukta Kulkarni,1,* Ajda Flašker,1,* Maruša Lokar,1 Katjuša Mrak-Poljšak,2 Anca Mazare,3 Andrej Artenjak,4 Saša Čučnik,2 Slavko Kralj,5 Aljaž Velikonja,1 Patrik Schmuki,3 Veronika Kralj-Iglič,6 Snezna Sodin-Semrl,2,7 Aleš Iglič11Laboratory of Biophysics, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia; 2Department of Rheumatology, University Medical Centre Ljubljana, Ljubljana, Slovenia; 3Department of Materials Science and Engineering, University of Erlangen Nuremberg, Erlangen, Germany; 4Sandoz Biopharmaceuticals Mengeš, Lek Pharmaceuticals dd, Menges, Slovenia; 5Department for Materials Synthesis, Institute Jožef Stefan (IJS, Ljubljana, Slovenia; 6Faculty of Health Studies, University of Ljubljana, Ljubljana, Slovenia; 7Faculty of Mathematics, Natural Science and Information Technology, University of Primorska, Koper, Slovenia *These authors contributed equally to this workAbstract: Titanium and titanium alloys are considered to be one of the most applicable materials in medical devices because of their suitable properties, most importantly high corrosion resistance and the specific combination of strength with biocompatibility. In order to improve the biocompatibility of titanium surfaces, the current report initially focuses on specifying the topography of titanium dioxide (TiO2 nanotubes (NTs by electrochemical anodization. The zeta potential (ζ-potential of NTs showed a negative value and confirmed the agreement between the measured and theoretically predicted dependence of ζ-potential on salt concentration, whereby the absolute value of ζ-potential diminished with increasing salt concentrations. We investigated binding of various plasma proteins with different sizes and charges using the bicinchoninic acid assay and immunofluorescence microscopy. Results showed effective and comparatively higher protein binding to NTs with 100 nm diameters (compared to 50 or 15 nm. We also showed a dose

  4. Sex differences in dopamine binding and modafinil conditioned place preference in mice.

    Science.gov (United States)

    Bernardi, Rick E; Broccoli, Laura; Spanagel, Rainer; Hansson, Anita C

    2015-10-01

    Studies in humans and rodents have demonstrated under certain conditions some reinforcing properties of modafinil, a drug being examined clinically for its potential to treat psychostimulant abuse. However, the majority of rodent studies examining the abuse potential of modafinil have used high doses that may not be clinically relevant. In fact, recent work has indicated that doses similar to those administered to humans are not reinforcing in mice. The current study examined sex differences in the ability of low-dose modafinil (0.75mg/kg, IP) to induce a conditioned place preference in mice, and assessed sex-dependent alterations in dopamine D1, D2 and DAT binding sites in reward-related regions in naïve and modafinil-treated mice. Low-dose modafinil failed to induce a conditioned place preference in male mice, while female mice demonstrated a significant modafinil place preference. Several dopamine binding differences were also detected in naïve and modafinil-treated mice, including sex differences in D1 and D2 availability in reward-related regions, and are discussed in relation to sex-dependent differences in the reinforcing effects of modafinil and psychostimulants in general. These findings implicate sex differences in the reinforcing properties of modafinil in mice, and indicate that clinical evaluation of the sex dependence of the reinforcing properties of modafinil in humans is warranted. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  5. Binding energies of the π-stacked anisole dimer: new molecular beam-laser spectroscopy experiments and CCSD(T) calculations.

    Science.gov (United States)

    Řezáč, Jan; Nachtigallová, Dana; Mazzoni, Federico; Pasquini, Massimiliano; Pietraperzia, Giangaetano; Becucci, Maurizio; Müller-Dethlefs, Klaus; Hobza, Pavel

    2015-04-27

    Among noncovalent interactions, π-π stacking is a very important binding motif governed mainly by London dispersion. Despite its importance, for instance, for the structure of bio-macromolecules, the direct experimental measurement of binding energies in π-π stacked complexes has been elusive for a long time. Only recently, an experimental value for the binding energy of the anisole dimer was presented, determined by velocity mapping ion imaging in a two-photon resonant ionisation molecular beam experiment. However, in that paper, a discrepancy was already noted between the obtained experimental value and a theoretical estimate. Here, we present an accurate recalculation of the binding energy based on the combination of the CCSD(T)/CBS interaction energy and a DFT-D3 vibrational analysis. This proves unambiguously that the previously reported experimental value is too high and a new series of measurements with a different, more sensitive apparatus was performed. The new experimental value of 1800±100 cm(-1) (5.15±0.29 kcal mol(-1)) is close to the present theoretical prediction of 5.04±0.40 kcal mol(-1). Additional calculations of the properties of the cationic and excited states involved in the photodissociation of the dimer were used to identify and rationalise the difficulties encountered in the experimental work. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. 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....

  7. Ropizine concurrently enhances and inhibits [3H] dextromethorpan binding to different structures of the guinea pig brain: Autoradiographic evidence for multiple binding sites

    International Nuclear Information System (INIS)

    Canoll, P.D.; Smith, P.R.; and Musacchio, J.M.

    1990-01-01

    Ropizine produces a simultaneous enhancement and inhibition of [ 3 H] dextromethorphan (DM) high-affinity binding to different areas of the guinea pig brain. These results imply that there are two distinct types of high-affinity [ 3 H]DM binding sites, which are present in variable proportions in different brain structures. The ropizine-enhances [ 3 H]DM binding type was preferentially inhibited by (+)-pentazocine. This is consistent with the presumption that the (+)-pentazocine-sensitive site is identical with the common site for DM and 3-(-3-Hydroxphenyl)-N-(1-propyl)piperidine ((+)-3-PPP). The second binding type, which is inhibited by ropizine and is not so sensitive to (+)- pentazocine, has not been fully characterized. This study demonstrates that the biphasic effects to ropizine are due, at least in part, to the effects of ropizine on two different types of [ 3 H]DM binding sites. However, this study does not rule out that the common DM/(+)-3-PPP site also might be inhibited by higher concentrations of ropizine

  8. Native mitochondrial RNA-binding complexes in kinetoplastid RNA editing differ in guide RNA composition.

    Science.gov (United States)

    Madina, Bhaskara R; Kumar, Vikas; Metz, Richard; Mooers, Blaine H M; Bundschuh, Ralf; Cruz-Reyes, Jorge

    2014-07-01

    Mitochondrial mRNAs in kinetoplastids require extensive U-insertion/deletion editing that progresses 3'-to-5' in small blocks, each directed by a guide RNA (gRNA), and exhibits substrate and developmental stage-specificity by unsolved mechanisms. Here, we address compositionally related factors, collectively known as the mitochondrial RNA-binding complex 1 (MRB1) or gRNA-binding complex (GRBC), that contain gRNA, have a dynamic protein composition, and transiently associate with several mitochondrial factors including RNA editing core complexes (RECC) and ribosomes. MRB1 controls editing by still unknown mechanisms. We performed the first next-generation sequencing study of native subcomplexes of MRB1, immunoselected via either RNA helicase 2 (REH2), that binds RNA and associates with unwinding activity, or MRB3010, that affects an early editing step. The particles contain either REH2 or MRB3010 but share the core GAP1 and other proteins detected by RNA photo-crosslinking. Analyses of the first editing blocks indicate an enrichment of several initiating gRNAs in the MRB3010-purified complex. Our data also indicate fast evolution of mRNA 3' ends and strain-specific alternative 3' editing within 3' UTR or C-terminal protein-coding sequence that could impact mitochondrial physiology. Moreover, we found robust specific copurification of edited and pre-edited mRNAs, suggesting that these particles may bind both mRNA and gRNA editing substrates. We propose that multiple subcomplexes of MRB1 with different RNA/protein composition serve as a scaffold for specific assembly of editing substrates and RECC, thereby forming the editing holoenzyme. The MRB3010-subcomplex may promote early editing through its preferential recruitment of initiating gRNAs. © 2014 Madina et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  9. Analysis on Binding Energy and Auger Parameter for Estimating Size and Stoichiometry of ZnO Nanorods

    Directory of Open Access Journals (Sweden)

    Santanu Bera

    2012-01-01

    Full Text Available ZnO nanorods prepared through chemical vapor deposition technique are characterized by microscopic and X-ray photoelectron spectroscopy (XPS techniques to correlate the effects of size on the binding energy of Zn 2p3/2 photoelectrons. A positive shift in Zn 2p3/2-binding energy as compared to that in bulk ZnO is assumed to be the effect of size of ZnO tips. The shift in binding energy has been explained in terms of relaxation energy in the photoemission process. Simultaneously, Auger parameter of the nanorods is evaluated for stoichiometric composition. The extra peak in O1s spectrum of nanorods is explained as adsorbed O-bearing species or surface contaminants.

  10. Relation between heat of vaporization, ion transport, molar volume, and cation-anion binding energy for ionic liquids.

    Science.gov (United States)

    Borodin, Oleg

    2009-09-10

    A number of correlations between heat of vaporization (H(vap)), cation-anion binding energy (E(+/-)), molar volume (V(m)), self-diffusion coefficient (D), and ionic conductivity for 29 ionic liquids have been investigated using molecular dynamics (MD) simulations that employed accurate and validated many-body polarizable force fields. A significant correlation between D and H(vap) has been found, while the best correlation was found for -log(DV(m)) vs H(vap) + 0.28E(+/-). A combination of enthalpy of vaporization and a fraction of the cation-anion binding energy was suggested as a measure of the effective cohesive energy for ionic liquids. A deviation of some ILs from the reported master curve is explained based upon ion packing and proposed diffusion pathways. No general correlations were found between the ion diffusion coefficient and molecular volume or the diffusion coefficient and cation/anion binding energy.

  11. Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations.

    Directory of Open Access Journals (Sweden)

    Yuzhen Niu

    Full Text Available As a promising target for the treatment of lung cancer, the MutT Homolog 1 (MTH1 protein can be inhibited by crizotinib. A recent work shows that the inhibitory potency of (S-crizotinib against MTH1 is about 20 times over that of (R-crizotinib. But the detailed molecular mechanism remains unclear. In this study, molecular dynamics (MD simulations and free energy calculations were used to elucidate the mechanism about the effect of chirality of crizotinib on the inhibitory activity against MTH1. The binding free energy of (S-crizotinib predicted by the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA and Adaptive biasing force (ABF methodologies is much lower than that of (R-crizotinib, which is consistent with the experimental data. The analysis of the individual energy terms suggests that the van der Waals interactions are important for distinguishing the binding of (S-crizotinib and (R-crizotinib. The binding free energy decomposition analysis illustrated that residues Tyr7, Phe27, Phe72 and Trp117 were important for the selective binding of (S-crizotinib to MTH1. The adaptive biasing force (ABF method was further employed to elucidate the unbinding process of (S-crizotinib and (R-crizotinib from the binding pocket of MTH1. ABF simulation results suggest that the reaction coordinates of the (S-crizotinib from the binding pocket is different from (R-crizotinib. The results from our study can reveal the details about the effect of chirality on the inhibition activity of crizotinib to MTH1 and provide valuable information for the design of more potent inhibitors.

  12. Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species.

    Science.gov (United States)

    Smith, Kathrine J; Petit, Chantal M; Aubart, Kelly; Smyth, Martin; McManus, Edward; Jones, Jo; Fosberry, Andrew; Lewis, Ceri; Lonetto, Michael; Christensen, Siegfried B

    2003-02-01

    Polypeptide deformylase (PDF) catalyzes the deformylation of polypeptide chains in bacteria. It is essential for bacterial cell viability and is a potential antibacterial drug target. Here, we report the crystal structures of polypeptide deformylase from four different species of bacteria: Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, and Escherichia coli. Comparison of these four structures reveals significant overall differences between the two Gram-negative species (E. coli and H. influenzae) and the two Gram-positive species (S. pneumoniae and S. aureus). Despite these differences and low overall sequence identity, the S1' pocket of PDF is well conserved among the four enzymes studied. We also describe the binding of nonpeptidic inhibitor molecules SB-485345, SB-543668, and SB-505684 to both S. pneumoniae and E. coli PDF. Comparison of these structures shows similar binding interactions with both Gram-negative and Gram-positive species. Understanding the similarities and subtle differences in active site structure between species will help to design broad-spectrum polypeptide deformylase inhibitor molecules.

  13. Inorganic mercury binding with different sulfur species in anoxic sediments and their gut juice extractions.

    Science.gov (United States)

    Zhong, Huan; Wang, Wen-Xiong

    2009-09-01

    To investigate the roles of different sulfur (S) species in controlling the partitioning and bioavailability of inorganic mercury (Hg) in anoxic sediments, we examined the differential binding of Hg with three key S species in anoxic sediment (mackinawite [FeS], pyrite [FeS2], and S(2-)) and then quantified their extraction by the gut juice of deposit-feeding sipunculans Sipunculus nudus. A sequential extraction method was simultaneously used to distinguish Hg sorption with different sediment components. All three S-containing sediment components could lead to a high binding of Hg in sediments, but most Hg was sorbed with FeS or FeS2 instead of formation of Hg sulfide despite the presence of S(2-) or humic acid. The gut juice extraction was relatively low and constant whenever FeS and FeS2 were in the sediment, indicating that both FeS and FeS2 controlled the Hg gut juice extraction and thus bioavailability. Mercury sorbed with FeS2 had higher gut juice extraction than that with FeS, while Hg sulfide was not extracted, strongly suggesting that Hg sorbed with FeS2 was more bioavailable than that with other S species. Mercury sorbed with FeS had very low bioavailability to sipunculans at a low Hg:S ratio in the sediment but was more bioavailable with increasing Hg:S ratio up to a maximum (approximately 1:10, mole based). The present study showed that different S species (FeS, FeS2) and Hg:S ratios significantly affected the binding and bioavailability of Hg in anoxic sediments.

  14. A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain

    Directory of Open Access Journals (Sweden)

    Nicolas Panel

    2017-09-01

    Full Text Available PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands. Here, we used experimental binding assays and molecular dynamics simulations to characterize 51 complexes involving the Tiam1 PDZ domain and to test the performance of a semi-empirical free energy function. The free energy function combined a Poisson-Boltzmann (PB continuum electrostatic term, a van der Waals interaction energy, and a surface area term. Each term was empirically weighted, giving a Linear Interaction Energy or “PB/LIE” free energy. The model yielded a mean unsigned deviation of 0.43 kcal/mol and a Pearson correlation of 0.64 between experimental and computed free energies, which was superior to a Null model that assumes all complexes have the same affinity. Analyses of the models support several experimental observations that indicate the orientation of the α2 helix is a critical determinant for peptide specificity. The models were also used to predict binding free energies for nine new variants, corresponding to point mutants of the Syndecan1 and Caspr4 peptides. The predictions did not reveal improved binding; however, they suggest that an unnatural amino acid could be used to increase protease resistance and peptide lifetimes in vivo. The overall performance of the model should allow its use in the design of new PDZ ligands in the future.

  15. A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain.

    Science.gov (United States)

    Panel, Nicolas; Sun, Young Joo; Fuentes, Ernesto J; Simonson, Thomas

    2017-01-01

    PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands. Here, we used experimental binding assays and molecular dynamics simulations to characterize 51 complexes involving the Tiam1 PDZ domain and to test the performance of a semi-empirical free energy function. The free energy function combined a Poisson-Boltzmann (PB) continuum electrostatic term, a van der Waals interaction energy, and a surface area term. Each term was empirically weighted, giving a Linear Interaction Energy or "PB/LIE" free energy. The model yielded a mean unsigned deviation of 0.43 kcal/mol and a Pearson correlation of 0.64 between experimental and computed free energies, which was superior to a Null model that assumes all complexes have the same affinity. Analyses of the models support several experimental observations that indicate the orientation of the α 2 helix is a critical determinant for peptide specificity. The models were also used to predict binding free energies for nine new variants, corresponding to point mutants of the Syndecan1 and Caspr4 peptides. The predictions did not reveal improved binding; however, they suggest that an unnatural amino acid could be used to increase protease resistance and peptide lifetimes in vivo . The overall performance of the model should allow its use in the design of new PDZ ligands in the future.

  16. Glucose Sensors Based on Microcapsules Containing an Orange/Red Competitive Binding Resonance Energy Transfer Assay

    Science.gov (United States)

    CHINNAYELKA, SWETHA; McSHANE, and MICHAEL J.

    2015-01-01

    Fluorescent sensing systems offer the potential for noninvasive monitoring with implantable devices, but they require carrier technologies that provide suitable immobilization, accessibility, and biocompatibility while maintaining adequate response characteristics. A recent development towards this goal is a highly specific and sensitive competitive binding assay for glucose using apo-glucose oxidase (apo-GOx) as the recognition element and dextran as the competing ligand; this has been demonstrated as a glucose sensor system by encapsulating the competitive binding assay in semipermeable microcapsule carriers. This paper describes the extension of this sensor design to longer wavelengths in an attempt to increase the applicability to in vivo monitoring. The glucose sensitivity of the tetramethylrhodamine isothiocyanate-dextran (TD) and cyanine Cy5-apo-GOx (CAG) complexes showed five to 10 times greater specificity for β-D-glucose over other sugars. Microcapsules loaded with TD/CAG complexes exhibited a linear, totally reversible response in the range of 0–720 mg/dL, with a sensitivity (percent change in intensity ratio) of 0.06%/(mg/dL). The decrease in sensitivity observed with the use of longer-wavelength dyes is most likely to be compensated with the deeper penetration of light and reduced tissue scattering. These findings imply that the encapsulation of sensing assay elements in microcapsules is a simple and translatable method for the fabrication of stable biosensors, and optimization of resonance energy transfer pairs and assay component preparation will further improve the response to approach clinically relevant performance. PMID:16800748

  17. The Antinociceptive Agent SBFI-26 Binds to Anandamide Transporters FABP5 and FABP7 at Two Different Sites

    Energy Technology Data Exchange (ETDEWEB)

    Hsu, Hao-Chi [Cryo-EM Structural; Tong, Simon [Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States; Zhou, Yuchen [Department of Applied Mathematics; Elmes, Matthew W. [Department of Biochemistry and; Yan, Su [Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States; Kaczocha, Martin [Department of Biochemistry and; Department of Anesthesiology, Stony Brook University, Stony; Deutsch, Dale G. [Department of Biochemistry and; Institute of Chemical Biology and; Rizzo, Robert C. [Department of Applied Mathematics; Institute of Chemical Biology and; Laufer; Ojima, Iwao [Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States; Institute of Chemical Biology and; Li, Huilin [Cryo-EM Structural; Institute of Chemical Biology and

    2017-06-28

    Human FABP5 and FABP7 are intracellular endocannabinoid transporters. SBFI-26 is an α-truxillic acid 1-naphthyl monoester that competitively inhibits the activities of FABP5 and FABP7 and produces antinociceptive and anti-inflammatory effects in mice. The synthesis of SBFI-26 yields several stereoisomers, and it is not known how the inhibitor binds the transporters. Here we report co-crystal structures of SBFI-26 in complex with human FABP5 and FABP7 at 2.2 and 1.9 Å resolution, respectively. We found that only (S)-SBFI-26 was present in the crystal structures. The inhibitor largely mimics the fatty acid binding pattern, but it also has several unique interactions. Notably, the FABP7 complex corroborates key aspects of the ligand binding pose at the canonical site previously predicted by virtual screening. In FABP5, SBFI-26 was unexpectedly found to bind at the substrate entry portal region in addition to binding at the canonical ligand-binding pocket. Our structural and binding energy analyses indicate that both R and S forms appear to bind the transporter equally well. We suggest that the S enantiomer observed in the crystal structures may be a result of the crystallization process selectively incorporating the (S)-SBFI-26–FABP complexes into the growing lattice, or that the S enantiomer may bind to the portal site more rapidly than to the canonical site, leading to an increased local concentration of the S enantiomer for binding to the canonical site. Our work reveals two binding poses of SBFI-26 in its target transporters. This knowledge will guide the development of more potent FABP inhibitors based upon the SBFI-26 scaffold.

  18. Estimating Parameter Uncertainty in Binding-Energy Models by the Frequency-Domain Bootstrap

    Science.gov (United States)

    Bertsch, G. F.; Bingham, Derek

    2017-12-01

    We propose using the frequency-domain bootstrap (FDB) to estimate errors of modeling parameters when the modeling error is itself a major source of uncertainty. Unlike the usual bootstrap or the simple χ2 analysis, the FDB can take into account correlations between errors. It is also very fast compared to the Gaussian process Bayesian estimate as often implemented for computer model calibration. The method is illustrated with a simple example, the liquid drop model of nuclear binding energies. We find that the FDB gives a more conservative estimate of the uncertainty in liquid drop parameters than the χ2 method, and is in fair accord with more empirical estimates. For the nuclear physics application, there are no apparent obstacles to apply the method to the more accurate and detailed models based on density-functional theory.

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

    Science.gov (United States)

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

    2017-06-01

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

  20. Binding energy of one [sup 4]He impurity in liquid [sup 3]He

    Energy Technology Data Exchange (ETDEWEB)

    Boronat, J. (Universitat Politecnica de Catalunya, Barcelona (Spain)); Saavedra, F.A. de; Buendia, E. (Universidad de Granola (Spain)); Polls, A. (Universitat de Barcelona (Spain))

    1994-02-01

    A variational microscopic calculation of the binding energy of a [sup 4]He impurity ([mu][sub I]) in homogeneous liquid [sup 3]He at zero temperature is presented. Starting on an extended Jastrow-Slater wave function including three-body correlations, the expression for [mu][sub I] is derived and the appropriated FHNC formalism for this problem is reviewed. In the framework of the Average Correlation Approximation (ACA), it is proved that it is possible to obtain the chemical potential of the impurity only from liquid [sup 3]He magnitudes with a good accuracy. The results are consistent with both a recent experimental determination of [mu][sub I] at zero pressure and the non-solubility of [sup 4]He in [sup 3]He. However, numerical uncertainties preclude a firm conclusion about the latter property.

  1. 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.

  2. The influence of different dietary energy concentrations on the ...

    African Journals Online (AJOL)

    The influence of different dietary energy concentrations on the production parameters of feedlot ostriches. T.S. Brand, S.F. Viviers, J van der Merwe, L.C. Hoffman. Abstract. Energy is essential for the continuous survival of any living organism. In ostrich diets, energy is usually derived from maize, which is often subject to ...

  3. Assessing Understanding of the Energy Concept in Different Science Disciplines

    Science.gov (United States)

    Park, Mihwa; Liu, Xiufeng

    2016-01-01

    Energy is one of the most central and richly connected ideas across all science disciplines. The purpose of this study was to develop a measurement instrument for assessing students' understanding of the energy concept within and across different science disciplines. To achieve this goal, the Inter-Disciplinary Energy concept Assessment (IDEA) was…

  4. 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.

  5. 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

  6. 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...

  7. Sperm and Spermatids Contain Different Proteins and Bind Distinct Egg Factors

    Directory of Open Access Journals (Sweden)

    Marta Teperek

    2014-09-01

    Full Text Available Spermatozoa are more efficient at supporting normal embryonic development than spermatids, their immature, immediate precursors. This suggests that the sperm acquires the ability to support embryonic development during spermiogenesis (spermatid to sperm maturation. Here, using Xenopus laevis as a model organism, we performed 2-D Fluorescence Difference Gel Electrophoresis (2D-DIGE and mass spectrometry analysis of differentially expressed proteins between sperm and spermatids in order to identify factors that could be responsible for the efficiency of the sperm to support embryonic development. Furthermore, benefiting from the availability of egg extracts in Xenopus, we also tested whether the chromatin of sperm could attract different egg factors compared to the chromatin of spermatids. Our analysis identified: (1 several proteins which were present exclusively in sperm; but not in spermatid nuclei and (2 numerous egg proteins binding to the sperm (but not to the spermatid chromatin after incubation in egg extracts. Amongst these factors we identified many chromatin-associated proteins and transcriptional repressors. Presence of transcriptional repressors binding specifically to sperm chromatin could suggest its preparation for the early embryonic cell cycles, during which no transcription is observed and suggests that sperm chromatin has a unique protein composition, which facilitates the recruitment of egg chromatin remodelling factors. It is therefore likely that the acquisition of these sperm-specific factors during spermiogenesis makes the sperm chromatin suitable to interact with the maternal factors and, as a consequence, to support efficient embryonic development.

  8. Analysis of Different Methods for Computing Source Energy in the Context of Zero Energy Buildings

    Energy Technology Data Exchange (ETDEWEB)

    Torcellini, Paul A.; Bonnema, Eric; Goldwasser, David; Pless, Shanti

    2016-08-26

    Building energy consumption can only be measured at the site or at the point of utility interconnection with a building. Often, to evaluate the total energy impact, this site-based energy consumption is translated into source energy, that is, the energy at the point of fuel extraction. Consistent with this approach, the U.S. Department of Energy's (DOE) definition of zero energy buildings uses source energy as the metric to account for energy losses from the extraction, transformation, and delivery of energy. Other organizations, as well, use source energy to characterize the energy impacts. Four methods of making the conversion from site energy to source energy were investigated in the context of the DOE definition of zero energy buildings. These methods were evaluated based on three guiding principles--improve energy efficiency, reduce and stabilize power demand, and use power from nonrenewable energy sources as efficiently as possible. This study examines relative trends between strategies as they are implemented on very low-energy buildings to achieve zero energy. A typical office building was modeled and variations to this model performed. The photovoltaic output that was required to create a zero energy building was calculated. Trends were examined with these variations to study the impacts of the calculation method on the building's ability to achieve zero energy status. The paper will highlight the different methods and give conclusions on the advantages and disadvantages of the methods studied.

  9. Perception of the energy question in different regions of France

    International Nuclear Information System (INIS)

    Fouque, B.; Villaret, J.M.

    1982-01-01

    The authors first outline the main variables which account for regional differences in the perception of the energy question, and go on to discuss these differences and the factors underlying them [fr

  10. Influence of different energy sources on the performance of broiler ...

    African Journals Online (AJOL)

    Influence of different energy sources on the performance of broiler chicks. PN Onu, LLC Ugwu, MO Otuma, EN Uchewa. Abstract. An experiment was conducted with 63 day-old Anak broiler chicks to investigate the growth response of broilers fed diets containing different energy sources. Three experimental diets were ...

  11. Reproductive Performance in Response to Different Energy and ...

    African Journals Online (AJOL)

    This study was conducted to investigate the effects of feeding different levels of energy and protein on the reproductive performance of Sudanese Nubian goats. Forty- four female Nubian goats (3-5 years old) were divided into four equal groups and fed on different levels of energy (2.22 -3.12 Mcal /kg DM) and protein (7.3% ...

  12. A Methodology to Allow Comparison among Different Energy Systems

    NARCIS (Netherlands)

    Colli, A.

    2009-01-01

    The work proposes a methodology to overcome diversity of risk expressions and allow comparison among different energy systems, being them connected to traditional or innovative technologies. The investigation started with the analysis of ten different energy chains along their steps, which has led

  13. Receptor-binding profiles of H7 subtype influenza viruses in different host species

    NARCIS (Netherlands)

    A.S. Gambaryan (Alexandra ); T.Y. Matrosovich (Tatyana); J. Philipp (Jennifer); V.J. Munster (Vincent); R.A.M. Fouchier (Ron); G. Cattoli (Giovanni); I. Capua (Ilaria); S.L. Krauss (Scott); R.G. Webster (Robert); J. Banks (James); N.V. Bovin (Nicolai); H.D. Klenk

    2012-01-01

    textabstractInfluenza viruses of gallinaceous poultry and wild aquatic birds usually have distinguishable receptor-binding properties. Here we used a panel of synthetic sialylglycopolymers and solid-phase receptor-binding assays to characterize receptor-binding profiles of about 70 H7 influenza

  14. Batteries for efficient energy extraction from a water salinity difference.

    Science.gov (United States)

    La Mantia, Fabio; Pasta, Mauro; Deshazer, Heather D; Logan, Bruce E; Cui, Yi

    2011-04-13

    The salinity difference between seawater and river water is a renewable source of enormous entropic energy, but extracting it efficiently as a form of useful energy remains a challenge. Here we demonstrate a device called "mixing entropy battery", which can extract and store it as useful electrochemical energy. The battery, containing a Na(2-x)Mn(5)O(10) nanorod electrode, was shown to extract energy from real seawater and river water and can be applied to a variety of salt waters. We demonstrated energy extraction efficiencies of up to 74%. Considering the flow rate of river water into oceans as the limiting factor, the renewable energy production could potentially reach 2 TW, or ∼13% of the current world energy consumption. The mixing entropy battery is simple to fabricate and could contribute significantly to renewable energy in the future.

  15. Batteries for Efficient Energy Extraction from a Water Salinity Difference

    KAUST Repository

    La Mantia, Fabio

    2011-04-13

    The salinity difference between seawater and river water is a renewable source of enormous entropic energy, but extracting it efficiently as a form of useful energy remains a challenge. Here we demonstrate a device called "mixing entropy battery", which can extract and store it as useful electrochemical energy. The battery, containing a Na2-xMn 5O10 nanorod electrode, was shown to extract energy from real seawater and river water and can be applied to a variety of salt waters. We demonstrated energy extraction efficiencies of up to 74%. Considering the flow rate of river water into oceans as the limiting factor, the renewable energy production could potentially reach 2 TW, or ∼13% of the current world energy consumption. The mixing entropy battery is simple to fabricate and could contribute significantly to renewable energy in the future. © 2011 American Chemical Society.

  16. Diabat Interpolation for Polymorph Free-Energy Differences.

    Science.gov (United States)

    Kamat, Kartik; Peters, Baron

    2017-02-02

    Existing methods to compute free-energy differences between polymorphs use harmonic approximations, advanced non-Boltzmann bias sampling techniques, and/or multistage free-energy perturbations. This work demonstrates how Bennett's diabat interpolation method ( J. Comput. Phys. 1976, 22, 245 ) can be combined with energy gaps from lattice-switch Monte Carlo techniques ( Phys. Rev. E 2000, 61, 906 ) to swiftly estimate polymorph free-energy differences. The new method requires only two unbiased molecular dynamics simulations, one for each polymorph. To illustrate the new method, we compute the free-energy difference between face-centered cubic and body-centered cubic polymorphs for a Gaussian core solid. We discuss the justification for parabolic models of the free-energy diabats and similarities to methods that have been used in studies of electron transfer.

  17. Energy difference space random walk to achieve fast free energy calculations.

    Science.gov (United States)

    Min, Donghong; Yang, Wei

    2008-05-21

    A method is proposed to efficiently obtain free energy differences. In the present algorithm, free energy calculations proceed by the realization of an energy difference space random walk. Thereby, this algorithm can greatly improve the sampling of the regions in phase space where target states overlap.

  18. 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.

  19. Selective binding of pyrene in subdomain IB of human serum albumin: Combining energy transfer spectroscopy and molecular modelling to understand protein binding flexibility

    Science.gov (United States)

    Ling, Irene; Taha, Mohamed; Al-Sharji, Nada A.; Abou-Zied, Osama K.

    2018-04-01

    The ability of human serum albumin (HSA) to bind medium-sized hydrophobic molecules is important for the distribution, metabolism, and efficacy of many drugs. Herein, the interaction between pyrene, a hydrophobic fluorescent probe, and HSA was thoroughly investigated using steady-state and time-resolved fluorescence techniques, ligand docking, and molecular dynamics (MD) simulations. A slight quenching of the fluorescence signal from Trp214 (the sole tryptophan residue in the protein) in the presence of pyrene was used to determine the ligand binding site in the protein, using Förster's resonance energy transfer (FRET) theory. The estimated FRET apparent distance between pyrene and Trp214 was 27 Å, which was closely reproduced by the docking analysis (29 Å) and MD simulation (32 Å). The highest affinity site for pyrene was found to be in subdomain IB from the docking results. The calculated equilibrium structure of the complex using MD simulation shows that the ligand is largely stabilized by hydrophobic interaction with Phe165, Phe127, and the nonpolar moieties of Tyr138 and Tyr161. The fluorescence vibronic peak ratio I1/I3 of bound pyrene inside HSA indicates the presence of polar effect in the local environment of pyrene which is less than that of free pyrene in buffer. This was clarified by the MD simulation results in which an average of 5.7 water molecules were found within 0.5 nm of pyrene in the binding site. Comparing the fluorescence signals and lifetimes of pyrene inside HSA to that free in buffer, the high tendency of pyrene to form dimer was almost completely suppressed inside HSA, indicating a high selectivity of the binding pocket toward pyrene monomer. The current results emphasize the ability of HSA, as a major carrier of several drugs and ligands in blood, to bind hydrophobic molecules in cavities other than subdomain IIA which is known to bind most hydrophobic drugs. This ability stems from the nature of the amino acids forming the binding

  20. Specific interactions and binding energies between thermolysin and potent inhibitors: molecular simulations based on ab initio molecular orbital method.

    Science.gov (United States)

    Hirakawa, Tatsuya; Fujita, Seiya; Ohyama, Tatsuya; Dedachi, Kenichi; Khan, Mahmud Tareq Hassan; Sylte, Ingebrigt; Kurita, Noriyuki

    2012-03-01

    Biochemical functions of the metalloprotease thermolysin (TLN) are controlled by various inhibitors. In a recent study we identified 12 compounds as TLN inhibitors by virtual screening and in vitro competitive binding assays. However, the specific interactions between TLN and these inhibitors have not been clarified. We here investigate stable structures of the solvated TLN-inhibitor complexes by classical molecular mechanics simulations and elucidate the specific interactions between TLN and these inhibitors at an electronic level by using ab initio fragment molecular orbital (FMO) calculations. The calculated binding energies between TLN and the inhibitors are qualitatively consistent with the experimental results, and the FMO results elucidate important amino acid residues of TLN for inhibitor binding. Based on the calculated results, we propose a novel potent inhibitor having a large binding affinity to TLN. Copyright © 2011 Elsevier Inc. All rights reserved.

  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. Binding Analysis of Some Classical Acetylcholinesterase Inhibitors: Insights for a Rational Design Using Free Energy Perturbation Method Calculations with QM/MM MD Simulations.

    Science.gov (United States)

    Nascimento, Érica C M; Oliva, Mónica; Świderek, Katarzyna; Martins, João B L; Andrés, Juan

    2017-04-24

    In the present study, the binding free energy of some classical inhibitors (DMT, DNP, GNT, HUP, THA) with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation (FEP) method based on hybrid quantum mechanics and molecular mechanics (QM/MM) potentials. The results highlight the key role of the van der Waals interaction for the inhibition process, since the contribution of this term to the binding free energy is almost as decisive as the electrostatic one. The analysis of the geometrical parameters and the interaction energy per residue along the QM/MM molecular dynamics (MD) simulations highlights the most relevant interactions in the different AChE-ligand systems, showing that the charged residues with a more prominent contribution to the interaction energy are Asp72 and Glu199, although the relative importance depends on the molecular size of the ligand. A correlation between the binding free energy and the number of cation-π interactions present in the systems has been established, DMT being the most potent inhibitor, capable of forming four cation-π interactions. A layer of water molecules surrounding the inhibitors has been observed, which act as bridges along a network formed by the ligands and the residues of the gorge and also between different residues. Although several hydrogen bonds between ligands and AChE do appear, no significant values of BIEs have been recorded. This behavior can be accounted for by the special features of AChE, such as the presence of several subsites of different natures in the gorge or the existence of several water molecules that act as bridges in the electrostatic interactions.

  3. Slow- and fast-binding inhibitors of thermolysin display different modes of binding: crystallographic analysis of extended phosphonamidate transition-state analogues.

    Science.gov (United States)

    Holden, H M; Tronrud, D E; Monzingo, A F; Weaver, L H; Matthews, B W

    1987-12-29

    The modes of binding to thermolysin of two phosphonamidate peptide inhibitors, carbobenzoxy-GlyP-L-Leu-L-Leu (ZGPLL) and carbobenzoxy-L-PheP-L-Leu-L-Ala (ZFPLA), have been determined by X-ray crystallography and refined at high resolution to crystallographic R-values of 17.7% and 17.0%, respectively. (GlyP is used to indicate that the trigonal carbon of the peptide linkage is replaced by the tetrahedral phosphorus of a phosphonamidate group.). These inhibitors were designed to be structural analogues of the presumed catalytic transition state and are potent inhibitors of thermolysin (ZGPLL, Ki = 9.1 nM; ZFPLA, Ki = 0.068 nM) [Bartlett, P. A., & Marlowe, C. K. (1987) Biochemistry (following paper in this issue)]. ZFPLA binds to thermolysin in the manner expected for the transition state and, for the first time, provides direct support for the presumed mode of binding of extended substrates in the S2 subsite. The mode of binding of ZFPLA displays all the interactions that are presumed to stabilize the transition state and supports the postulated mechanism of catalysis [Hangauer, D. G., Monzingo, A. F., & Matthews, B. W. (1984) Biochemistry 23, 5730-5741]. The two oxygens of the phosphonamidate moiety are liganded to the zinc to give overall pentacoordination of the metal. For the second inhibitor the situation is different. Although both ZFPLA and ZGPLL have similar modes of binding in the S1' and S2' subsites, the configurations of the carbobenzoxy-Phe and carbobenzoxy-Gly moieties are different. For ZFPLA the carbonyl group of the carbobenzoxy group is hydrogen bonded directly to the enzyme, whereas in ZGPLL the carbonyl group is rotated 117 degrees, and there is a water molecule interposed between the inhibitor and the enzyme. For ZGPLL only one of the phosphonamidate oxygens is liganded to the zinc. Correlated with the change in inhibitor-zinc ligation from monodentate in ZGPLL to bidentate in ZFPLA there is an increase in the phosphorus-nitrogen bond length of

  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. A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations.

    Science.gov (United States)

    Abel, Robert; Wang, Lingle; Mobley, David L; Friesner, Richard A

    2017-01-01

    Protein-ligand binding is among the most fundamental phenomena underlying all molecular biology, and a greater ability to more accurately and robustly predict the binding free energy of a small molecule ligand for its cognate protein is expected to have vast consequences for improving the efficiency of pharmaceutical drug discovery. We briefly reviewed a number of scientific and technical advances that have enabled alchemical free energy calculations to recently emerge as a preferred approach, and critically considered proper validation and effective use of these techniques. In particular, we characterized a selection bias effect which may be important in prospective free energy calculations, and introduced a strategy to improve the accuracy of the free energy predictions. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  6. Structure-based simulations of kinesin motor domain for the study and characterization of its different microtubule and ligand-binding states

    Science.gov (United States)

    Chakraborty, Srirupa; Zheng, Wenjun

    2014-03-01

    Kinesins are molecular motors acting as enzyme-based nanomachines that transport intracellular cargo along microtubules (MT). To obtain a detailed structural and energetic picture of the various conformations of the kinesin motor domain, we built atomistic models using available crystal structures, homology modeling and flexible fitting into cryo-electron microscopy (EM) maps. These models depict the various biochemical states of the kinesin head, such as - with the neck-linker docked and undocked in the MT-free state, and the different nucleotide (ADP, ATP and APO) bound states in the kinesin-MT complex. Here we perform molecular dynamics simulation techniques and large-scale computational probing of differences in these states, by an exhaustive search of interactions that differ between them, identify key residues in the active site and binding interface, and investigate the binding free-energy between kinesin and MT, and kinesin and ligand to compare with experimentally obtained results.

  7. Binding energy and dynamics of Be acceptor levels in AlAs/GaAs multiple quantum wells

    NARCIS (Netherlands)

    Halsall, M. P.; Zheng, W. M.; Harrison, P.; Wells, J. P. R.; Steer, M. J.; Orlova, E. E.

    2004-01-01

    We report an infrared study of the effect of quantum well confinement on the binding energy and dynamics of shallow Be acceptors in both bulk GaAs and a series of delta-doped AlAs/GaAs multiquantum well samples with well thicknesses of 20,15 and 10 nm. Low temperature far-infrared absorption

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

    International Nuclear Information System (INIS)

    Benvenuto, O.G.; Civitarese, O.; Reboiro, M.

    1993-01-01

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

  9. Correlation between the binding energy of neutrons in nuclei and anomalous fractionation of isotopes in medico-biological objects

    International Nuclear Information System (INIS)

    Bykovskij, Yu.A.; Timoshin, V.T.; Laptev, I.D.; Manykin, Eh.A.

    1986-01-01

    Laser mass-spectrometry is used to investigate isotope ratio in medico-biological objects (MBO). Anomalous fractionation of carbon, oxygen, silicon, sulphur, potassium and calcium isotopes in MBO is detected. Correlation between neutron binding energy in isotopic nuclei and isotope anomalous fractionation of some elements in MBO is determined

  10. Applications of SOECs in different types of energy systems

    DEFF Research Database (Denmark)

    Mathiesen, Brian Vad; Ridjan, Iva; Hansen, Kenneth

    for using combined capacities of SOEC and SOFC was investigated as this can potentially improve the profitability of the investment, but also improve the stability of the energy system by offering grid-balancing capacity when intermittent resources cannot meet the demand for electricity. Finally, five......Different aspects of electrolyser integration in energy systems was investigated in order to determine the potential of using this technology in the future. The first analysis examined the influence of the use of co-electrolysis for the fuel production process in comparison with using steam...... different energy systems were analysed in order to determine the operation of electrolysers: Danish 100% renewable scenario for 2050, smart energy system Germany 2050 and three nuclear scenarios for Germany with different shares of nuclear energy (15%, 30% and 45%) of the electricity production...

  11. Mutated primer binding sites interacting with different tRNAs allow efficient murine leukemia virus replication

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M; Lovmand, J

    1993-01-01

    Two Akv murine leukemia virus-based retroviral vectors with primer binding sites matching tRNA(Gln-1) and tRNA(Lys-3) were constructed. The transduction efficiency of these mutated vectors was found to be comparable to that of a vector carrying the wild-type primer binding site matching t......RNA(Pro). Polymerase chain reaction amplification and sequence analysis of transduced proviruses confirmed the transfer of vectors with mutated primer binding sites and further showed that tRNA(Gln-2) may act efficiently in conjunction with the tRNA(Gln-1) primer binding site. We conclude that murine leukemia virus...... can replicate by using various tRNA molecules as primers and propose primer binding site-tRNA primer interactions to be of major importance for tRNA primer selection. However, efficient primer selection does not require perfect Watson-Crick base pairing at all 18 positions of the primer binding site....

  12. 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.

  13. Binding energy and momentum distribution of nuclear matter using Green's function methods

    International Nuclear Information System (INIS)

    Ramos, A.; Dickhoff, W.H.; Polls, A.

    1991-01-01

    The influence of hole-hole (h-h) propagation in addition to the conventional particle-particle (p-p) propagation, on the energy per particle and the momentum distribution is investigated for the v 2 central interaction which is derived from Reid's soft-core potential. The results are compared to Brueckner-Hartree-Fock calculations with a continuous choice for the single-particle (SP) spectrum. Calculation of the energy from a self-consistently determined SP spectrum leads to a lower saturation density. This result is not corroborated by calculating the energy from the hole spectral function, which is, however, not self-consistent. A generalization of previous calculations of the momentum distribution, based on a Goldstone diagram expansion, is introduced that allows the inclusion of h-h contributions to all orders. From this result an alternative calculation of the kinetic energy is obtained. In addition, a direct calculation of the potential energy is presented which is obtained from a solution of the ladder equation containing p-p and h-h propagation to all orders. These results can be considered as the contributions of selected Goldstone diagrams (including p-p and h-h terms on the same footing) to the kinetic and potential energy in which the SP energy is given by the quasiparticle energy. The results for the summation of Goldstone diagrams leads to a different momentum distribution than the one obtained from integrating the hole spectral function which in general gives less depletion of the Fermi sea. Various arguments, based partly on the results that are obtained, are put forward that a self-consistent determination of the spectral functions including the p-p and h-h ladder contributions (using a realistic interaction) will shed light on the question of nuclear saturation at a nonrelativistic level that is consistent with the observed depletion of SP orbitals in finite nuclei

  14. Binding energy and momentum distribution of nuclear matter using Green's function methods

    International Nuclear Information System (INIS)

    Ramos, A.; Dickhoff, W.H.; Polls, A.

    1990-07-01

    The influence of hole-hole (hh) propagation in addition to the conventional particle-particle (pp) propagation on the energy per particle and the momentum distribution is investigated for two central interactions (v 2 and v 2 l=0 ) which are derived from Reid's soft core potential. The results are compared to Brueckner-Hartree-Fock calculations with a continuous choice for the single-particle (sp) spectrum. Calculation of the energy from a self-consistently determined sp spectrum leads to a lower saturation density. This result is not corroborated by calculating the energy from the hole spectral function which is, however, not self-consistent. A generalization of previous calculations of the momentum distribution based on a Goldstone diagram expansion is introduced which allows the inclusion of hh contributions to all orders. From this result an alternative calculation of the kinetic energy is obtained. In addition, a direct calculation of the potential energy is presented which is obtained from a solution of the ladder equation containing pp and hh propagation to all orders. These results can be considered as the contributions of selected Goldstone diagrams (including pp and hh terms on the same footing) to the kinetic and potential energy in which the sp energy is given by the quasi-article energy. The results for the summation of Goldstone diagrams leads to a different momentum distribution than the one obtained from integrating the hole spectral function which in general gives less depletion of the Fermi sea. Various arguments, based partly on the results that are obtained, are put forward that a self-consistent determination of the spectral functions including the pp and hh ladder contributions (using a realistic interaction) will shed light on the question of nuclear saturation at a non-relativistic level which is consistent with the observed depletion of sp orbitals in finite nuclei. (Author) (51 refs., 3 tabs., 15 figs)

  15. Direct determination of monolayer MoS2 and WSe2 exciton binding energies on insulating and metallic substrates

    KAUST Repository

    Park, Soohyung

    2018-01-03

    Understanding the excitonic nature of excited states in two-dimensional (2D) transition-metal dichalcogenides (TMDCs) is of key importance to make use of their optical and charge transport properties in optoelectronic applications. We contribute to this by the direct experimental determination of the exciton binding energy (E b,exc) of monolayer MoS2 and WSe2 on two fundamentally different substrates, i.e. the insulator sapphire and the metal gold. By combining angle-resolved direct and inverse photoelectron spectroscopy we measure the electronic band gap (E g), and by reflectance measurements the optical excitonic band gap (E exc). The difference of these two energies is E b,exc. The values of E g and E b,exc are 2.11 eV and 240 meV for MoS2 on sapphire, and 1.89 eV and 240 meV for WSe2 on sapphire. On Au E b,exc is decreased to 90 meV and 140 meV for MoS2 and WSe2, respectively. The significant E b,exc reduction is primarily due to a reduction of E g resulting from enhanced screening by the metal, while E exc is barely decreased for the metal support. Energy level diagrams determined at the K-point of the 2D TMDCs Brillouin zone show that MoS2 has more p-type character on Au as compared to sapphire, while WSe2 appears close to intrinsic on both. These results demonstrate that the impact of the dielectric environment of 2D TMDCs is more pronounced for individual charge carriers than for a correlated electron–hole pair, i.e. the exciton. A proper dielectric surrounding design for such 2D semiconductors can therefore be used to facilitate superior optoelectronic device function.

  16. Direct determination of monolayer MoS2 and WSe2 exciton binding energies on insulating and metallic substrates

    Science.gov (United States)

    Park, Soohyung; Mutz, Niklas; Schultz, Thorsten; Blumstengel, Sylke; Han, Ali; Aljarb, Areej; Li, Lain-Jong; List-Kratochvil, Emil J. W.; Amsalem, Patrick; Koch, Norbert

    2018-04-01

    Understanding the excitonic nature of excited states in two-dimensional (2D) transition-metal dichalcogenides (TMDCs) is of key importance to make use of their optical and charge transport properties in optoelectronic applications. We contribute to this by the direct experimental determination of the exciton binding energy (E b,exc) of monolayer MoS2 and WSe2 on two fundamentally different substrates, i.e. the insulator sapphire and the metal gold. By combining angle-resolved direct and inverse photoelectron spectroscopy we measure the electronic band gap (E g), and by reflectance measurements the optical excitonic band gap (E exc). The difference of these two energies is E b,exc. The values of E g and E b,exc are 2.11 eV and 240 meV for MoS2 on sapphire, and 1.89 eV and 240 meV for WSe2 on sapphire. On Au E b,exc is decreased to 90 meV and 140 meV for MoS2 and WSe2, respectively. The significant E b,exc reduction is primarily due to a reduction of E g resulting from enhanced screening by the metal, while E exc is barely decreased for the metal support. Energy level diagrams determined at the K-point of the 2D TMDCs Brillouin zone show that MoS2 has more p-type character on Au as compared to sapphire, while WSe2 appears close to intrinsic on both. These results demonstrate that the impact of the dielectric environment of 2D TMDCs is more pronounced for individual charge carriers than for a correlated electron-hole pair, i.e. the exciton. A proper dielectric surrounding design for such 2D semiconductors can therefore be used to facilitate superior optoelectronic device function.

  17. On the specificity of heparin/heparan sulfate binding to proteins. Anion-binding sites on antithrombin and thrombin are fundamentally different.

    Directory of Open Access Journals (Sweden)

    Philip D Mosier

    Full Text Available The antithrombin-heparin/heparan sulfate (H/HS and thrombin-H/HS interactions are recognized as prototypic specific and non-specific glycosaminoglycan (GAG-protein interactions, respectively. The fundamental structural basis for the origin of specificity, or lack thereof, in these interactions remains unclear. The availability of multiple co-crystal structures facilitates a structural analysis that challenges the long-held belief that the GAG binding sites in antithrombin and thrombin are essentially similar with high solvent exposure and shallow surface characteristics.Analyses of solvent accessibility and exposed surface areas, gyrational mobility, symmetry, cavity shape/size, conserved water molecules and crystallographic parameters were performed for 12 X-ray structures, which include 12 thrombin and 16 antithrombin chains. Novel calculations are described for gyrational mobility and prediction of water loci and conservation.The solvent accessibilities and gyrational mobilities of arginines and lysines in the binding sites of the two proteins reveal sharp contrasts. The distribution of positive charges shows considerable asymmetry in antithrombin, but substantial symmetry for thrombin. Cavity analyses suggest the presence of a reasonably sized bifurcated cavity in antithrombin that facilitates a firm 'hand-shake' with H/HS, but with thrombin, a weaker 'high-five'. Tightly bound water molecules were predicted to be localized in the pentasaccharide binding pocket of antithrombin, but absent in thrombin. Together, these differences in the binding sites explain the major H/HS recognition characteristics of the two prototypic proteins, thus affording an explanation of the specificity of binding. This provides a foundation for understanding specificity of interaction at an atomic level, which will greatly aid the design of natural or synthetic H/HS sequences that target proteins in a specific manner.

  18. The effect of binding energy and resolution in simulations of the common envelope binary interaction

    Science.gov (United States)

    Iaconi, Roberto; De Marco, Orsola; Passy, Jean-Claude; Staff, Jan

    2018-03-01

    The common envelope binary interaction remains one of the least understood phases in the evolution of compact binaries, including those that result in Type Ia supernovae and in mergers that emit detectable gravitational waves. In this work we continue the detailed and systematic analysis of 3D hydrodynamic simulations of the common envelope interaction aimed at understanding the reliability of the results. Our first set of simulations replicate the 5 simulations of Passy et al. (a 0.88 M⊙, 90 R⊙ RGB primary with companions in the range 0.1 to 0.9 M⊙) using a new AMR gravity solver implemented on our modified version of the hydrodynamic code ENZO. Despite smaller final separations obtained, these more resolved simulations do not alter the nature of the conclusions that are drawn. We also carry out 5 identical simulations but with a 2.0 M⊙ primary RGB star with the same core mass as the Passy et al. simulations, isolating the effect of the envelope binding energy. With a more bound envelope all the companions in-spiral faster and deeper though relatively less gas is unbound. Even at the highest resolution, the final separation attained by simulations with a heavier primary is similar to the size of the smoothed potential even if we account for the loss of some angular momentum by the simulation. As a result we suggest that a ˜2.0 M⊙ RGB primary may possibly end in a merger with companions as massive as 0.6 M⊙, something that would not be deduced using analytical arguments based on energy conservation.

  19. Electron momentum distributions and binding energies for the valence orbitals of hydrogen bromide and hydrogen iodide

    International Nuclear Information System (INIS)

    Brion, C.E.; McCarthy, I.E.; Suzuki, I.H.; Weigold, E.; Williams, G.R.J.; Bedford, K.L.; Kunz, A.B.; Weidman, R.

    1981-12-01

    The electron binding energy spectra and momentum distributions have been obtained for the valence orbitals of HBr and HI using noncoplanar symmetric electron coincidence spectroscopy at 1200eV. The weakly bonding inner valence ns orbitals, which have not been previously observed, have their spectroscopic (pole) strength severely split among a number of ion states. For HBr the strength of the main inner valence (ns) transition is 0.42 0.03 whereas for HI it is 0.37 0.04, in close agreement with that observed for the valence s orbitals of the corresponding isoelectronic inert gas atoms. The spectroscopic strength for the two outermost orbitals is found to be close to unity, in agreement with many body Green's function calculations. The measured momentum distributions are compared with several spherically averaged MO momentum distributions, as well as (for HBr) with a Green's function calculation of the generalized overlap amplitude (GOA). The GOA momentum distributions are in excellent agreement with the HBr data, both in shape and relative magnitude. Not all of the MO momentum distributions are in reasonable agreement with the data. Comparison is also made with the calculated momentum distributions for Kr, Br, Xe and I

  20. 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.

  1. Characterization of atrazine binding to dissolved organic matter of soil under different types of land use.

    Science.gov (United States)

    Zhu, Long-Ji; Zhao, Yue; Chen, Yan-Ni; Cui, Hong-Yang; Wei, Yu-Quan; Liu, Hai-Long; Chen, Xiao-Meng; Wei, Zi-Min

    2018-01-01

    Atrazine is widely used in agriculture. In this study, dissolved organic matter (DOM) from soils under four types of land use (forest (F), meadow (M), cropland (C) and wetland (W)) was used to investigate the binding characteristics of atrazine. Fluorescence excitation-emission matrix-parallel factor (EEM-PARAFAC) analysis, two-dimensional correlation spectroscopy (2D-COS) and Stern-Volmer model were combined to explore the complexation between DOM and atrazine. The EEM-PARAFAC indicated that DOM from different sources had different structures, and humic-like components had more obvious quenching effects than protein-like components. The Stern-Volmer model combined with correlation analysis showed that log K values of PARAFAC components had a significant correlation with the humification of DOM, especially for C3 component, and they were all in the same order as follows: meadow soil (5.68)>wetland soil (5.44)>cropland soil (5.35)>forest soil (5.04). The 2D-COS further confirmed that humic-like components firstly combined with atrazine followed by protein-like components. These findings suggest that DOM components can significantly influence the bioavailability, mobility and migration of atrazine in different land uses. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? An evaluation of the linear interaction energy (LIE) method

    NARCIS (Netherlands)

    Stjernschantz, E.M.; Marelius, J.; Medina, C.; Jacobsson, M.; Vermeulen, N.P.E.; Oostenbrink, C.

    2006-01-01

    An extensive evaluation of the linear interaction energy (LIE) method for the prediction of binding affinity of docked compounds has been performed, with an emphasis on its applicability in lead optimization. An automated setup is presented, which allows for the use of the method in an industrial

  3. Net energy analysis of different electricity generation systems

    International Nuclear Information System (INIS)

    1994-07-01

    This document is a report on the net energy analysis of nuclear power and other electricity generation systems. The main objectives of this document are: To provide a comprehensive review of the state of knowledge on net energy analysis of nuclear and other energy systems for electricity generation; to address traditional questions such as whether nuclear power is a net energy producer or not. In addition, the work in progress on a renewed application of the net energy analysis method to environmental issues is also discussed. It is expected that this work could contribute to the overall comparative assessment of different energy systems which is an ongoing activity at the IAEA. 167 refs, 9 figs, 5 tabs

  4. Heterogeneity of [3H]phorbol 12,13-dibutyrate binding in primary mouse keratinocytes at different stages of maturation

    International Nuclear Information System (INIS)

    Dunn, J.A.; Jeng, A.Y.; Yuspa, S.H.; Blumberg, P.M.

    1985-01-01

    Mouse keratinocytes respond heterogeneously to phorbol esters with distinct subpopulations stimulated to proliferate or induced to differentiate. The maturation state of the epidermal cell at the time of exposure may determine its response. The binding of phorbol esters to primary mouse keratinocytes was studied under culture conditions selecting for proliferating cells or differentiating cells. [20- 3 H]-12-Deoxyphorbol 13-isobutyrate ([ 3 H]-DPB) bound to both types of cells at one class of binding sites. The dissociation constant (Kd) for [ 3 H]DPB in the proliferative cells was 69 nM and the binding at saturation (Bmax) was 1.3 pmol/mg of protein. The corresponding values in the differentiative cells were 96 nM and 1.5 pmol/mg of protein, respectively. In contrast to the results obtained with [ 3 H]DPB, [20- 3 H]phorbol 12,13-dibutyrate ([ 3 H]PDBU) bound to both cell types in a heterogeneous fashion. The site for [ 3 H]DPB binding seemed to correspond to the higher affinity [ 3 H]PDBU binding site. The major difference in the cells grown in the medium containing 1.2 mM CaCl 2 was an increase in the Bmax of the lower affinity binding site with the other three parameters remaining similar. The state of epidermal differentiation thus appears to modulate the amount of the lower affinity binding sites for phorbol esters

  5. Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points.

    Science.gov (United States)

    Harris, Robert C; Deng, Nanjie; Levy, Ronald M; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2017-06-05

    Many biomolecules undergo conformational changes associated with allostery or ligand binding. Observing these changes in computer simulations is difficult if their timescales are long. These calculations can be accelerated by observing the transition on an auxiliary free energy surface with a simpler Hamiltonian and connecting this free energy surface to the target free energy surface with free energy calculations. Here, we show that the free energy legs of the cycle can be replaced with energy representation (ER) density functional approximations. We compute: (1) The conformational free energy changes for alanine dipeptide transitioning from the right-handed free energy basin to the left-handed basin and (2) the free energy difference between the open and closed conformations of β-cyclodextrin, a "host" molecule that serves as a model for molecular recognition in host-guest binding. β-cyclodextrin contains 147 atoms compared to 22 atoms for alanine dipeptide, making β-cyclodextrin a large molecule for which to compute solvation free energies by free energy perturbation or integration methods and the largest system for which the ER method has been compared to exact free energy methods. The ER method replaced the 28 simulations to compute each coupling free energy with two endpoint simulations, reducing the computational time for the alanine dipeptide calculation by about 70% and for the β-cyclodextrin by > 95%. The method works even when the distribution of conformations on the auxiliary free energy surface differs substantially from that on the target free energy surface, although some degree of overlap between the two surfaces is required. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  6. Species Differences in the Carbohydrate Binding Preferences of Surfactant Protein D

    DEFF Research Database (Denmark)

    Crouch, Erika C.; Smith, Kelly; McDonald, Barbara

    2006-01-01

    Interactions of surfactant protein D (SP-D) with micro-organisms and organic antigens involve binding to the trimeric neck plus carbohydrate recognition domain (neck+CRD). In these studies, we compared the ligand binding of homologous human, rat, and mouse trimeric neck+CRD fusion proteins, each...

  7. Species Differences in the Carbohydrate Binding Preferences of Surfactant Protein D

    DEFF Research Database (Denmark)

    Crouch, Erika C.; Smith, Kelly; McDonald, Barbara

    2006-01-01

    Interactions of surfactant protein D (SP-D) with micro-organisms and organic antigens involve binding to the trimeric neck plus carbohydrate recognition domain (neck+CRD). In these studies, we compared the ligand binding of homologous human, rat, and mouse trimeric neck+CRD fusion proteins, each ...

  8. Binding free-energy calculation is a powerful tool for drug optimization: calculation and measurement of binding free energy for 7-azaindole derivatives to glycogen synthase kinase-3β.

    Science.gov (United States)

    Kitamura, Kunihiro; Tamura, Yunoshin; Ueki, Tomokazu; Ogata, Koji; Noda, Shigeho; Himeno, Ryutaro; Chuman, Hiroshi

    2014-06-23

    Present computational lead (drug)-optimization is lacking in thermodynamic tactics. To examine whether calculation of binding free-energy change (ΔG) is effective for the lead-optimization process, binding ΔGs of 7-azaindole derivatives to the ATP binding site of glycogen synthase kinase-3β (GSK-3β) were calculated. The result was a significant correlation coefficient of r = 0.895 between calculated and observed ΔGs. This indicates that calculated ΔG reflects the inhibitory activities of 7-azaindole derivatives. In addition to quantitative estimation of activity, ΔG calculation characterizes the thermodynamic behavior of 7-azaindole derivatives, providing also useful information for inhibitor optimization on affinity to water molecules.

  9. Optimal selection among different domestic energy consumption patterns based on energy and exergy analysis

    International Nuclear Information System (INIS)

    Lu, S.; Wu, J.Y.

    2010-01-01

    In China market, people have many choices for air conditioning of their apartments, including heat-pump systems or gas-fired boilers for heating and air conditioners for cooling. Domestic hot water is usually provided by domestic water heaters making use of electricity or natural gas, which are known for their great energy costs. These systems consume much energy and increase the total cost of required domestic energy. A novel system combining heat pump with water heater is proposed in this paper, and it is named domestic energy system. The system can realize the provision of space heating, cooling and domestic hot water throughout a year. Based on different types of air conditioners, space heating equipments and water heaters, domestic energy consumption patterns are concluded to be eight categories. This study describes and compares the eight domestic energy consumption patterns by economic analysis and prime energy analysis method. Results show that the domestic energy system can provide good economy and save energy significantly. Furthermore, exergy analysis method is employed to compare the exergy efficiencies of different energy consumption systems. The results show that the domestic energy system has the highest energy conversion efficiency and can make remarkable contribution to social energy saving.

  10. 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...

  11. Energy Efficiency of Biogas Produced from Different Biomass Sources

    International Nuclear Information System (INIS)

    Begum, Shahida; Nazri, A H

    2013-01-01

    Malaysia has different sources of biomass like palm oil waste, agricultural waste, cow dung, sewage waste and landfill sites, which can be used to produce biogas and as a source of energy. Depending on the type of biomass, the biogas produced can have different calorific value. At the same time the energy, being used to produce biogas is dependent on transportation distance, means of transportation, conversion techniques and for handling of raw materials and digested residues. An energy systems analysis approach based on literature is applied to calculate the energy efficiency of biogas produced from biomass. Basically, the methodology is comprised of collecting data, proposing locations and estimating the energy input needed to produce biogas and output obtained from the generated biogas. The study showed that palm oil and municipal solid waste is two potential sources of biomass. The energy efficiency of biogas produced from palm oil residues and municipal solid wastes is 1.70 and 3.33 respectively. Municipal solid wastes have the higher energy efficiency due to less transportation distance and electricity consumption. Despite the inherent uncertainties in the calculations, it can be concluded that the energy potential to use biomass for biogas production is a promising alternative.

  12. A self-interaction-free local hybrid functional: Accurate binding energies vis-à-vis accurate ionization potentials from Kohn-Sham eigenvalues

    International Nuclear Information System (INIS)

    Schmidt, Tobias; Kümmel, Stephan; Kraisler, Eli; Makmal, Adi; Kronik, Leeor

    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 potentials is not yet satisfactory, and if we choose to optimize their prediction, a rather different value of the functional's parameter is obtained. We put this finding in a larger context by discussing similar observations for other functionals and possible directions for further functional development that our findings suggest

  13. Dark energy as consequence of release of cosmological nuclear binding-energy, and its further extension towards a new theory of inflation

    International Nuclear Information System (INIS)

    Gupta, R.C.; Pradhan, Anirudh; Gupta, Sushant

    2012-01-01

    Comparatively recent observations on Type-Ia supernovae and low density (Um = 0.3) measurement of matter including dark matter suggest that the present day universe consists mainly of repulsive-gravity type 'exotic matter' with negative-pressure often said 'dark energy' (Ux = O7). But the nature of dark energy is mysterious and its puzzling questions, such as why, how, where and when about the dark energy, are intriguing. In the present paper the authors attempt to answer these questions while making an effort to reveal the genesis of dark energy, and suggest that the cosmological nuclear binding energy liberated during primordial nucleo-synthesis remains trapped dormant for a long time and then is released free which manifests itself as dark energy in the universe. It is also explained why for dark energy the parameter w = -2/3. Noting that w = 1 for stiff matter and w = 1/3 for radiation; w = -2/3 is for dark energy because '- 1' is due to 'deficiency of stiff- nuclear-matter' and that this binding energy is ultimately released as 'radiation' contributing '+ 1/3', making w = -1+ 1/3 = -2/3. When dark energy is released free at Z = 80, w = -2/3. But as on present day at Z = 0 when radiation strength has diminished to ä ? 0, the parameter w = -1 + ä 1/3 = -1. This, thus almost solves the dark- energy mystery of negative pressure and repulsive-gravity. The proposed theory makes several estimates/predictions which agree reasonably well with the astrophysical constraints and observations. Though there are many candidate-theories, the proposed model of this paper presents an entirely new approach (cosmological nuclear energy) as a possible candidate for dark energy. The secret of acceleration of big-universe is hidden in the small-nucleus. (author)

  14. A review of different strategies for HVAC energy saving

    International Nuclear Information System (INIS)

    Vakiloroaya, Vahid; Samali, Bijan; Fakhar, Ahmad; Pishghadam, Kambiz

    2014-01-01

    Highlights: • Various strategies for HVAC energy saving are described and reviewed. • The influence of each strategy on the HVAC energy saving is investigated. • Combination of existing air conditioning technologies appears to be effective for the energy conservation and comfort. • A comparison study between these approaches is carried out. • Changing the HVAC configuration has the potential to increase or reduce energy savings, depending on several factors. - Abstract: Decreasing the energy consumption of heating, ventilation and air conditioning (HVAC) systems is becoming increasingly important due to rising cost of fossil fuels and environmental concerns. Therefore, finding novel ways to reduce energy consumption in buildings without compromising comfort and indoor air quality is an ongoing research challenge. One proven way of achieving energy efficiency in HVAC systems is to design systems that use novel configurations of existing system components. Each HVAC discipline has specific design requirements and each presents opportunities for energy savings. Energy efficient HVAC systems can be created by re-configuring traditional systems to make more strategic use of existing system parts. Recent research has demonstrated that a combination of existing air conditioning technologies can offer effective solutions for energy conservation and thermal comfort. This paper investigates and reviews the different technologies and approaches, and demonstrates their ability to improve the performance of HVAC systems in order to reduce energy consumption. For each strategy, a brief description is first presented and then by reviewing the previous studies, the influence of that method on the HVAC energy saving is investigated. Finally, a comparison study between these approaches is carried out

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

    Science.gov (United States)

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

    2014-03-01

    Understanding the mechanism of drug-DNA binding is crucial for predicting the potential genotoxicity of drugs. Agarose gel electrophoresis, absorption, steady state fluorescence, and circular dichroism have been used in exploring the interaction of cationic amphiphilic drugs (CADs) such as amitriptyline hydrochloride (AMT), imipramine hydrochloride (IMP), and promethazine hydrochloride (PMT) with calf thymus or pUC19 DNA. Agarose gel electrophoresis assay, along with absorption and steady state fluorescence studies, reveal interaction between the CADs and DNA. A comparative study of the drugs with respect to the effect of urea, iodide induced quenching, and ethidium bromide (EB) exclusion assay reflects binding of CADs to the DNA primarily in an intercalative fashion. Circular dichroism data also support the intercalative mode of binding. Besides quenching, there is fluorescence exchange energy transfer (FRET) in between CADs and EB using DNA as a template.

  16. Different mechanisms are involved in the antibody mediated inhibition of ligand binding to the urokinase receptor

    DEFF Research Database (Denmark)

    List, K; Høyer-Hansen, G; Rønne, E

    1999-01-01

    or interference with conformational properties of the receptor critical for ligand binding. This distinction is central when employing the antibodies as tools in the elucidation of the structure-function relationship of the protein in question. We have studied the effect of monoclonal antibodies against......PA/uPAR complex. The continuous recording of binding and dissociation, obtained in BIA, is central in characterizing these phenomena. The identification of a non-competitive inhibitory mechanism against this receptor reveals the presence of a determinant which influences the binding properties of a remote site...

  17. Sex differences of human cortical blood flow and energy metabolism

    DEFF Research Database (Denmark)

    Aanerud, Joel; Borghammer, Per; Rodell, Anders

    2017-01-01

    Brain energy metabolism is held to reflect energy demanding processes in neuropil related to the density and activity of synapses. There is recent evidence that men have higher density of synapses in temporal cortex than women. One consequence of these differences would be different rates...... cerebral blood flow and cerebral metabolic rate of oxygen as functions of age in healthy volunteers of both sexes. Cerebral metabolic rate of oxygen did not change with age for either sex and there were no differences of mean values of cerebral metabolic rate of oxygen between men and women in cerebral...

  18. Effect of dietary dilution of energy and nutrients during different ...

    African Journals Online (AJOL)

    A completely randomized design was conducted to evaluate the effect of dietary dilution of energy and nutrients during different growing periods on compensatory growth of Ross broilers. Four replicant pens were assigned per seven treatments. Chicks in each treatment received concentrated and diluted diets in different ...

  19. Relation of cigarette smoking in males of different ages to sex hormone binding globulin and testosterone

    International Nuclear Information System (INIS)

    El-Nabarawy, F.S.

    2002-01-01

    The relationship of cigarette smoking, age, total testosterone free testosterone and sex hormone binding globulin (SHBG) were examined by solid phase radioimmunoassay in 90 randomly chosen healthy males of different ages. The serum levels of these hormones were investigated for smokers compared with non-smokers, of the same ages in 3 groups (adolescent males, middle aged males, and old aged males). Results indicated that cigarette smokers showed increased serum levels of testosterone (60.0% higher, P> 0.05), free testosterone (51.0 higher, P > 0.005) in young adolescent males group, testosterone (27.8% higher, P > 0.001), free testosterone (21.3% higher, P > 0.001) in middle aged males group, and testosterone (21.0% higher, P > 0.001), free testosterone (16.8% higher, P > 0.4) in old ages males group. SHBG was calculated as a mean of free and total testosterone in each group. smokers showed higher mean values of SHBG than non-smokers. Age was positively associated with serum SHBG, it was found that SHBG increased by 17.2% from the youngest (> 18 years) to the oldest age (> 65 years)

  20. Comparison of energy consumption and specific energy requirements of different methods for drying mushroom slices

    International Nuclear Information System (INIS)

    Motevali, Ali; Minaei, Saeid; Khoshtaghaza, Mohammad Hadi; Amirnejat, Hamed

    2011-01-01

    Energy consumption for drying of mushroom slices was evaluated using various drying methods including hot air, microwave, vacuum, infrared, microwave-vacuum and hot air-infrared. Results of data analysis showed that the lowest and highest energy consumption levels in drying mushroom slices were associated with microwave and vacuum dryers, respectively. The use of vacuum in conjunction with microwave drying increased energy consumption relative to microwave drying alone. Energy consumption in the hot air dryer showed a downward trend with increasing temperature and an upward trend with increasing air velocity. In drying mushroom using infrared radiation, it was observed that increased air velocity increases drying time and consequently the amount of consumed energy. Using a combination of hot air and infrared drying decreased energy consumption relative to infrared drying alone and increased it relative to hot air drying. In the combined microwave-vacuum dryer, drying time and consequently energy consumption decreased in comparison to the vacuum dryer. Hot air-infrared drying of mushroom slices proved to have the lowest energy consumption. -- Highlights: ► In this study we comparing the amount of energy used and specific energy consumption in different drying methods. ► Six drying methods including Hot air, Infrared, Hot air-infrared, Microwave, Vacuum and microwave-vacuum were used. ► The maximum and minimum energy consumption was obtained in vacuum and microwave dryer, respectively. ► The best drying method in terms of energy consumption and specific energy consumption is the microwave dryer.

  1. Longitudinal investigation of source memory reveals different developmental trajectories for item memory and binding

    OpenAIRE

    Riggins, Tracy

    2013-01-01

    The present study used a cohort-sequential design to examine developmental changes in children's ability to bind items in memory during early and middle childhood. Three cohorts of children (aged 4, 6, or 8 years) were followed longitudinally for three years. Each year, children completed a source memory paradigm assessing memory for items and binding. Results suggest linear increases in memory for individual items (facts or sources) between 4 and 10 years of age, but that memory for correct ...

  2. Single-molecule fluorescence resonance energy transfer shows uniformity in TATA binding protein-induced DNA bending and heterogeneity in bending kinetics.

    Science.gov (United States)

    Blair, Rebecca H; Goodrich, James A; Kugel, Jennifer F

    2012-09-25

    TATA binding protein (TBP) is a key component of the eukaryotic RNA polymerase II transcription machinery that binds to TATA boxes located in the core promoter regions of many genes. Structural and biochemical studies have shown that when TBP binds DNA, it sharply bends the DNA. We used single-molecule fluorescence resonance energy transfer (smFRET) to study DNA bending by human TBP on consensus and mutant TATA boxes in the absence and presence of TFIIA. We found that the state of the bent DNA within populations of TBP-DNA complexes is homogeneous; partially bent intermediates were not observed. In contrast to the results of previous ensemble studies, TBP was found to bend a mutant TATA box to the same extent as the consensus TATA box. Moreover, in the presence of TFIIA, the extent of DNA bending was not significantly changed, although TFIIA did increase the fraction of DNA molecules bound by TBP. Analysis of the kinetics of DNA bending and unbending revealed that on the consensus TATA box two kinetically distinct populations of TBP-DNA complexes exist; however, the bent state of the DNA is the same in the two populations. Our smFRET studies reveal that human TBP bends DNA in a largely uniform manner under a variety of different conditions, which was unexpected given previous ensemble biochemical studies. Our new observations led to us to revise the model for the mechanism of DNA binding by TBP and for how DNA bending is affected by TATA sequence and TFIIA.

  3. Rebound effect of improved energy efficiency for different energy types: A general equilibrium analysis for China

    International Nuclear Information System (INIS)

    Lu, Yingying; Liu, Yu; Zhou, Meifang

    2017-01-01

    This paper explores the rebound effect of different energy types in China based on a static computable general equilibrium model. A one-off 5% energy efficiency improvement is imposed on five different types of energy, respectively, in all the 135 production sectors in China. The rebound effect is measured both on the production level and on the economy-wide level for each type of energy. The results show that improving energy efficiency of using electricity has the largest positive impact on GDP among the five energy types. Inter-fuel substitutability does not affect the macroeconomic results significantly, but long-run impact is usually greater than the short-run impact. For the exports-oriented sectors, those that are capital-intensive get big negative shock in the short run while those that are labour-intensive get hurt in the long run. There is no “backfire” effect; however, improving efficiency of using electricity can cause negative rebound, which implies that improving the energy efficiency of using electricity might be a good policy choice under China's current energy structure. In general, macro-level rebound is larger than production-level rebound. Primary energy goods show larger rebound effect than secondary energy goods. In addition, the paper points out that the policy makers in China should look at the rebound effect in the long term rather than in the short term. The energy efficiency policy would be a good and effective policy choice for energy conservation in China when it still has small inter-fuel substitution. - Highlights: • Primary energy goods show larger rebound effect than secondary energy goods. • Improving efficiency of using electricity can cause negative rebound. • The energy efficiency policy would be an effective policy choice for China. • Policy-makers should consider the rebound effect in the longer term.

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

    Science.gov (United States)

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

    2018-02-01

    The interaction of HIV-1 transactivator protein Tat with its cognate transactivation response (TAR) RNA has emerged as a promising target for developing antiviral compounds and treating HIV infection, since it is a crucial step for efficient transcription and replication. In the present study, molecular dynamics (MD) simulations and MM/GBSA calculations have been performed on a series of neamine derivatives in order to estimate appropriate MD simulation time for acceptable correlation between ΔG bind and experimental pIC 50 values. Initially, all inhibitors were docked into the active site of HIV-1 TAR RNA. Later to explore various conformations and examine the docking results, MD simulations were carried out. Finally, binding free energies were calculated using MM/GBSA method and were correlated with experimental pIC 50 values at different time scales (0-1 to 0-10 ns). From this study, it is clear that in case of neamine derivatives as simulation time increased the correlation between binding free energy and experimental pIC 50 values increased correspondingly. Therefore, the binding energies which can be interpreted at longer simulation times can be used to predict the bioactivity of new neamine derivatives. Moreover, in this work, we have identified some plausible critical nucleotide interactions with neamine derivatives that are responsible for potent inhibitory activity. Furthermore, we also provide some insights into a new class of oxadiazole-based back bone cyclic peptides designed by incorporating the structural features of neamine derivatives. On the whole, this approach can provide a valuable guidance for designing new potent inhibitors and modify the existing compounds targeting HIV-1 TAR RNA.

  5. Risk of the different activities related to energy production

    International Nuclear Information System (INIS)

    Tenaglia, G.

    1983-01-01

    After recalling briefly the concept of risk and explaining the relevant terminology currently in use, the paper deals with the application of the concept of risk to the activities related to energy production. Particular emphasis is placed on the necessity of considering the entire cycle of an energy source, the different aspects that the negative consequences of an activity may entail, as well as the context, mainly territorial and socio-economical, in wich an activity is performed. Moreover the paper presents, schematically and in qualitative terms, the main risk of the different activities related to energy production. More details are given about potentially dangerous activities, nowdays emerging, like -for example- transportation and storage of flammable liquids, whether refrigerated or not. Finally, the difficulties of comparing risks having different probabilities and consequences are considered, as well as the meaning to be assigned, in any case, to comparison among riks [fr

  6. Comparing the health and environmental hazards of different energy systems

    International Nuclear Information System (INIS)

    Hamilton, L.D.

    1982-01-01

    Energy and environment can pose difficult challenges for policy makers and scientists. Assessing health impacts of different energy sources requires synthesis of research results from many different disciplines into a rational framework. Information is often scanty; qualitatively different risks, or energy systems with quite different end uses, must be put on a common footing. Risk-assessment methods reviewed include examples drawn from work of the Biomedical and Environmental Assessment Division at Brookhaven National Laboratory and elsewhere. Coal and nuclear fuel cycles are compared in respect to morbidity and mortality. Other cycles (oil, gas and renewables) are also examined. In broadening comparisons to include new technologies, one must include the impact of manufacturing the energy-producing devices as part of an expanded fuel cycle, via input-output methods. Input-output analysis allows comparisons of direct and system-wide impacts. Throughout the analysis, uncertainties must be explicitly recognized in the results, including uncertainty in validity of data and uncertainty in choice of appropriate models. No single method of comparative risk assessment is fully satisfactory; each has its limitations. By use of several methods progress has been made in understanding the relative impact of energy technologies

  7. Comparing the health and environmental hazards of different energy systems

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, L.D.

    1982-01-01

    Energy and environment can pose difficult challenges for policy makers and scientists. Assessing health impacts of different energy sources requires synthesis of research results from many different disciplines into a rational framework. Information is often scanty; qualitatively different risks, or energy systems with quite different end uses, must be put on a common footing. Risk-assessment methods reviewed include examples drawn from work of the Biomedical and Environmental Assessment Division at Brookhaven National Laboratory and elsewhere. Coal and nuclear fuel cycles are compared in respect to morbidity and mortality. Other cycles (oil, gas and renewables) are also examined. In broadening comparisons to include new technologies, one must include the impact of manufacturing the energy-producing devices as part of an expanded fuel cycle, via input-output methods. Input-output analysis allows comparisons of direct and system-wide impacts. Throughout the analysis, uncertainties must be explicitly recognized in the results, including uncertainty in validity of data and uncertainty in choice of appropriate models. No single method of comparative risk assessment is fully satisfactory; each has its limitations. By use of several methods progress has been made in understanding the relative impact of energy technologies.

  8. Comparing the health impacts of different energy sources

    International Nuclear Information System (INIS)

    Hamilton, L.D.

    1982-01-01

    Assessing health impacts of different energy sources requires synthesis of research results from many different disciplines into a rational framework. Information is often scanty; qualitatively different risks, or energy systems with substantially different end uses, must be put on a common footing. Historically institutional constraints have inhibited agencies from making incisive intercomparisons necessary for formulating energy policy; this has exacerbated public controversy over appropriate energy sources. Risk assessment methods reviewed include examples drawn from work of the Biomedical and Environmental Assessment Division at Brookhaven National Laboratory and elsewhere. Uncertainty over the mechanism and size of air pollution health damage is addressed through a probabilistic health-damage function, using sulphate-particle exposure as an indicator. This facilitates intercomparison through analysis of each step in the whole fuel cycle between a typical coal and nuclear power plant. Occupational health impacts, a significant fraction of overall damage, are illustrated by accident trends in coal-mining. In broadening comparisons to include new technologies, one must include the impact of manufacturing the energy-producing device as part of an expanded fuel cycle, via input/output methods. Throughout the analysis, uncertainties must be made explicit in the results, including uncertainty of data and uncertainty in choice of appropriate models and methods. No single method of comparative risk assessment is fully satisfactory; each has its limitations. Several methods must be compared if decision-making is to be realistic. (author)

  9. Application of the step-wise regression procedure to the semi-empirical formulae of the nuclear binding energy

    International Nuclear Information System (INIS)

    Eissa, E.A.; Ayad, M.; Gashier, F.A.B.

    1984-01-01

    Most of the binding energy semi-empirical terms without the deformation corrections used by P.A. Seeger are arranged in a multiple linear regression form. The stepwise regression procedure with 95% confidence levels for acceptance and rejection of variables is applied for seeking a model for calculating binding energies of even-even (E-E) nuclei through a significance testing of each basic term. Partial F-values are taken as estimates for the significance of each term. The residual standard deviation and the overall F-value are used for selecting the best linear regression model. (E-E) nuclei are taken into sets lying between two successive proton and neutron magic numbers. The present work is in favour of the magic number 126 followed by 164 for the neutrons and indecisive in supporting the recently predicted proton magic number 114 rather than the previous one, 126. (author)

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

    International Nuclear Information System (INIS)

    El Ghazi, Haddou; Jorio, Anouar; Zorkani, Izeddine

    2013-01-01

    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

  11. Absence of a Scott correction for the total binding energy of noninteracting fermions in a smooth potential well

    International Nuclear Information System (INIS)

    Huxtable, B.D.

    1988-01-01

    It is shown, for V in a particular class of smooth functions, that the total binding energy, E(Z), of Z noninteracting Fermions in the potential well Z 4/3 V(Z 1/3 X) obeys E(Z) = c TF (V)Z 7/3 + O(Z 5/3 ) as Z → ∞. Here c TF (V) is the coefficient predicted by Thomas-Fermi theory. This result is consistent with the conjectured Scott correction, which occurs at order Z 2 , to the total binding energy of an atomic number Z. This correction is thought to arise only because V(x)∼ - |x| -1 near x = 0 in the atomic problem, and so V is not a smooth function

  12. Comparision between different metal oxide nanostructures and nanocomposites for sensing, energy generation, and energy harvesting

    Science.gov (United States)

    Willander, Magnus; Alnoor, Hatim; Elhag, Sami; Ibupoto, Zafar Hussain; Nour, Eiman Satti; Nur, Omer

    2016-02-01

    Highlights from research on different nanocomposites and nanostructures for sensing and other energy related applications will be presented. The synthesized nanostructures and nanocomposites presented here were all obtained using the low temperature (textile and paper. We here present results from different metal oxide nanostructures employed for chemical sensing and some innovative energy related applications. Efficient sensitive and selective sensing of dopamine, melamine, and glucose are presented as some examples of self-powered sensors utilizing the electrochemical phenomenon i.e. transferring chemical energy into electrical signal. Further the use of nanomaterials for developing selfpowered devices utilizing mechanical ambient energy is presented via piezoelectric and triboelectric effects. Here the self-powered devices and systems were relying on utilizing the electormechanical phenomenon i.e. transferring ambient mechanical energy into useful electrical energy. Finally the visibility of nanomaterials prepared by the low temperature chemical synthesis as possible low cost replacement of Pt electrodes for hydrogen production is briefly presented and discussed.

  13. Behavioral and Electrophysiological Correlates of Memory Binding Deficits in Patients at Different Risk Levels for Alzheimer's Disease.

    Science.gov (United States)

    Pietto, Marcos; Parra, Mario A; Trujillo, Natalia; Flores, Facundo; García, Adolfo M; Bustin, Julian; Richly, Pablo; Manes, Facundo; Lopera, Francisco; Ibáñez, Agustín; Baez, Sandra

    2016-06-30

    Deficits in visual short-term memory (VSTM) binding have been proposed as an early and specific marker for Alzheimer's disease (AD). However, no studies have explored the neural correlates of this domain in clinical categories involving prodromal stages with different risk levels of conversion to AD. We assessed underlying electrophysiological modulations in patients with mild cognitive impairment (MCI), patients in the MCI stages of familial AD carrying the mutation E280A of the presenilin-1 gene (MCI-FAD), and healthy controls. Moreover, we compared the behavioral performance and neural correlates of both patient groups. Participants completed a change-detection VSTM task assessing recognition of changes between shapes or shape-color bindings, presented in two consecutive arrays (i.e., study and test) while event related potentials (ERPs) were recorded. Changes always occurred in the test array and consisted of new features replacing studied features (shape-only) or features swapping across items (shape-color binding). Both MCI and MCI-FAD patients performed worse than controls in the shape-color binding condition. Early electrophysiological activity (100-250 ms) was significantly reduced in both clinical groups, particularly over fronto-central and parieto-occipital regions. However, shape-color binding performance and their reduced neural correlates were similar between MCI and MCI-FAD. Our results support the validity of the VSTM binding test and their neural correlates in the early detection of AD and highlight the importance of studies comparing samples at different risk for AD conversion. The combined analysis of behavioral and ERP data gleaned with the VSTM binding task can offer a valuable memory biomarker for AD.

  14. Computation of Hemagglutinin Free Energy Difference by the Confinement Method

    Science.gov (United States)

    2017-01-01

    Hemagglutinin (HA) mediates membrane fusion, a crucial step during influenza virus cell entry. How many HAs are needed for this process is still subject to debate. To aid in this discussion, the confinement free energy method was used to calculate the conformational free energy difference between the extended intermediate and postfusion state of HA. Special care was taken to comply with the general guidelines for free energy calculations, thereby obtaining convergence and demonstrating reliability of the results. The energy that one HA trimer contributes to fusion was found to be 34.2 ± 3.4kBT, similar to the known contributions from other fusion proteins. Although computationally expensive, the technique used is a promising tool for the further energetic characterization of fusion protein mechanisms. Knowledge of the energetic contributions per protein, and of conserved residues that are crucial for fusion, aids in the development of fusion inhibitors for antiviral drugs. PMID:29151344

  15. Binding matrix: a novel approach for binding site recognition.

    Science.gov (United States)

    Kim, Jan T; Gewehr, Jan E; Martinetz, Thomas

    2004-06-01

    Recognition of protein-DNA binding sites in genomic sequences is a crucial step for discovering biological functions of genomic sequences. Explosive growth in availability of sequence information has resulted in a demand for binding site detection methods with high specificity. The motivation of the work presented here is to address this demand by a systematic approach based on Maximum Likelihood Estimation. A general framework is developed in which a large class of binding site detection methods can be described in a uniform and consistent way. Protein-DNA binding is determined by binding energy, which is an approximately linear function within the space of sequence words. All matrix based binding word detectors can be regarded as different linear classifiers which attempt to estimate the linear separation implied by the binding energy function. The standard approaches of consensus sequences and profile matrices are described using this framework. A maximum likelihood approach for determining this linear separation leads to a novel matrix type, called the binding matrix. The binding matrix is the most specific matrix based classifier which is consistent with the input set of known binding words. It achieves significant improvements in specificity compared to other matrices. This is demonstrated using 95 sets of experimentally determined binding words provided by the TRANSFAC database.

  16. Analysis of angiotensin II binding to human platelets: Differences in young and old subjects

    International Nuclear Information System (INIS)

    Siebers, M.J.; Goodfriend, T.L.; Ball, D.; Elliott, M.E.

    1990-01-01

    We examined the binding of radiolabeled angiotensin II (AII) to human platelets to characterize the apparent increase in AII receptors observed in older subjects. At 22 degrees C, the amount of radioactivity associated with platelets from older subjects increased continuously for more than 2 hours. The same amount of radioactivity was displaced by addition of unlabeled AII at 30 min and 60 min. In the presence of phenylarsine oxide, in the cold, or when labeled antagonist was the ligand, binding came to equilibrium by 30 min. High pressure liquid chromatography demonstrated that 125 I-AII was the major radioactive compound in the supernatant and platelets after incubation, but the platelets also contained radiolabeled AII fragments. Thus, some degradation accompanied interaction of AII and platelets. Phenylarsine oxide did not prevent degradation of bound AII, suggesting that degradation precedes internalization. On average, maximum binding was greater in older subjects whether platelets were incubated with 125 I-AII alone, with 125 I-AII and phenylarsine oxide to prevent internalization, or when the competitive inhibitor 125 I-sar1,ile8-AII was the radioligand. Variability of binding among subjects also increased with age. Thus, platelets bind, degrade, and internalize AII, and the three processes occur to a greater extent in platelets from some, but not all older subjects

  17. Electron binding energies of organic azides: Green’s function and density functional theory versus Hartree Fock calculations

    Science.gov (United States)

    Mateus, Margarida P. S.; Cabral, Benedito J. C.

    2007-11-01

    Theoretical calculations for the electron binding energies (EBEs) of several organic azides including hydrazoic acid, methyl azide, ethyl azide, 2-chloroethyl azide, 2-azidoethanol, azidoacetone, 2-azidoacetic acid, 3-azido-2-butanone, and 2-azidoethyl acetate are reported. EBEs were calculated with ab initio Green's function (GF) and density functional theory (DFT). Complete basis-set extrapolated coupled cluster calculations with single, double, and perturbative triple excitations [CCSD(T)] for the first ionization energy of azides are also reported. It is shown that EBEs from GF and DFT calculations are in better agreement with experiment than Hartree-Fock predictions.

  18. Charge transfer, lattice distortion, and quantum confinement effects in Pd, Cu, and Pd-Cu nanoparticles; size and alloying induced modifications in binding energy

    International Nuclear Information System (INIS)

    Sengar, Saurabh K.; Mehta, B. R.; Gupta, Govind

    2011-01-01

    In this letter, effect of size and alloying on the core and valence band shifts of Pd, Cu, and Pd-Cu alloy nanoparticles has been studied. It has been shown that the sign and magnitude of the binding energy shifts is determined by the contributions of different effects; with quantum confinement and lattice distortion effects overlapping for size induced shifts in case of core levels and lattice distortion and charge transfer effects overlapping for alloying induced shifts at smaller sizes. These results are important for understanding gas molecule-solid surface interaction in metal and alloy nanoparticles in terms of valance band positions.

  19. Energy and Environmental Performance of Bioethanol from Different Lignocelluloses

    Directory of Open Access Journals (Sweden)

    Lin Luo

    2010-01-01

    Full Text Available Climate change and the wish to reduce the dependence on oil are the incentives for the development of alternative energy sources. The use of lignocellulosic biomass together with cellulosic processing technology provides opportunities to produce fuel ethanol with less competition with food and nature. Many studies on energy analysis and life cycle assessment of second-generation bioethanol have been conducted. However, due to the different methodology used and different system boundary definition, it is difficult to compare their results. To permit a direct comparison of fuel ethanol from different lignocelluloses in terms of energy use and environmental impact, seven studies conducted in our group were summarized in this paper, where the same technologies were used to convert biomass to ethanol, the same system boundaries were defined, and the same allocation procedures were followed. A complete set of environmental impacts ranging from global warming potential to toxicity aspects is used. The results provide an overview on the energy efficiency and environmental performance of using fuel ethanol derived from different feedstocks in comparison with gasoline.

  20. Renewable Energy in the Baltic States. Different Situations

    International Nuclear Information System (INIS)

    Streimikiene, Dalia

    2007-01-01

    In many ways, the Baltic nations seem to be good students with ambitious objectives for applying European directives and the Kyoto Protocol. For example, in 2006, renewable energies already accounted for 9 % in Lithuania, 10 % in Estonia and 43 % in Latvia (5.2 % in the EU-15) of primary energy output. This should increase to 12 %, 15 % and 50 % in 2010 (12 % in the EU-15) respectively. While all are dependent on oil imports, their own resources vary: nuclear power in Lithuania (at least until 2009 when the last reactor of the Ignalina power station will close, with EU compensation), oil shale feeds Estonian power stations, wood in Latvia. The latter must import electricity while the two other countries produce double their domestic demand. All three are linked to the Russian power grid built up during the Soviet era rather than the European. Nevertheless, the share of renewable energy produced electricity is very small in these two producer countries, unlike Latvia which has hydraulic resources. The three countries have very different taxation on energy and electrical products, including renewable energy price support. All were granted transitional periods of differing lengths to apply European standard. The Baltic nations produce low greenhouse gas emissions and only Estonia has organized an emission rights trading market

  1. Diagnostic group differences in temporomandibular joint energy densities.

    Science.gov (United States)

    Gallo, L M; Iwasaki, L R; Gonzalez, Y M; Liu, H; Marx, D B; Nickel, J C

    2015-04-01

    Cartilage fatigue, due to mechanical work, may account for precocious development of degenerative joint disease in the temporomandibular joint (TMJ). This study compared energy densities (mJ/mm³) in TMJs of three diagnostic groups. Sixty-eight subjects (44 women, 24 men) gave informed consent. Diagnostic criteria for temporomandibular disorders (DC/TMD) and imaging were used to group subjects according to presence of jaw muscle or joint pain (+P) and bilateral disk displacement (+DD). Subjects (+P+DD, n=16; -P+DD, n=16; and -P-DD, n=36) provided cone-beam computed tomography and magnetic resonance images, and jaw-tracking data. Numerical modeling was used to determine TMJ loads (Fnormal). Dynamic stereometry was used to characterize individual-specific data of stress-field dynamics during 10 symmetrical jaw-closing cycles. These data were used to estimate tractional forces (Ftraction). Energy densities were then calculated as W/Q (W=work done or mechanical energy input=tractional force×distance of stress-field translation, Q=volume of cartilage). anova and Tukey-Kramer post hoc analyses tested for intergroup differences. Mean±standard error energy density for the +P+DD group was 12.7±1.5 mJ/mm³ and significantly greater (all adjusted p<0.04) when compared to -P+DD (7.4±1.4 mJ/mm³) and -P-DD (5.8±0.9 mJ/mm³) groups. Energy densities in -P+DD and -P-DD groups were not significantly different. Diagnostic group differences in energy densities suggest that mechanical work may be a unique mechanism, which contributes to cartilage fatigue in subjects with pain and disk displacement. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  2. Comparison of the kinetics of different Markov models for ligand binding under varying conditions

    Science.gov (United States)

    Martini, Johannes W. R.; Habeck, Michael

    2015-03-01

    We recently derived a Markov model for macromolecular ligand binding dynamics from few physical assumptions and showed that its stationary distribution is the grand canonical ensemble [J. W. R. Martini, M. Habeck, and M. Schlather, J. Math. Chem. 52, 665 (2014)]. The transition probabilities of the proposed Markov process define a particular Glauber dynamics and have some similarity to the Metropolis-Hastings algorithm. Here, we illustrate that this model is the stochastic analog of (pseudo) rate equations and the corresponding system of differential equations. Moreover, it can be viewed as a limiting case of general stochastic simulations of chemical kinetics. Thus, the model links stochastic and deterministic approaches as well as kinetics and equilibrium described by the grand canonical ensemble. We demonstrate that the family of transition matrices of our model, parameterized by temperature and ligand activity, generates ligand binding kinetics that respond to changes in these parameters in a qualitatively similar way as experimentally observed kinetics. In contrast, neither the Metropolis-Hastings algorithm nor the Glauber heat bath reflects changes in the external conditions correctly. Both converge rapidly to the stationary distribution, which is advantageous when the major interest is in the equilibrium state, but fail to describe the kinetics of ligand binding realistically. To simulate cellular processes that involve the reversible stochastic binding of multiple factors, our pseudo rate equation model should therefore be preferred to the Metropolis-Hastings algorithm and the Glauber heat bath, if the stationary distribution is not of only interest.

  3. Comparison of the kinetics of different Markov models for ligand binding under varying conditions

    International Nuclear Information System (INIS)

    Martini, Johannes W. R.; Habeck, Michael

    2015-01-01

    We recently derived a Markov model for macromolecular ligand binding dynamics from few physical assumptions and showed that its stationary distribution is the grand canonical ensemble [J. W. R. Martini, M. Habeck, and M. Schlather, J. Math. Chem. 52, 665 (2014)]. The transition probabilities of the proposed Markov process define a particular Glauber dynamics and have some similarity to the Metropolis-Hastings algorithm. Here, we illustrate that this model is the stochastic analog of (pseudo) rate equations and the corresponding system of differential equations. Moreover, it can be viewed as a limiting case of general stochastic simulations of chemical kinetics. Thus, the model links stochastic and deterministic approaches as well as kinetics and equilibrium described by the grand canonical ensemble. We demonstrate that the family of transition matrices of our model, parameterized by temperature and ligand activity, generates ligand binding kinetics that respond to changes in these parameters in a qualitatively similar way as experimentally observed kinetics. In contrast, neither the Metropolis-Hastings algorithm nor the Glauber heat bath reflects changes in the external conditions correctly. Both converge rapidly to the stationary distribution, which is advantageous when the major interest is in the equilibrium state, but fail to describe the kinetics of ligand binding realistically. To simulate cellular processes that involve the reversible stochastic binding of multiple factors, our pseudo rate equation model should therefore be preferred to the Metropolis-Hastings algorithm and the Glauber heat bath, if the stationary distribution is not of only interest

  4. Ligand binding and thermostability of different allosteric states of the insulin zinc-hexamer

    DEFF Research Database (Denmark)

    Huus, Kasper; Havelund, Svend; Olsen, Helle B

    2006-01-01

    The influence of ligand binding and conformation state on the thermostability of hexameric zinc-insulin was studied by differential scanning calorimetry (DSC). The insulin hexamer exists in equilibrium between the forms T6, T3R3, and R6. Phenolic ligands induce and stabilize the T3R3- and R6-stat...

  5. Different types of working memory binding in epilepsy patients with unilateral anterior temporal lobectomy

    NARCIS (Netherlands)

    Geldorp, B. van; Bouman, Z.; Hendriks, M.; Kessels, R.P.C.

    2014-01-01

    The medial temporal lobe is an important structure for long-term memory formation, but its role in working memory is less clear. Recent studies have shown hippocampal involvement during working memory tasks requiring binding of information. It is yet unclear whether this is limited to tasks

  6. New insights into structure and function of the different types of fatty acid-binding protein

    NARCIS (Netherlands)

    Zimmerman, Augusta Wilhelmina

    2002-01-01

    Fatty acid binding proteins (FABPs) are small cytosolic proteins with virtually identical backbone structures that facilitate the solubility and intracellular transport of fatty acids. They may also modulate the effect of fatty acids on various metabolic enzymes and receptors and on cellular

  7. Longitudinal Investigation of Source Memory Reveals Different Developmental Trajectories for Item Memory and Binding

    Science.gov (United States)

    Riggins, Tracy

    2014-01-01

    The present study used a cohort-sequential design to examine developmental changes in children's ability to bind items in memory during early and middle childhood. Three cohorts of children (aged 4, 6, or 8 years) were followed longitudinally for 3 years. Each year, children completed a source memory paradigm assessing memory for items and…

  8. Optimal portfolio selection between different kinds of Renewable energy sources

    Energy Technology Data Exchange (ETDEWEB)

    Zakerinia, MohammadSaleh; Piltan, Mehdi; Ghaderi, Farid

    2010-09-15

    In this paper, selection of the optimal energy supply system in an industrial unit is taken into consideration. This study takes environmental, economical and social parameters into consideration in modeling along with technical factors. Several alternatives which include renewable energy sources, micro-CHP systems and conventional system has been compared by means of an integrated model of linear programming and three multi-criteria approaches (AHP, TOPSIS and ELECTRE III). New parameters like availability of sources, fuels' price volatility, besides traditional factors are considered in different scenarios. Results show with environmental preferences, renewable sources and micro-CHP are good alternatives for conventional systems.

  9. On the atomic-number similarity of the binding energies of electrons in filled shells of elements of the periodic table

    Science.gov (United States)

    Karpov, V. Ya.; Shpatakovskaya, G. V.

    2017-03-01

    An expression for the binding energies of electrons in the ground state of an atom is derived on the basis of the Bohr-Sommerfeld quantization rule within the Thomas-Fermi model. The validity of this relation for all elements from neon to uranium is tested within a more perfect quantum-mechanical model with and without the inclusion of relativistic effects, as well as with experimental binding energies. As a result, the ordering of electronic levels in filled atomic shells is established, manifested in an approximate atomic-number similarity. It is proposed to use this scaling property to analytically estimate the binding energies of electrons in an arbitrary atom.

  10. Identification of potential inhibitors of Fasciola gigantica thioredoxin1: computational screening, molecular dynamics simulation, and binding free energy studies.

    Science.gov (United States)

    Shukla, Rohit; Shukla, Harish; Kalita, Parismita; Sonkar, Amit; Pandey, Tripti; Singh, Dev Bukhsh; Kumar, Awanish; Tripathi, Timir

    2017-07-04

    Fasciola gigantica is the causative organism of fascioliasis and is responsible for major economic losses in livestock production globally. F. gigantica thioredoxin1 (FgTrx1) is an important redox-active enzyme involved in maintaining the redox homeostasis in the cell. To identify a potential anti-fasciolid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,67,740) against the FgTrx1 structure. The ligands were docked against FgTrx1 and 309 ligands were found to have better docking score. These compounds were evaluated for Lipinski and ADMET prediction, and 30 compounds were found to fit well for re-docking studies. After refinement by molecular docking and drug-likeness analysis, three potential inhibitors (ZINC15970091, ZINC9312362, and ZINC9312661) were identified. These three ligands were further subjected to molecular dynamics simulation (MDS) to compare the dynamics and stability of the protein structure after binding of the ligands. The binding free energy analyses were calculated to determine the intermolecular interactions. The results suggested that the two compounds had a binding free energy of -82.237, and -109.52 kJ.mol -1 for compounds with IDs ZINC9312362 and ZINC9312661, respectively. These predicted compounds displayed considerable pharmacological and structural properties to be drug candidates. We concluded that these two compounds could be potential drug candidates to fight against F. gigantica parasites.

  11. Binding energies and structures of Ca-He2 weakly bound triatomic complexes

    Science.gov (United States)

    López-Durán, David; Rodríguez-Cantano, Rocío; González-Lezana, Tomás; Delgado-Barrio, Gerardo; Villarreal, Pablo; Gianturco, Franco A.

    2012-08-01

    Bound states of 40Ca-nHe2, n=3,4, triatomic complexes are investigated. The potential-energy surface, represented as the addition of atomic-pair interactions, is that recently used to study these systems by Gou and Li, Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.85.012510 85, 012510 (2012). The results obtained from three different methods, in fair agreement, profoundly disagree with those reported in the reference above. In addition, we address the feasibility of two Ca-He interactions existing in the literature by analyzing the characteristics of their ground and excited vibrorotational states. To this end, simulated absorption spectra in the region of microwaves are also presented and discussed.

  12. Oligomerization domains in the glycan-binding receptors DC-SIGN and DC-SIGNR: Sequence variation and stability differences.

    Science.gov (United States)

    Dos Santos, Ália; Hadjivasiliou, Andreas; Ossa, Felipe; Lim, Novandy K; Turgut, Aylin; Taylor, Maureen E; Drickamer, Kurt

    2017-02-01

    Human dendritic cell-specific intercellular adhesion molecule-1 grabbing nonintegrin, DC-SIGN, and the sinusoidal endothelial cell receptor DC-SIGNR or L-SIGN, are closely related sugar-binding receptors. DC-SIGN acts both as a pathogen-binding endocytic receptor and as a cell adhesion molecule, while DC-SIGNR has only the pathogen-binding function. In addition to differences in the sugar-binding properties of the carbohydrate-recognition domains in the two receptors, there are sequence differences in the adjacent neck domains, which are coiled-coil tetramerization domains comprised largely of 23-amino acid repeat units. A series of model polypeptides consisting of uniform repeat units have been characterized by gel filtration, differential scanning calorimetry and circular dichroism. The results demonstrate that two features characterize repeat units which form more stable tetramers: a leucine reside in the first position of the heptad pattern of hydrophobic residues that pack on the inside of the coiled coil and an arginine residue on the surface of the coiled coil that forms a salt bridge with a glutamic acid residue in the same polypeptide chain. In DC-SIGNR from all primates, very stable repeat units predominate, so the carbohydrate-recognition domains must be held relatively closely together. In contrast, stable repeat units are found only near the membrane in DC-SIGN. The presence of residues that disrupt tetramer formation in repeat units near the carbohydrate-recognition domains of DC-SIGN would allow these domains to splay further apart. Thus, the neck domains of DC-SIGN and DC-SIGNR can contribute to the different functions of these receptors by presenting the sugar-binding sites in different contexts. © 2016 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  13. Regional energy consumption and income differences in Denmark

    DEFF Research Database (Denmark)

    Klinge Jacobsen, Henrik

    2003-01-01

    documents that rural populations have higher energy bills also compared to income, but there is no income inequality between rural and urban areas in Denmark. In countries with higher inequality in income distribution and a higher proportion of low-income households in rural areas, the impact of energy...... and transport taxes might be more uneven. In such cases, the environmental tax structure should compensate the low-income rural households. For countries with a high proportion of low-income households living in urban areas and little income inequality, this issue might, as in the Danish case, not be a problem......Internationally a debate on the distributional impact of energy taxation has focused on the tax burden relative to income. The general conclusion is that taxes are regressive, but at a varying degree for different countries. This study examines the relationship between location, income, heating...

  14. A Smarter Grid for Renewable Energy: Different States of Action

    Directory of Open Access Journals (Sweden)

    Clark Koenigs

    2013-11-01

    Full Text Available Smart grid has strong potential to advance and encourage renewable energy deployment, but given the multiple motivations for smart grid, renewables are not always central in smart grid policy discussions. The term “smart grid” represents a set of technologies, including advanced meters, sensors and energy storage that are crucial for the integration of more renewable and low carbon electricity into the electric power grid. However, developing and building a smart grid is jurisdictionally complex, path dependent and context specific; states and regions are approaching grid modernization in different ways. This paper reports on a comparative analysis of smart grid development in seven U.S. states. We use state-level policy documents to learn what motivates smart grid development and how smart grid is framed in relation to renewable energy. In some states, renewable technologies are presented as an integral part of the smart grid policy discussion, while in others they are largely absent.

  15. Energy behavior of solar hot water systems under different conditions

    International Nuclear Information System (INIS)

    Fuentes Lombá, Osmanys; Torres Ten, Alonso; Arzuaga Machado, Yusnel; Hernández, Massipe J. Raúl; Cueva Gonzales, Wagner

    2017-01-01

    By means of numerical simulations in TRNSYS v14 the influence of the solar absorption area of a system for heating water with solar energy, composed by a flat solar collector and a tank thermo-accumulator, on its energy efficiency. For the study, the solar collectors EDWARDS, ISOFOTÓN 1, ISOFOTÓN 2, MADE, ROLDAN and IBERSOLAR of absorption area 2, 1,9, 1,88, 2, 1,9 and 2,3 m2 respectively were chosen. For each collector, the energy performance was simulated for one year, setting 200 L for the accumulation volume and 50 °C for the intake temperature. Despite the different characteristics of each collector, their behavior is quite similar showing a very mature technology. (author)

  16. Ions in size-selected aqueous nanodrops: sequential water molecule binding energies and effects of water on ion fluorescence.

    Science.gov (United States)

    Donald, William A; Leib, Ryan D; Demireva, Maria; Williams, Evan R

    2011-11-23

    The effects of water on ion fluorescence were investigated, and average sequential water molecule binding energies to hydrated ions, M(z)(H(2)O)(n), at large cluster size were measured using ion nanocalorimetry. Upon 248-nm excitation, nanodrops with ~25 or more water molecules that contain either rhodamine 590(+), rhodamine 640(+), or Ce(3+) emit a photon with average energies of approximately 548, 590, and 348 nm, respectively. These values are very close to the emission maxima of the corresponding ions in solution, indicating that the photophysical properties of these ions in the nanodrops approach those of the fully hydrated ions at relatively small cluster size. As occurs in solution, these ions in nanodrops with 8 or more water molecules fluoresce with a quantum yield of ~1. Ce(3+) containing nanodrops that also contain OH(-) fluoresce, whereas those with NO(3)(-) do not. This indirect fluorescence detection method has the advantages of high sensitivity, and both the size of the nanodrops as well as their constituents can be carefully controlled. For ions that do not fluoresce in solution, such as protonated tryptophan, full internal conversion of the absorbed 248-nm photon occurs, and the average sequential water molecule binding energies to the hydrated ions can be accurately obtained at large cluster sizes. The average sequential water molecule binding energies for TrpH(+)(H(2)O)(n) and a doubly protonated tripeptide, [KYK + 2H](2+)(H(2)O)(n), approach asymptotic values of ~9.3 (n ≥ 11) and ~10.0 kcal/mol (n ≥ 25), respectively, consistent with a liquidlike structure of water in these nanodrops.

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

    Science.gov (United States)

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

    2018-01-01

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

  18. 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.

  19. Colloquium on the risks of different energy sources

    International Nuclear Information System (INIS)

    1980-01-01

    Four subjects, each taking up one session, were dealt with in this Colloquium. The first is the definition of the health risk concept which is only obvious on the surface. It was shown how within the medical world itself, apparently the most competent to discover and evaluate these risks, this definition is still approximate both in theory and in practice. The second theme dealt with concerns the way in which risks are viewed by the general public. By a psychological and sociological approach it is possible to form an idea of how differently opinion reacts to risks of similar gravity and probability. The apprehension of risks and the opposition to nuclear energy were analysed in detail in this session. The third subject, more analytical and probably one of the most topical is concerned with the inventory of risks due to each industrial energy sector. This session was in two parts, the first devoted to problems specific to each source of energy including nuclear, the second to common problems (pollution of air, fresh water and sea water, and long-term effects (nuclear wastes for example). The fourth and last session dealt with a fundamental problem, methods of studying these risks. The conclusions of different enquiries are always very similar: the energy source hierarchy, in order of diminishing risks, is as follows: coal, liquid hydrocarbons, nuclear and gaseous hydrocarbons [fr

  20. Forskolin- and dihydroalprenolol (DHA) binding sites and adenylate cyclase activity in heart of rats fed diets containing different oils

    International Nuclear Information System (INIS)

    Alam, S.Q.; Ren, Y.F.; Alam, B.S.

    1987-01-01

    The purpose of the present investigation was to determine if dietary lipids can induce changes in the adenylate cyclase system in rat heart. Three groups of male young Sprague-Dawley rats were fed for 6 weeks diets containing 10% corn oil (I), 8% coconut oil + 2% corn oil (II) or 10% menhaden oil (III). Adenylate cyclase activity (basal, fluoride-, isoproterenol-, and forskolin-stimulated) was higher in heart homogenates of rats in group III than in the other two groups. Concentration of the [ 3 H]-forskolin binding sites in the cardiac membranes were significantly higher in rats fed menhaden oil. The values (pmol/mg protein) were 4.8 +/- 0.2 (I), 4.5 +/- 0.7 (II) and 8.4 +/- 0.5 (III). There was no significant difference in the affinity of the forskolin binding sites among the 3 dietary groups. When measured at different concentrations of forskolin, the adenylate cyclase activity in cardiac membranes of rats fed menhaden oil was higher than in the other 2 groups. Concentrations of the [ 3 H]DHA binding sites were slightly higher but their affinity was lower in cardiac membranes of rats fed menhaden oil. The results suggest that diets containing fish oil increase the concentration of the forskolin binding sites and may also affect the characteristics of the β-adrenergic receptor in rat heart

  1. Halide Binding and Inhibition of Laccase Copper Clusters: The Role of Reorganization Energy

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2015-01-01

    complicate characterization. Understanding these processes at the molecular level is thus desirable but theoretically unexplored. This paper reports systematic calculations of geometries, reorganization energies, and ionization energies for all partly oxidized states of the trinuclear copper clusters...

  2. Energy and environmental consciousness. Differences between advanced and developing countries

    International Nuclear Information System (INIS)

    Takeshita, Takashi

    1999-01-01

    The purpose of the present study is to understand how much differences there are between advanced countries and developing countries in terms of environmental and energy consciousness. We are experiencing now a big dilemma of the human desire to continue to exist and, at the same time, to develop the economy against the worsening of the Earth's environmental conditions. Understanding international differences of environmental and energy consciousness is a short way to solve this dilemma. The results of the present study were that peoples from advanced countries feel that science and technology are sometimes unreliable, while those from developing countries, are willing to rely upon them. However regardless of the country, people share the same consciousness about Earth's environment. In both, advanced and developing countries, people are reluctant to give up living comforts, unless this leads to a higher standard of living. Based on this result, the author would like to conduct another survey concerning the consciousness of future lifestyle. (author)

  3. Structure-Based Inhibitor Design for an Enzyme That Binds Different Steriods

    Energy Technology Data Exchange (ETDEWEB)

    Qiu,W.; Zhou, M.; Mazumdar, M.; Azzi, A.; Ghanmi, D.; Luu-The, V.; Labrie, F.; Lin, S.

    2007-01-01

    Human type 5 17{beta}-hydroxysteroid dehydrogenase plays a crucial role in local androgen formation in prostate tissue. Several chemicals were synthesized and tested for their ability to inhibit this enzyme, and a series of estradiol derivatives bearing a lactone on the D-ring were found to inhibit its activity efficiently. The crystal structure of the type 5 enzyme in complex with NADP and such a novel inhibitor, EM1404, was determined to a resolution of 1.30 {angstrom}. Significantly more hydrogen bonding and hydrophobic interactions were defined between EM1404 and the enzyme than in the substrate ternary complex. The lactone ring of EM1404 accounts for important interactions with the enzyme, whereas the amide group at the opposite end of the inhibitor contributes to the stability of three protein loops involved in the construction of the substrate binding site. EM1404 has a strong competitive inhibition, with a K{sub i} of 6.9 {+-} 1.4 nM, demonstrating 40 times higher affinity than that of the best inhibitor previously reported. This is observed despite the fact that the inhibitor occupies only part of the binding cavity. Attempts to soak the inhibitor into crystals of the binary complex with NADP were unsuccessful, yielding a structure with a polyethylene glycol fragment occupying the substrate binding site. The relative crystal packing is discussed. Combined studies of small molecule inhibitor synthesis, x-ray crystallography, enzyme inhibition, and molecular modeling make it possible to analyze the plasticity of the substrate binding site of the enzyme, which is essential for developing more potent and specific inhibitors for hormone-dependent cancer therapy.

  4. Partitioning of metals in different binding phases of tropical estuarine sediments: importance of metal chemistry

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, P.; Chakraborty, S.; Vudamala, K.; Sarkar, Arindam; Nath, B.N.

    binding phases of tropical estuarine sediments. Materials and Methods: Study area: The sediment samples were collected from the Vembanad Lake in Kerala, west coast of India. It is the longest (stretching about 90 km) and largest brackish-water lake... of the European Communities. International journal of environmental analytical chemistry, 51(1-4), 135-151. Verma, A., & Subramanian, V. (2002). Organic matter and amino acid concentrations in surface sediments of Vembanad Lake–a tropical estuary, west coast...

  5. Analogues of doxanthrine reveal differences between the dopamine D 1 receptor binding properties of chromanoisoquinolines and hexahydrobenzo[a]phenanthridines

    Science.gov (United States)

    Cueva, J.P.; Chemel, B.R.; Juncosa, J.I.; Lill, M.A.; Watts, V.J.; Nichols, D.E.

    2012-01-01

    Efforts to develop selective agonists for dopamine D 1-like receptors led to the discovery of dihydrexidine and doxanthrine, two bioisosteric ??-phenyldopamine-type full agonist ligands that display selectivity and potency at D 1-like receptors. We report herein an improved methodology for the synthesis of substituted chromanoisoquinolines (doxanthrine derivatives) and the evaluation of several new compounds for their ability to bind to D 1- and D 2-like receptors. Identical pendant phenyl ring substitutions on the dihydrexidine and doxanthrine templates surprisingly led to different effects on D 1-like receptor binding, suggesting important differences between the interactions of these ligands with the D 1 receptor. We propose, based on the biological results and molecular modeling studies, that slight conformational differences between the tetralin and chroman-based compounds lead to a shift in the location of the pendant ring substituents within the receptor. ?? 2011 Elsevier Ltd. All rights reserved.

  6. Environmental evaluation of different forms of electric energy generation

    International Nuclear Information System (INIS)

    Guena, Ana Maria de Oliveira

    2007-01-01

    Electric energy has an important function in the modem world; it is fundamental for progress and development. The electricity discovery allowed improvements in several areas: health, water and food supply, quality of life and sanitary conditions, and contributed also to the establishment of the capitalist and consumption society. The use of oil as an energy generation source was the impulse for the industrial revolution and machines, motors and generators were developed contributing to the progress This also brought the pollutant gases emission (CO 2 , CO, SO x and NO x ) and other substances that had contributed to the greenhouse effect, the ozone hole and the acid rain, modifying the balance of the planet. The development and implementation of other forms of energy generation caused local changes, where they were installed, giving rise to environmental impacts. This work presents an evaluation about different forms of electrical energy generation and the environmental impacts relative to each one of them. Five forms of electric energy generation were considered: thermoelectric, nuclear, hydroelectric, wind and solar energy. The implementation and the development of the petroleum industry in the world and in Brazil are presented. The geology of the oil, its extraction and quality improvement, besides details of the functioning of three types of thermoelectric power plants - coal, gas and oil - are also discussed. The specific as well as the environmental impacts they have in common are highlighted. The impacts originated from the deactivation of each one of them are also pointed out. The discovery and the development of nuclear energy in Brazil and in the world as well as the functioning of a nuclear power plant, the impacts generated by its operation and decommissioning are presented. The history, functioning and development of hydroelectric energy generation in Brazil, characterized by the great plants, are related to environmental aspects The environmental

  7. In vitro binding of [³H]PIB to human amyloid deposits of different types.

    Science.gov (United States)

    Hellström-Lindahl, Ewa; Westermark, Per; Antoni, Gunnar; Estrada, Sergio

    2014-03-01

    Systemic amyloidosis is caused by extracellular deposition of insoluble fibrillar proteins arranged in β-pleated sheets. [(11)C]PIB has been used in PET studies to assess Aβ deposition in brain of patients with Alzheimer's disease (AD). The possibility to visualize other types of amyloid deposits with [(11)C]PIB would be of potential clinical importance in early diagnosis and for following therapeutic effects. In the present study, we evaluated in vitro binding of [(3)H]PIB to tissues containing transthyretin (ATTR), immunoglobulin light-chain (AL), amyloid protein A (AA) and Aβ amyloid. We found significantly higher binding of [(3)H]PIB in tissue from systemic amyloidoses than in control tissue, i.e. 4.7 times higher (p PIB showed the highest affinity to cortex of AD brain (IC50 = 3.84 nM), while IC50 values were much higher for ATTR, AA and AL type of amyloidosis and large variations in affinity were observed even within tissues having the same type of amyloidosis. Extraction with guanidine-HCl, which disrupts the β-sheet structure, decreased the protein levels and, concomitantly, the binding of [(3)H]PIB in all four types of amyloidoses.

  8. Roles of binding energy and diffusion length of singlet and triplet excitons in organic heterojunction solar cells

    International Nuclear Information System (INIS)

    Narayan, Monishka Rita; Singh, Jai

    2012-01-01

    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.)

  9. 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.)

  10. Crystallography aided by atomic core-level binding energies: proton transfer versus hydrogen bonding in organic crystal structures.

    Science.gov (United States)

    Stevens, Joanna S; Byard, Stephen J; Seaton, Colin C; Sadiq, Ghazala; Davey, Roger J; Schroeder, Sven L M

    2011-10-10

    Ionic bond or hydrogen bridge? Brønsted proton transfer to nitrogen acceptors in organic crystals causes strong N1s core-level binding energy shifts. A study of 15 organic cocrystal and salt systems shows that standard X-ray photoelectron spectroscopy (XPS) can be used as a complementary method to X-ray crystallography for distinguishing proton transfer from H-bonding in organic condensed matter. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. 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.

  12. Amine-hydrogen halide complexes: experimental electric dipole moments and a theoretical decomposition of dipole moments and binding energies.

    Science.gov (United States)

    Brauer, Carolyn S; Craddock, Matthew B; Kilian, Jacob; Grumstrup, Erik M; Orilall, M Christopher; Mo, Yirong; Gao, Jiali; Leopold, Kenneth R

    2006-08-24

    The Stark effect has been observed in the rotational spectra of several gas-phase amine-hydrogen halide complexes and the following electric dipole moments have been determined: H(3)(15)N-H(35)Cl (4.05865 +/- 0.00095 D), (CH(3))(3)(15)N-H(35)Cl (7.128 +/- 0.012 D), H(3)(15)N-H(79)Br (4.2577 +/- 0.0022 D), and (CH(3))(3)(15)N-H(79)Br (8.397 +/- 0.014 D). Calculations of the binding energies and electric dipole moments for the full set of complexes R(n)()(CH(3))(3)(-)(n)()N-HX (n = 0-3; X = F, Cl, Br) at the MP2/aug-cc-pVDZ level are also reported. The block localized wave function (BLW) energy decomposition method has been used to partition the binding energies into contributions from electrostatic, exchange, distortion, polarization, and charge-transfer terms. Similarly, the calculated dipole moments have been decomposed into distortion, polarization, and charge-transfer components. The complexes studied range from hydrogen-bonded systems to proton-transferred ion pairs, and the total interaction energies vary from 7 to 17 kcal/mol across the series. The individual energy components show a much wider variation than this, but cancellation of terms accounts for the relatively narrow range of net binding energies. For both the hydrogen-bonded complexes and the proton-transferred ion pairs, the electrostatic and exchange terms have magnitudes that increase with the degree of proton transfer but are of opposite sign, leaving most of the net stabilization to arise from polarization and charge transfer. In all of the systems studied, the polarization terms contribute the most to the induced dipole moment, followed by smaller but still significant contributions from charge transfer. A significant contribution to the induced moment of the ion pairs also arises from distortion of the HX monomer.

  13. Analysis of Energy Demand for Low-Energy Multi-Dwelling Buildings of Different Configuration

    Directory of Open Access Journals (Sweden)

    Giedrė Streckienė

    2014-10-01

    Full Text Available To meet the goals established by Directive 2010/31/EU of the European Parliament and of the Council on the energy performance of buildings, the topics of energy efficiency in new and old buildings must be solved. Research and development of new energy solutions and technology are necessary for increasing energy performance of buildings. Three low-energy multi-dwelling buildings have been modelled and analyzed in the presented study. All multi-dwelling houses are made of similar single-family house cells. However, multi-dwelling buildings are of different geometry, flat number and height. DesignBuilder software was used for simulating and determining heating, cooling and electricity demand for buildings. Three different materials (silicate, ceramic and clay concrete blocks as bearing constructions of external walls have been analyzed. To decrease cooling demand for buildings, the possibility of mounting internal or external louvers has been considered. Primary energy savings for multi-dwelling buildings using passive solar measures have been determined.

  14. Full energy chain analysis of greenhouse gas emissions from different energy sources

    International Nuclear Information System (INIS)

    Vate, J.F. van de

    1996-01-01

    The field of work of the Advisory Group Meeting/Workshop, i.e. full-energy chain emissions of greenhouse gases, is defined, and its environment, i.e. the Earth Summit -the 1992 UN Conference on Environment and Development in Rio-, is discussed. It is inferred that countries that ratified the Earth Summit's Convention on Climate Change have committed themselves to lower the greenhouse gas emissions from their energy use, and that this can be done most effectively by accounting in energy planning for the full-energy chain emissions of all greenhouse gases. The scatter in literature values of greenhouse gas emission factors of the full energy chain of individual energy sources is discussed. The scatter among others is due to different analytical methods, data bases and system boundaries, and due to neglect of the non-CO 2 greenhouse gases and professional biases. Generic values for greenhouse gas emission factors of energy and materials use are proposed. (author). 10 refs, 2 tabs

  15. Ligand-induced structural changes in TEM-1 probed by molecular dynamics and relative binding free energy calculations.

    Science.gov (United States)

    Pimenta, A C; Martins, J M; Fernandes, R; Moreira, I S

    2013-10-28

    The TEM family of enzymes has had a crucial impact on the pharmaceutical industry due to their important role in antibiotic resistance. Even with the latest technologies in structural biology and genomics, no 3D structure of a TEM-1/antibiotic complex is known previous to acylation. Therefore, the comprehension of their capability in acylate antibiotics is based on the protein macromolecular structure uncomplexed. In this work, molecular docking, molecular dynamic simulations, and relative free energy calculations were applied in order to get a comprehensive and thorough analysis of TEM-1/ampicillin and TEM-1/amoxicillin complexes. We described the complexes and analyzed the effect of ligand binding on the overall structure. We clearly demonstrate that the key residues involved in the stability of the ligand (hot-spots) vary with the nature of the ligand. Structural effects such as (i) the distances between interfacial residues (Ser70-Oγ and Lys73-Nζ, Lys73-Nζ and Ser130-Oγ, and Ser70-Oγ-Ser130-Oγ), (ii) side chain rotamer variation (Tyr105 and Glu240), and (iii) the presence of conserved waters can be also influenced by ligand binding. This study supports the hypothesis that TEM-1 suffers structural modifications upon ligand binding.

  16. Differences in energy capacities between tennis players and runners.

    Science.gov (United States)

    Novak, Dario; Vucetić, Vlatko; Zugaj, Sanja

    2013-05-01

    The primary purpose of this study was to determine differences between elite athletes and tennis players in order to provide a clearer picture regarding the energy demands in modern tennis. Forty-eight (48) athletes and 24 tennis players from Croatian national leagues were compared in morphological and physiological parameters of an all-out incremental treadmill test with gas exchange measurements. Tennis players' HRmax (192.96+/-7.75 bpm) shows values that are most different to 400-meters sprinters (200.13+/-6.95 bpm). Maximum running speed of tennis players on the treadmill (vmax) is no different with the speed achieved by sprinters, while there are significant differences among other athletes. Values in running speed at anaerobic threshold (vAnT) show no statistically significant difference with the values for athlete sprinters and 400-m sprinters. Values of RvO2max for tennis players indicate significant similarities with athlete sprinters and 400-m sprinters while the values of RvO2AnT are nearly identical with the values for sprinters and show no statistically significant differences (p<0.05). The results indicate that values achieved by tennis players approximate most different those of the middle and long distance runners. This singles out the possible importance of the anaerobic capacity and the high level of sprint endurance in tennis players. Knowing these characteristics is the basis for planning and implementing training systems that will enable the increase and optimal usage of energy capacities of tennis players in possibly improving sports results.

  17. Structure of production costs of different energy sources (fossile fuels and nuclear energy) (group 11)

    International Nuclear Information System (INIS)

    Girard, Ph.

    2002-01-01

    This article is the work of a group of students from the ''Ecole Nationale d'Administration'', they had to study the structure of the costs of the different energy sources. This analysis shows some common features between the energy sources. The cost is very dependent on the partial costs of technological constraints due to exploration, production, transport and distribution. For primary energies the market appears to be not very competitive, the price depends strongly on the market power of the operator and benefits are generally important. In France, taxes play a role to assure competitiveness of gas and coal against oil. Uranium fuel presents the lowest production and transformation costs at the same energy content. Transport costs are important for natural gas which implies a strong mutual dependence between gas producers and consumers. The irreplaceable use of oil in transport assures regular high revenues for oil companies. (A.C.)

  18. Sex differences in obesity and the regulation of energy homeostasis.

    Science.gov (United States)

    Lovejoy, J C; Sainsbury, A

    2009-03-01

    Obesity prevalence is generally higher in women than in men, and there is also a sex difference in body fat distribution. Sex differences in obesity can be explained in part by the influence of gonadal steroids on body composition and appetite; however, behavioural, socio-cultural and chromosomal factors may also play a role. This review, which evolved from the 2008 Stock Conference on sex differences in obesity, summarizes current research and recommendations related to hormonal and neuroendocrine influences on energy balance and fat distribution. A number of important gaps in the research are identified, including a need for more studies on chromosomal sex effects on energy balance, the role of socio-cultural (i.e. gender) factors in obesity and the potential deleterious effects of high-fat diets during pregnancy on the foetus. Furthermore, there is a paucity of clinical trials examining sex-specific approaches and outcomes of obesity treatment (lifestyle-based or pharmacological), and research is urgently needed to determine whether current weight loss programmes, largely developed and tested on women, are appropriate for men. Last, it is important that both animal and clinical research on obesity be designed and analysed in such a way that data can be separately examined in both men and women.

  19. Communication: Towards the binding energy and vibrational red shift of the simplest organic hydrogen bond: Harmonic constraints for methanol dimer

    International Nuclear Information System (INIS)

    Heger, Matthias; Suhm, Martin A.; Mata, Ricardo A.

    2014-01-01

    The discrepancy between experimental and harmonically predicted shifts of the OH stretching fundamental of methanol upon hydrogen bonding to a second methanol unit is too large to be blamed mostly on diagonal and off-diagonal anharmonicity corrections. It is shown that a decisive contribution comes from post-MP2 electron correlation effects, which appear not to be captured by any of the popular density functionals. We also identify that the major deficiency is in the description of the donor OH bond. Together with estimates for the electronic and harmonically zero-point corrected dimer binding energies, this work provides essential constraints for a quantitative description of this simple hydrogen bond. The spectroscopic dissociation energy is predicted to be larger than 18 kJ/mol and the harmonic OH-stretching fundamental shifts by about −121 cm −1 upon dimerization, somewhat more than in the anharmonic experiment (−111 cm −1 )

  20. Calculating the Na⁺ translocating V-ATPase catalytic site affinity for substrate binding by homology modeled NtpA monomer using molecular dynamics/free energy calculation.

    Science.gov (United States)

    Muhammed, Zahed; Arai, Satoshi; Saijo, Shinya; Yamato, Ichiro; Murata, Takeshi; Suenaga, Atsushi

    2012-07-01

    Vacuolar ATPase (V-ATPase) of Enterococcus hirae is composed of a soluble catalytic domain (V₁; NtpA₃-B₃-D-G) and an integral membrane domain (V₀; NtpI-K₁₀) connected by a central and two peripheral stalks (NtpC, NtpD-G and NtpE-F). Recently nucleotide binding of catalytic NtpA monomer has been reported (Arai et al.). In the present study, we calculated the nucleotide binding affinity of NtpA by molecular dynamics (MD) simulation/free energy calculation using MM-GBSA approach based on homology modeled structure of NtpA monomer docked with ATP analogue, adenosine 5'-[β, γ-imido] triphosphate (AMP-PNP). The calculated binding free energies showed qualitatively good agreement with experimental data. The calculation was cross-validated further by the rigorous method, thermodynamic integration (TI) simulation. Finally, the interaction between NtpA and nucleotides at the atomic level was investigated by the analyses of components of free energy and the optimized model structures obtained from MD simulations, suggesting that electrostatic contribution is responsible for the difference in nucleotide binding to NtpA monomer. This is the first observation and suggestion to explain the difference of nucleotide binding properties in V-ATPase NtpA subunit, and our method can be a valuable primary step to predict nucleotide binding affinity to other subunits (NtpAB, NtpA₃B₃) and to explore subunit interactions and eventually may help to understand energy transduction mechanism of E. hirae V-ATPase. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Testing and evaluation of different energy storage devices for piezoelectric energy harvesting under road conditions

    Science.gov (United States)

    Gopalakrishnan, Pratheek

    The increasing needs in green technology have propelled the rapid development in energy conversion and the advancement of electric energy storage systems. A viable storage technology is needed to store intermittent electrical energy in different electronic applications. In this thesis, recent progress on the chemistry and design of batteries is summarized with their challenges and improvements. Along with that, electrolytic capacitors are also reviewed with their types, advantages and disadvantages of each in short. Super capacitors having higher surface area and thinner dielectrics than conventional capacitors along with hybrid capacitors, are discussed in detail. The potential of a hybrid capacitor, Ni(OH)2/ Active Carbon, compared with Ni-Cd batteries and electrolytic capacitors in the application of energy storage for high way energy harvesting has been explored in this work. Both the battery and the hybrid capacitor has been tested under various experimental conditions and their properties in relation to their chemical compositions are compared. The results obtained from the experiments have been analyzed and the most suitable energy storage devices have been selected with their application potential evaluated before drawing conclusion reported in this thesis.

  2. A cation-π interaction at a phenylalanine residue in the glycine receptor binding site is conserved for different agonists

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Hanek, Ariele P; Price, Kerry L

    2011-01-01

    . In the current study, we investigated whether the lower efficacy agonists of the human GlyR β-alanine and taurine also form cation-π interactions with Phe159. By incorporating a series of unnatural amino acids, we found cation-π interactions between Phe159 and the amino groups of β-alanine and taurine....... The strengths of these interactions were significantly weaker than for glycine. Modeling studies suggest that β-alanine and taurine are orientated subtly differently in the binding pocket, with their amino groups further from Phe159 than that of glycine. These data therefore show that similar agonists can have...... similar but not identical orientations and interactions in the binding pocket and provide a possible explanation for the lower potencies of β-alanine and taurine....

  3. Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site.

    Directory of Open Access Journals (Sweden)

    Nan eZhao

    2013-08-01

    Full Text Available Previously we have shown that ONIOM type (QM/MM calculations can be used to simulate isotope edited FTIR difference spectra for neutral ubiquinone in the QA binding site in Rhodobacter sphaeroides photosynthetic reaction centers. Here we considerably extend upon this previous work by calculating isotope edited FTIR difference spectra for reaction centers with a variety of unlabeled and 18O labeled foreign quinones incorporated into the QA binding site. Isotope edited spectra were calculated for reaction centers with 2,3-dimethoxy-5,6-dimethyl-1,4-benzoquinone (MQ0, 2,3,5,6-tetramethyl-1,4-benzoquinone (duroquinone, DQ, and 2,3-dimethyl-l,4-naphthoquinone (DMNQ incorporated, and compared to corresponding experimental spectra. The calculated and experimental spectra agree well, further demonstrating the utility and applicability of our ONIOM approach for calculating the vibrational properties of pigments in protein binding sites.The normal modes that contribute to the bands in the calculated spectra, their composition, frequency and intensity, and how these quantities are modified upon 18O labeling, are presented. This computed information leads to a new and more detailed understanding/interpretation of the experimental FTIR difference spectra. Hydrogen bonding to the carbonyl groups of the incorporated quinones is shown to be relatively weak. It is also shown that there is some asymmetry in hydrogen bonding, accounting for 10-13 cm-1 separation in the frequencies of the carbonyl vibrational modes of the incorporated quinones. The extent of asymmetry H-bonding could only be established by considering the spectra for various types of quinones incorporated into the QA binding site. The quinones listed above are tail-less. Spectra were also calculated for reaction centers with corresponding tail containing quinones incorporated, and it is found that replacement of the quinone methyl group by a phytyl or prenyl chain does not alter ONIOM calculated s

  4. The health cost of energy. The health impacts of the different energy sources

    International Nuclear Information System (INIS)

    Masse, Roland

    2017-01-01

    This publication proposes an assessment of impacts of the different energy sources on public health. After a discussion of general aspects regarding this issue, the author addresses the identification and assessment of risks. While referring to different statistical data, he discusses the impacts of accidents in terms of dead, injured or evacuated people. He also addresses health impacts during a normal operation of power plants, i.e. in the case of nuclear plants (issue of exposure to various levels of radiation at the different steps of fuel cycle), of carbon-based plants (health risks and impacts during coal extraction, due to CO 2 emissions and to other toxic emissions, due to atmospheric pollution, identified risks, modelling attempts, assessment of a loss in life expectancy), and of other energies. While acknowledging that there are still many unknowns to assess these health impacts, the author compares these assessments. A summarized version of this article is proposed, in which the author briefly comments data regarding severe accidents related to energy production, discusses health consequences of electric power production and use, and makes a distinction between the most and less hazardous energies as far as public health is concerned

  5. Different Reliability Assessment Approaches for Wave Energy Converters

    DEFF Research Database (Denmark)

    Ambühl, Simon; Kramer, Morten Mejlhede; Sørensen, John Dalsgaard

    2015-01-01

    Reliability assessments are of importance for wave energy converters (WECs) due to the fact that accessibility might be limited in case of failure and maintenance. These failure rates can be adapted by reliability considerations. There are two different approaches to how reliability can be estima......Reliability assessments are of importance for wave energy converters (WECs) due to the fact that accessibility might be limited in case of failure and maintenance. These failure rates can be adapted by reliability considerations. There are two different approaches to how reliability can...... be estimated: the so-called classical reliability theory and the probabilistic reliability theory. The classical reliability theory is often used for failure rate estimations of mechanical and electrical components, whereas the probabilistic reliability theory is commonly used for structural components....... For WECs, mechanical/electrical components as well as structural components are of importance. Therefore, both reliability theories need to be incorporated in WEC designs, WEC developments and improvements of WECs. This paper gives an overview of the two reliability theories and how they can be combined...

  6. Energy expenditure on recreational visits to different natural environments.

    Science.gov (United States)

    Elliott, Lewis R; White, Mathew P; Taylor, Adrian H; Herbert, Stephen

    2015-08-01

    Physical inactivity poses a significant challenge to physical and mental health. Environmental approaches to tackle physical inactivity have identified natural environments as potentially important public health resources. Despite this, little is known about characteristics of the activity involved when individuals visit different types of natural environment. Using Natural England's Monitor of Engagement with the Natural Environment Survey, we examined 71,603 English respondents' recreational visits to natural environments in the past week. Specifically, we examined the intensity of the activities they undertook on the visits (METs), the duration of their visit, and the associated total energy expenditure (MET minutes). Visits to countryside and urban greenspace environments were associated with more intense activities than visits to coastal environments. However, visits to coastal environments were associated with the most energy expenditure overall due to their relatively long duration. Results differed by the urbanity or rurality of the respondent's residence and also how far respondents travelled to their destination. Knowledge of what types of natural environment afford the highest volumes and intensities of physical activity could inform landscape architecture and exercise prescriptions. Isolating activity-supporting characteristics of natural environments that can be translated into urban design is important in providing physical activity opportunities for those less able to access expansive environments. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  7. Developing a Novel Hydrogen Sponge with Ideal Binding Energy and High Surface Area for Practical Hydrogen Storage

    Energy Technology Data Exchange (ETDEWEB)

    Chung, T. C. Mike

    2018-04-19

    This Phase I (5 quarters) research project was to examine the validity of a new class of boron-containing polymer (B-polymer) frameworks, serving as the adsorbents for the practical onboard H2 storage applications. Three B-polymer frameworks were synthesized and investigated, which include B-poly(butyenylstyrene) (B-PBS) framework (A), B-poly(phenyldiacetyene) (B-PPDA) framework (B), and B-poly(phenyltriacetylene) (B-PPTA) framework (C). They are 2-D polymer structures with the repeating cyclic units that spontaneously form open morphology and the B-doped (p-type) π-electrons delocalized surfaces. The ideal B-polymer framework shall exhibit open micropores (pore size in the range of 1-1.5nm) with high surface area (>3000 m2/g), and the B-dopants in the conjugated framework shall provide high surface energy for interacting with H2 molecules (an ideal H2 binding energy in the range of 15-25 kJ/mol). The pore size distribution and H2 binding energy were investigated at both Penn State and NREL laboratories. So far, the experimental results show the successful synthesis of B-polymer frameworks with the relatively well-defined planar (2-D) structures. The intrinsically formed porous morphology exhibits a broad pore size distribution (in the range of 0.5-10 nm) with specific surface area (~1000 m2/g). The miss-alignment between 2-D layers may block some micropore channels and limit gas diffusion throughout the entire matrix. In addition, the 2-D planar conjugated structure may also allow free π-electrons delocalization throughout the framework, which significantly reduces the acidity of B-moieties (electron-deficiency).The resulting 2-D B-polymer frameworks only exhibit a small increase of H2 binding energy in the range of 8-9 KJ/mole (quite constant over the whole sorption range).

  8. Binding energies and isomerization in metallocene ions from threshold photoelectron photoion coincidence spectroscopy.

    Science.gov (United States)

    Révész, Agnes; Szepes, László; Baer, Tomas; Sztáray, Bálint

    2010-12-22

    Metallocene ions (Cp(2)M(+), M = Cr, Co, Ni) were studied by threshold photoelectron photoion coincidence spectroscopy (TPEPICO) to investigate the mechanism, energetics, and kinetics of the ionic dissociation processes. The examined energy-selected Cp(2)M(+) ions fragment by losing the neutral cyclopentadienyl ligand. In addition, CH and C(2)H(2) losses appear as minor channels, while the cobaltocene ion also loses an H atom. A possible isomerization pathway has also been observed for Cp(2)Ni(+), yielding a complex with pentafulvalene (C(10)H(8)) with a loss of H(2). In order to determine the 0 K appearance energies for the CpM(+) fragment ions, the asymmetric time-of-flight peak shapes and the breakdown diagrams of the energy-selected metallocene ions were modeled by both the rigid activated complex (RAC) Rice-Ramsperger-Kassel-Marcus (RRKM) theory and the simplified statistical adiabatic channel model (SSACM). The following appearance energies were obtained with SSACM, which is more reliable for loose transition states: 10.57 ± 0.14, 11.01 ± 0.13, and 10.18 ± 0.13 eV for M = Cr, Co, and Ni, respectively. These values combined with the corresponding adiabatic ionization energies yield M-Cp bond dissociation energies in Cp(2)M(+) ions of 5.04 ± 0.16, 5.77 ± 0.15, and 3.96 ± 0.15 eV. Density functional calculations at the B3LYP/6-311G(d,p) level of theory were used to determine the structures of these complexes and to provide parameters necessary for the analysis of the experimental data. The trends in the M-Cp bond energies can be related to the electronic structures of the metallocene ions based on a simple molecular orbital picture.

  9. Sequestration of maize crop straw C in different soils: role of oxyhydrates in chemical binding and stabilization as recalcitrance.

    Science.gov (United States)

    Song, Xiangyun; Li, Lianqing; Zheng, Jufeng; Pan, Genxing; Zhang, Xuhui; Zheng, Jinwei; Hussain, Qaiser; Han, Xiaojun; Yu, Xinyan

    2012-05-01

    While biophysical controls on the sequestration capacity of soils have been well addressed with physical protection, chemical binding and stabilization processes as well as microbial community changes, the role of chemical binding and stabilization has not yet well characterized for soil organic carbon (SOC) sequestration in rice paddies. In this study, a 6-month laboratory incubation with and without maize straw amendment (MSA) was conducted using topsoil samples from soils with different clay mineralogy and free oxy-hydrate contents collected across Southern China. The increase in SOC under MSA was found coincident with that in Fe- and Al-bound OC (Fe/Al-OC) after incubation for 30 d (R(2)=0.90, P=0.05), and with sodium dithionate-citrate-bicarbonate (DCB) extractable Fe after incubation for 180 d (R(2)=0.99, Phumin (R(2)=0.87, P=0.06) observed after incubation for 180 d may indicate a chemical stabilization of sequestered SOC as humin in the long run. These results improved our understanding of SOC sequestration in China's rice paddies that involves an initial chemical binding of amended C and a final stabilization as recalcitrant C of humin. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks.

    Directory of Open Access Journals (Sweden)

    Mathilde de Taffin

    Full Text Available Collier, the single Drosophila COE (Collier/EBF/Olf-1 transcription factor, is required in several developmental processes, including head patterning and specification of muscle and neuron identity during embryogenesis. To identify direct Collier (Col targets in different cell types, we used ChIP-seq to map Col binding sites throughout the genome, at mid-embryogenesis. In vivo Col binding peaks were associated to 415 potential direct target genes. Gene Ontology analysis revealed a strong enrichment in proteins with DNA binding and/or transcription-regulatory properties. Characterization of a selection of candidates, using transgenic CRM-reporter assays, identified direct Col targets in dorso-lateral somatic muscles and specific neuron types in the central nervous system. These data brought new evidence that Col direct control of the expression of the transcription regulators apterous and eyes-absent (eya is critical to specifying neuronal identities. They also showed that cross-regulation between col and eya in muscle progenitor cells is required for specification of muscle identity, revealing a new parallel between the myogenic regulatory networks operating in Drosophila and vertebrates. Col regulation of eya, both in specific muscle and neuronal lineages, may illustrate one mechanism behind the evolutionary diversification of Col biological roles.

  11. Functional roles and clinical values of insulin-like growth factor-binding protein-5 in different types of cancers.

    Science.gov (United States)

    Güllü, Gökçe; Karabulut, Sevgi; Akkiprik, Mustafa

    2012-06-01

    Insulin-like growth factor-binding proteins(IGFBPs) are critical regulators of the mitogenic activity of insulin-like growth factors (IGFs). IGFBP5, one of these IGFBPs, has special structural features, including a nuclear transport domain, heparin-binding motif, and IGF/extracellular matrix/acid-labile subunit-binding sites. Furthermore, IGFBP5 has several functional effects on carcinogenesis and even normal cell processes, such as cell growth, death, motility, and tissue remodeling. These biological effects are sometimes related with IGF (IGF-dependent effects) and sometimes not (IGF-independent effects). The functional role of IGFBP5 is most likely determined in a cell-type and tissue-type specific manner but also depends on cell context, especially in terms of the diversity of interacting proteins and the potential for nuclear localization. Clinical findings show that IGFBP5 has the potential to be a useful clinical biomarker for predicting response to therapy and clinical outcome of cancer patients. In this review, we summarize the functional diversity and clinical importance of IGFBP5 in different types of cancers.

  12. Effect of dietary dilution of energy and nutrients during different ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    Nov 16, 2009 ... energy increase, poultry consumes more energy that lead to increase fat storing in their bodies (Robbins, ... birds while consuming diluted diets, improve their energy intake productivity with reducing energy ..... Farell DJ, Mannion PF, Maldonado RAP (1999). A comparison of total and digestible amino acid ...

  13. Evasin-displaying lactic acid bacteria bind different chemokines and neutralize CXCL8 production in Caco-2 cells.

    Science.gov (United States)

    Škrlec, Katja; Pucer Janež, Anja; Rogelj, Boris; Štrukelj, Borut; Berlec, Aleš

    2017-11-01

    Chemokines are key signals in the immune system and play an important role as proinflammatory mediators in the pathology of inflammatory bowel disease and colorectal cancer, making them an important target for therapy. Recombinant lactic acid bacteria (LAB) were engineered to bind CC and CXC chemokines by displaying chemokine-binding proteins evasin-1, evasin-3 and evasin-4 on their surface. Evasin genes were cloned into lactococcal surface display vector and overexpressed in L. lactis NZ9000 and NZ9000ΔhtrA in fusion with secretion signal and surface anchor. Evasin-displaying bacteria removed from 15% to 90% of 11 different chemokines from the solution as determined with ELISA and Luminex multiplexing assays, whereby L. lactis NZ9000ΔhtrA proved more efficient. Lactobacillus salivarius ATCC 11741 was coated with L. . lactis-expressed evasin fusion protein, and its ability to bind chemokines was also confirmed. Evasin-3-displaying L. lactis removed 76.0% of IL-1β-induced CXCL8 from the supernatant of Caco-2 epithelial cells. It also prevented secretion of CXCL8 from Caco-2 cells in a time-dependent manner when added before induction with IL-1β. Evasin-displaying LAB have the ability to bind multiple chemokines simultaneously and exert synergistic activity. This innovative treatment approach therefore has the potential for mucosal therapy of inflammatory bowel disease or colorectal cancer. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  14. Different forms of soluble cytoplasmic mRNA binding proteins and particles in Xenopus laevis oocytes and embryos

    Energy Technology Data Exchange (ETDEWEB)

    Murray, M.T.; Krohne, G.; Franke, W.W. (Institute of Cell and Tumor Biology, Heidelberg (Germany, F.R.))

    1991-01-01

    To gain insight into the mechanisms involved in the formation of maternally stored mRNPs during Xenopus laevis development, we searched for soluble cytoplasmic proteins of the oocyte that are able to selectively bind mRNAs, using as substrate radiolabeled mRNA. In vitro mRNP assembly in solution was followed by UV-cross-linking and RNase digestion, resulting in covalent tagging of polypeptides by nucleotide transfer. Five polypeptides of approximately 54, 56 60, 70, and 100 kD (p54, p56, p60, p70, and p100) have been found to selectively bind mRNA and assemble into mRNPs. These polypeptides, which correspond to previously described native mRNP components, occur in three different particle classes of approximately 4.5S, approximately 6S, and approximately 15S, as also determined by their reactions with antibodies against p54 and p56. Whereas the approximately 4.5S class contains p42, p60, and p70, probably each in the form of individual molecules or small complexes, the approximately 6S particles appears to consist only of p54 and p56, which occur in a near-stoichiometric ratio suggestive of a heterodimer complex. The approximately 15S particles contain, in addition to p54 and p56, p60 and p100 and this is the single occurring form of RNA-binding p100. We have also observed changes in the in vitro mRNA binding properties of these polypeptides during oogenesis and early embryonic development, in relation to their phosphorylation state and to the activity of an approximately 15S particle-associated protein kinase, suggesting that these proteins are involved in the developmental translational regulation of maternal mRNAs.

  15. Differential stability of TATA box binding proteins from archaea with different optimal growth temperatures

    Science.gov (United States)

    Kopitz, Annette; Soppa, Jörg; Krejtschi, Carsten; Hauser, Karin

    2009-09-01

    The TATA box binding protein (TBP) is involved in promoter recognition, the first step of transcription initiation. TBP is universally conserved and essential in archaea and eukaryotes. In archaea, TBPs have to be stable and to function in species that cover an extremely wide range of optimal growth temperatures (OGTs), from below 0 °C to more than 100 °C. Thus, the archaeal TBP family is ideally suited to study the evolutionary adaptation of proteins to an extremely wide range of temperatures. We characterized the thermostability of one mesophilic and one thermophilic TBP by infrared spectroscopy. Transition temperatures ( Tms) of thermal unfolding have been determined using TBPs from Methanosarcina mazei (OGT 37 °C) and from Methanothermobacter thermautotrophicus (OGT 65 °C). Furthermore, the influence of protein and salt concentration on thermostability has been characterized. Together with previous studies, our results reveal that the Tms of archaeal TBPs are closely correlated with the OGTs of the respective species. Noteworthy, this is also true for the TBP from M. mazei representing the first characterized TBP from a mesophilic archaeon. In contrast, the only characterized eukaryotic TBP of the mesophilic plant Arabidopsis thaliana has a Tm more than 40 °C above the OGT.

  16. Gi- and Gs-coupled GPCRs show different modes of G-protein binding.

    Science.gov (United States)

    Van Eps, Ned; Altenbach, Christian; Caro, Lydia N; Latorraca, Naomi R; Hollingsworth, Scott A; Dror, Ron O; Ernst, Oliver P; Hubbell, Wayne L

    2018-03-06

    More than two decades ago, the activation mechanism for the membrane-bound photoreceptor and prototypical G protein-coupled receptor (GPCR) rhodopsin was uncovered. Upon light-induced changes in ligand-receptor interaction, movement of specific transmembrane helices within the receptor opens a crevice at the cytoplasmic surface, allowing for coupling of heterotrimeric guanine nucleotide-binding proteins (G proteins). The general features of this activation mechanism are conserved across the GPCR superfamily. Nevertheless, GPCRs have selectivity for distinct G-protein family members, but the mechanism of selectivity remains elusive. Structures of GPCRs in complex with the stimulatory G protein, G s , and an accessory nanobody to stabilize the complex have been reported, providing information on the intermolecular interactions. However, to reveal the structural selectivity filters, it will be necessary to determine GPCR-G protein structures involving other G-protein subtypes. In addition, it is important to obtain structures in the absence of a nanobody that may influence the structure. Here, we present a model for a rhodopsin-G protein complex derived from intermolecular distance constraints between the activated receptor and the inhibitory G protein, G i , using electron paramagnetic resonance spectroscopy and spin-labeling methodologies. Molecular dynamics simulations demonstrated the overall stability of the modeled complex. In the rhodopsin-G i complex, G i engages rhodopsin in a manner distinct from previous GPCR-G s structures, providing insight into specificity determinants. Copyright © 2018 the Author(s). Published by PNAS.

  17. Differences in energy transfer of a cyanobacterium, Synechococcus sp. PCC 7002, grown in different cultivation media.

    Science.gov (United States)

    Niki, Kenta; Aikawa, Shimpei; Yokono, Makio; Kondo, Akihiko; Akimoto, Seiji

    2015-08-01

    Currently, cyanobacteria are regarded as potential biofuel sources. Large-scale cultivation of cyanobacteria in seawater is of particular interest because seawater is a low-cost medium. In the present study, we examined differences in light-harvesting and energy transfer processes in the cyanobacterium Synechococcus sp. PCC 7002 grown in different cultivation media, namely modified A medium (the optimal growth medium for Synechococcus sp. PCC 7002) and f/2 (a seawater medium). The concentrations of nitrate and phosphate ions were varied in both media. Higher nitrate ion and/or phosphate ion concentrations yielded high relative content of phycobilisome. The cultivation medium influenced the energy transfers within phycobilisome, from phycobilisome to photosystems, within photosystem II, and from photosystem II to photosystem I. We suggest that the medium also affects charge recombination at the photosystem II reaction center and formation of a chlorophyll-containing complex.

  18. Technological learning in offshore wind energy: Different roles of the government

    International Nuclear Information System (INIS)

    Smit, Thijs; Junginger, Martin; Smits, Ruud

    2007-01-01

    Offshore wind energy is a promising source of renewable electricity, even though its current costs prevent large-scale implementation. Technological learning has improved the technology and its economic performance already, and could result in significant further improvements. This study investigates how technological learning takes place in offshore wind energy and how technological learning is related to different policy regimes. Offshore wind energy developments in Denmark and the United Kingdom have been analysed with a technology-specific innovation systems approach. The results reveal that the dominant forms of learning are learning by doing and learning by using. At the same time, learning by interacting is crucial to achieve the necessary binding elements in the technology-specific innovation system. Generally, most learning processes were performed by self-organizing entities. However, sometimes cultural and technical barriers occurred, excluding component suppliers and knowledge institutes from the innovation system. Danish policies successfully anticipated these barriers and removed them; therefore, the Danish policies can be characterized as pro-active. British policies shaped stable conditions for learning only; therefore, they can be characterized as active. In the future, barriers could hinder learning by interacting between the oil and gas industry, the offshore wind industry and academia. Based on this study, we suggest national and international policy makers to design long-term policies to anticipate these barriers, in order to contribute to technological learning

  19. Comparison between the classical interaction energy and periodic Hartree-Fock binding energies for the interaction between molecules and surfaces

    International Nuclear Information System (INIS)

    Chacon-Taylor, M.R.; McCarthy, M.I.

    1995-01-01

    The energetics of the H 2 O/MgO(001), HCl/MgO(001), and NH 3 /MgO(001) interface were investigated using the ab initio periodic Hartree-Fock LCAO method and a classical interaction energy model. The QM calculations treated a system that was periodic in two dimensions with the adsorbate approaching a three-layer slab of MgO(001). The authors used an approximation to the classical interaction energy, where the surface is represented by its potential, electric field, and electric field derivatives at the positions of the molecule center of mass, and the molecule is described by its charge, electric dipole, electric quadrupole and polarizability. The potential, electric field and electric field gradient are obtained for the clean three-layer slab using the ab initio periodic Hartree-Fock LCAO method (CRYSTAL) and an optimized split valence basis 8-61G on Mg and 8-51G on O. The charge, electric dipole, and electric quadrupole are calculated using ab initio Hartree-Fock theory (GAUSSIAN-92) with a 6-31G* basis set while the SCF polarizability is determined analytically using the same basis set

  20. Phase transition in the Jarzynski estimator of free energy differences.

    Science.gov (United States)

    Suárez, Alberto; Silbey, Robert; Oppenheim, Irwin

    2012-05-01

    The transition between a regime in which thermodynamic relations apply only to ensembles of small systems coupled to a large environment and a regime in which they can be used to characterize individual macroscopic systems is analyzed in terms of the change in behavior of the Jarzynski estimator of equilibrium free energy differences from nonequilibrium work measurements. Given a fixed number of measurements, the Jarzynski estimator is unbiased for sufficiently small systems. In these systems the directionality of time is poorly defined and the configurations that dominate the empirical average, but which are in fact typical of the reverse process, are sufficiently well sampled. As the system size increases the arrow of time becomes better defined. The dominant atypical fluctuations become rare and eventually cannot be sampled with the limited resources that are available. Asymptotically, only typical work values are measured. The Jarzynski estimator becomes maximally biased and approaches the exponential of minus the average work, which is the result that is expected from standard macroscopic thermodynamics. In the proper scaling limit, this regime change has been recently described in terms of a phase transition in variants of the random energy model. In this paper this correspondence is further demonstrated in two examples of physical interest: the sudden compression of an ideal gas and adiabatic quasistatic volume changes in a dilute real gas.

  1. Ignition in net for different energy confinement time scalings

    International Nuclear Information System (INIS)

    Johner, J.; Prevot, F.

    1988-06-01

    A zero-dimensional profile dependent model is used to assess the feasibility of ignition in the extended version of NET. Five recent scalings for the energy confinement time (Goldston, Kaye All, Kaye Big, Shimomura-Odajima, Rebut-Lallia) are compared in the frame of two different scenarii, i.e., H-mode with a flat density profile or L-mode with a peaked density profile. For the flat density H-mode case, ignition is accessible with none of the scalings except Rebut-Lallia's. For the peaked density L-mode case, ignition is accessible with none of the scalings except Rebut-Lallia's. For the two Kaye's scalings, ignition is forbidden in H-mode even with the peaked density profile. For the Rebut-Lallia scaling, ignition is allowed in L-mode even with the flat density profile

  2. Pomegranate ( Punica granatum L.) expresses several nsLTP isoforms characterized by different immunoglobulin E-binding properties.

    Science.gov (United States)

    Bolla, Michela; Zenoni, Sara; Scheurer, Stephan; Vieths, Stefan; San Miguel Moncin, Maria Del Mar; Olivieri, Mario; Antico, Andrea; Ferrer, Marta; Berroa, Felicia; Enrique, Ernesto; Avesani, Linda; Marsano, Francesco; Zoccatelli, Gianni

    2014-01-01

    Pomegranate allergy is associated with sensitization to non-specific lipid transfer proteins (nsLTPs). Our aim was to identify and characterize the non-specific nsLTPs expressed in pomegranate at the molecular level and to study their allergenic properties in terms of immunoglobulin E (IgE)-binding and cross-reactivity with peach nsLTP (Pru p 3). A non-equilibrium two-dimensional (2-D) electrophoretic approach based on acid-urea PAGE and sodium dodecyl sulfate PAGE was set up to separate pomegranate nsLTPs. Their immunoreactivity was tested by immunoblotting carried out with anti-Pru p 3 polyclonal antibodies and sera from pomegranate-allergic patients. For final identification, pomegranate nsLTPs were purified by chromatography and subjected to trypsin digestion and mass spectrometry (MS) analysis. For this purpose, the sequences obtained by cDNA cloning of three pomegranate nsLTPs were integrated in the database that was subsequently searched for MS data interpretation. Four nsLTPs were identified by 2-D immunoblotting. The detected proteins showed different IgE-binding capacity and partial cross-reactivity with Pru p 3. cDNA cloning and MS analyses led to the identification of three nsLTP isoforms with 66-68% amino acid sequence identity named Pun g 1.0101, Pun g 1.0201 and Pun g 1.0301. By 2-D electrophoresis, we could separate different nsLTP isoforms possessing different IgE-binding properties, which might reflect peculiar allergenic potencies. The contribution of Pru p 3 to prime sensitization is not central as in other plant nsLTPs. © 2014 S. Karger AG, Basel.

  3. Hypernuclear interactions and the binding energies of Λ and ΛΛ hypernuclei

    International Nuclear Information System (INIS)

    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 Λ/ 9 Be, and of the well depth, with ΛN forces which are consistent with Λp scattering and which are quite strongly spin-dependent, with reasonable TPE ΛNN forces with strongly repulsive dispersive-type ΛNN forces. For the latter we also consider a spin-dependent version which is somewhat favored by our analysis. /sub Λ/ 9 Be is treated as a 2α + Λ system and is significantly overbound, ≅1 MeV, if only αα and αΛ potentials are used. An ααΛ potential obtained from the ΛNN forces nicely accounts for this overbinding. The ΛΛ hypernuclei /sub ΛΛ/ 6 He and /sub ΛΛ/ 10 Be are treated as α + 2Λ and 2α + 2Λ systems. Use of the /sub ΛΛ/ 10 Be event gives ≅1.5 MeV too little binding for /sub ΛΛ/ 6 He. The 1 S 0 ΛΛ potential obtained from /sub ΛΛ/ 10 Be is quite strongly attractive, comparable to the ΛN and also to the NN potential without OPE. 18 refs

  4. Differences in the Antinociceptive Effects and Binding Properties of Propranolol and Bupranolol Enantiomers.

    Science.gov (United States)

    Martin, Loren J; Piltonen, Marjo H; Gauthier, Josee; Convertino, Marino; Acland, Erinn L; Dokholyan, Nikolay V; Mogil, Jeffrey S; Diatchenko, Luda; Maixner, William

    2015-12-01

    Recent efforts have suggested that the β-adrenergic receptor (β-AR) system may be a novel and viable therapeutic target for pain reduction; however, most of the work to date has focused on the β(2)-adrenergic receptor (AR). Here, we compared the antinociceptive effects of enantiomeric configurations of propranolol and bupranolol, two structurally similar nonselective β-blocking drugs, against mouse models of inflammatory and chronic pain. In addition, we calculated in silico docking and measured the binding properties of propranolol and bupranolol for all 3 β-ARs. Of the agents examined, S-bupranolol is superior in terms of its antinociceptive effect and exhibited fewer side effects than propranolol or its associated enantiomers. In contrast to propranolol, S-bupranolol exhibited negligible β-AR intrinsic agonist activity and displayed a full competitive antagonist profile at β(1)/β(2)/β(3)-ARs, producing a unique blockade of β(3)-ARs. We have shown that S-bupranolol is an effective antinociceptive agent in mice without negative side effects. The distinctive profile of S-bupranolol is most likely mediated by its negligible β-AR intrinsic agonist activity and unique blockade of β(3)-AR. These findings suggest that S-bupranolol instead of propranolol may represent a new and effective treatment for a variety of painful conditions. The S enantiomer of bupranolol, a β-receptor antagonist, shows greater antinociceptive efficacy and a superior preclinical safety profile and it should be considered as a unique β-adrenergic receptor compound to advance future clinical pain studies. Copyright © 2015 American Pain Society. Published by Elsevier Inc. All rights reserved.

  5. Donor impurity binding energies of coaxial GaAs / Alx Ga1 - x As cylindrical quantum wires in a parallel applied magnetic field

    Science.gov (United States)

    Tshipa, M.; Winkoun, D. P.; Nijegorodov, N.; Masale, M.

    2018-04-01

    Theoretical investigations are carried out of binding energies of a donor charge assumed to be located exactly at the center of symmetry of two concentric cylindrical quantum wires. The intrinsic confinement potential in the region of the inner cylinder is modeled in any one of the three profiles: simple parabolic, shifted parabolic or the polynomial potential. The potential inside the shell is taken to be a potential step or potential barrier of a finite height. Additional confinement of the charge carriers is due to the vector potential of the axial applied magnetic field. It is found that the binding energies attain maxima in their variations with the radius of the inner cylinder irrespective of the particular intrinsic confinement of the inner cylinder. As the radius of the inner cylinder is increased further, the binding energies corresponding to either the parabolic or the polynomial potentials attain minima at some critical core-radius. Finally, as anticipated, the binding energies increase with the increase of the parallel applied magnetic field. This behaviour of the binding energies is irrespective of the particular electric potential of the nanostructure or its specific dimensions.

  6. In silico analysis of different generation β lactams antibiotics with penicillin binding protein-2 of Neisseria meningitidis for curing meningococcal disease.

    Science.gov (United States)

    Tripathi, Vijay; Tripathi, Pooja; Srivastava, Navita; Gupta, Dwijendra

    2014-12-01

    Neisseria meningitidis is a gram negative, diplococcic pathogen responsible for the meningococcal disease and fulminant septicemia. Penicillin-binding proteins-2 (PBPs) is crucial for the cell wall biosynthesis during cell proliferation of N. meningitidis and these are the target for β-lactam antibiotics. For many years penicillin has been recognized as the antibiotic for meningococcal disease but the meningococcus has seemed to be antibiotic resistance. In the present work we have verified the molecular interaction of Penicillin binding protein-2 N. meningitidis to different generation of β-lactam antibiotics and concluded that the third generation of β-lactam antibiotics shows efficient binding with Penicillin binding protein-2 of N. meningitidis. On the basis of binding efficiency and inhibition constant, ceftazidime emerged as the most efficient antibiotic amongst the other advanced β-lactam antibiotics against Penicillin-binding protein-2 of N. meningitidis.

  7. Electron binding energies of aqueous alkali and halide ions: EUV photoelectron spectroscopy of liquid solutions and combined ab initio and molecular dynamics calculations.

    Science.gov (United States)

    Winter, Bernd; Weber, Ramona; Hertel, Ingolf V; Faubel, Manfred; Jungwirth, Pavel; Brown, Eric C; Bradforth, Stephen E

    2005-05-18

    Photoelectron spectroscopy combined with the liquid microjet technique enables the direct probing of the electronic structure of aqueous solutions. We report measured and calculated lowest vertical electron binding energies of aqueous alkali cations and halide anions. In some cases, ejection from deeper electronic levels of the solute could be observed. Electron binding energies of a given aqueous ion are found to be independent of the counterion and the salt concentration. The experimental results are complemented by ab initio calculations, at the MP2 and CCSD(T) level, of the ionization energies of these prototype ions in the aqueous phase. The solvent effect was accounted for in the electronic structure calculations in two ways. An explicit inclusion of discrete water molecules using a set of snapshots from an equilibrium classical molecular dynamics simulations and a fractional charge representation of solvent molecules give good results for halide ions. The electron binding energies of alkali cations computed with this approach tend to be overestimated. On the other hand, the polarizable continuum model, which strictly provides adiabatic binding energies, performs well for the alkali cations but fails for the halides. Photon energies in the experiment were in the EUV region (typically 100 eV) for which the technique is probing the top layers of the liquid sample. Hence, the reported energies of aqueous ions are closely connected with both structures and chemical reactivity at the liquid interface, for example, in atmospheric aerosol particles, as well as fundamental bulk solvation properties.

  8. Study of lysozyme mobility and binding free energy during adsorption on a graphene surface

    International Nuclear Information System (INIS)

    Nakano, C. Masato; Ma, Heng; Wei, Tao

    2015-01-01

    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

  9. 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.

  10. Effects of the atomic environment on the electron binding energies in samarium

    Czech Academy of Sciences Publication Activity Database

    Inoyatov, A. K.; Kovalík, Alojz; Filosofov, D. V.; Ryšavý, Miloš; Vénos, Drahoslav; Yushkevich, Y. V.; Perevoshchikov, L. L.; Zhdanov, V. S.

    2016-01-01

    Roč. 207, FEB (2016), s. 38-49 ISSN 0368-2048 R&D Projects: GA ČR(CZ) GAP203/12/1896; GA MŠk LG14004 Institutional support: RVO:61389005 Keywords : Sm-149 * atomic environment * electron ginding energy * intermediate-valence state * chemical shift * natural atomic level width Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.661, year: 2016

  11. The analysis of security cost for different energy sources

    International Nuclear Information System (INIS)

    Jun, Eunju; Kim, Wonjoon; Chang, Soon Heung

    2009-01-01

    Global concerns for the security of energy have steadily been on the increase and are expected to become a major issue over the next few decades. Urgent policy response is thus essential. However, little attempt has been made at defining both energy security and energy metrics. In this study, we provide such metrics and apply them to four major energy sources in the Korean electricity market: coal, oil, liquefied natural gas, and nuclear. In our approach, we measure the cost of energy security in terms of supply disruption and price volatility, and we consider the degree of concentration in energy supply and demand using the Hirschman-Herfindahl index (HHI). Due to its balanced fuel supply and demand, relatively stable price, and high abundance, we find nuclear energy to be the most competitive energy source in terms of energy security in the Korean electricity market. LNG, on the other hand, was found to have the highest cost in term of energy security due to its high concentration in supply and demand, and its high price volatility. In addition, in terms of cost, we find that economic security dominates supply security, and as such, it is the main factor in the total security cost. Within the confines of concern for global energy security, our study both broadens our understanding of energy security and enables a strategic approach in the portfolio management of energy consumption.

  12. Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package.

    Science.gov (United States)

    Mermelstein, Daniel J; Lin, Charles; Nelson, Gard; Kretsch, Rachael; McCammon, J Andrew; Walker, Ross C

    2018-03-12

    Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD-based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907-atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  13. A comparison study on polysaccharides extracted from Laminaria japonica using different methods: structural characterization and bile acid-binding capacity.

    Science.gov (United States)

    Gao, Jie; Lin, Lianzhu; Sun, Baoguo; Zhao, Mouming

    2017-09-20

    In this study, the structural characterization and bile acid-binding capacity of Laminaria japonica polysaccharides (LP), obtained by seven different extraction methods, were investigated. The results indicated that extraction methods exhibited significant effects on extraction yield, molecular weight, monosaccharide composition and the content of neutral sugar, fucose, uronic acid and sulfate of LP. AFM analysis indicated that LP extracted by different methods exhibited certain different, flexible and worm-like chains with many branches. Rheological measurements showed that the LP, obtained by pressurized hot water extraction and acid assisted extraction, exhibited lower viscosity due to their lower molecular weight, compared to other extracted polysaccharides. The bile acid-binding capacity of acid assisted extracted LP was significantly higher than other LP samples tested, which was probably ascribed to its highly branched structure, low molecular weight, low viscosity and abundant uronic acid and fucose in total monosaccharides. The present study provides scientific evidence and advances in the preparation technology and a method for evaluating hypolipidemic activities of L. japonica polysaccharides.

  14. Malaysian cockle (Anadara granosa) allergy: Identification of IgE-binding proteins and effects of different cooking methods.

    Science.gov (United States)

    Zailatul, H M Y; Rosmilah, M; Faizal, B; Noormalin, A; Shahnaz, M

    2015-06-01

    The purpose of this study was to evaluate the effect of different cooking methods on the allergenicity of cockle and to identify proteins most frequently bound by IgE antibodies using a proteomics approach. Raw, boiled, fried and roasted extracts of the cockle were prepared. The protein profiles of the extracts were obtained by separation using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and 2-dimensional gel electrophoresis (2-DE). IgE-immunoblotting was then performed with the use of individual sera from patients with cockle allergy and the major IgE-binding proteins were analyzed by mass-spectrometry. SDS-PAGE of raw extract showed 13 protein bands. Smaller numbers of protein bands were detected in the boiled, fried and roasted extracts. The 2-DE gel profile of the raw extract further separated the protein bands to ~50 protein spots with molecular masses between 13 to 180 kDa and isoelectric point (pI) values ranging from 3 to 10. Immunoblotting of raw extract exhibited 11 IgE-binding proteins with two proteins of 36 and 40 kDa as the major IgE-binding proteins, while the boiled extract revealed 3 IgE-binding proteins. Fried and roasted extracts only showed a single IgE-binding protein at 36 kDa. 2-DE immunoblotting of raw extract demonstrated 5 to 20 IgE reactive spots. Mass spectrometry analysis led to identification of 2 important allergens, tropomyosin (36 kDa) and arginine kinase (40 kDa). Heated extracts showed a reduction in the number of IgE-reactive bands compared with raw extract, which suggest that thermal treatment can be used as a tool in attempting to reduce cockle allergenicity. The degree of allergenicity of cockle was demonstrated in the order raw > boiled > fried ≈ roasted. Two important allergens reacting with more than 50% of patients' sera identified using mass spectrometric approaches were tropomyosin and arginine kinase. Thus, allergens found in this study would help in component based diagnosis, management of

  15. Field use of D218O to measure energy expenditure of soldiers at different energy intakes

    International Nuclear Information System (INIS)

    DeLany, J.P.; Schoeller, D.A.; Hoyt, R.W.; Askew, E.W.; Sharp, M.A.

    1989-01-01

    To test the application of doubly labeled water under adverse field conditions, energy expenditures of 16 special operations soldiers were measured during a 28-day field training exercise. Subjects were matched by fat-free mass and divided equally between an ad libitum ready-to-eat meal diet and a 2,000 kcal/day lightweight ration. Subjects recorded intakes daily, and body composition was measured before and after the exercise. At the beginning of the study, subjects moved to a new northerly location and, therefore, a new water supply. To compensate for this, a group of soldiers who did not receive heavy water was followed to measure isotopic base-line changes. Energy expenditure by doubly labeled water was in agreement with intake/balance (3,400 ± 260 vs. 3,230 ± 520 kcal/day). The overall coefficient of variation of energy expenditure by doubly labeled water was half that of intake/balance (7.6 vs. 16.1%). The coefficient of variation of repeat measures with doubly labeled water was 7.3%. Energy expenditure of the ready-to-eat meal group, 3,540 ± 180 kcal/day, was not significantly different from the lightweight ration group, 3,330 ± 301 kcal/day. Doubly labeled water was valid under field conditions

  16. Energy utitlzation by broilers fed different micro-nutrient mixtures ...

    African Journals Online (AJOL)

    Feeding micro-nutrient mixture B improved energy efficiency. It was concluded that the poor performance and the poor energy efficiency of C-fed broilers was as a result of the micronutrient imbalance of the mixture since the mixture is deficient in Zinc and four B-vitamins that affect energy utilization. It also contains ...

  17. Supplementation of grazing suckling beef calves receiving different energy sources

    Directory of Open Access Journals (Sweden)

    Josilaine Aparecida da Costa Lima

    2016-06-01

    Full Text Available The aim of this study was to evaluate the effect of different energy sources - corn, sorghum, and wheat bran - on performance, intake, digestibility, and nitrogen utilization efficiency of beef calves subjected to creep feeding. Thirty-four calves (12 males and 22 females with initial age and weight of four months and 108±3.9 kg, respectively, were used in a randomized-block experimental design with four treatments and two blocks (males and females. Treatments were control (MM, a mineral mixture ad libitum; corn (C; corn + sorghum (C+S; and corn + sorghum + wheat bran (C+S+WB. Supplements contained approximately 20% crude protein (CP, and were fed in the amount of 0.5% of body weight. Supplemented animals had higher performance (P < 0.05 when compared with those on treatment MM. Supplementation increased (P < 0.05 the intakes of dry matter (DM, organic matter (OM, crude protein (CP, neutral detergent fiber corrected for ash and protein (NDFap, non-fibrous carbohydrates (NFC, digestible neutral detergent fiber (dNDF, and digestible organic matter (dOM. The digestibility of NFC was higher (P < 0.05 in the supplemented treatments. The C+S and C+S+WB treatments provided increased digestibility (P < 0.05 of OM, CP, and NDFap. The synthesis of nitrogen compounds was higher (P < 0.05 in animals on treatment C as compared with those on the other supplemented treatments. Animals on treatments C+S and C+S+WB had higher (P < 0.05 nitrogen utilization efficiency compared with those on the other treatments. Concentrate supplementation improved the animal performance. The use of other energy sources (sorghum or wheat bran in association with corn is recommended for suckling calves.

  18. Urban energy consumption: Different insights from energy flow analysis, input–output analysis and ecological network analysis

    International Nuclear Information System (INIS)

    Chen, Shaoqing; Chen, Bin

    2015-01-01

    Highlights: • Urban energy consumption was assessed from three different perspectives. • A new concept called controlled energy was developed from network analysis. • Embodied energy and controlled energy consumption of Beijing were compared. • The integration of all three perspectives will elucidate sustainable energy use. - Abstract: Energy consumption has always been a central issue for sustainable urban assessment and planning. Different forms of energy analysis can provide various insights for energy policy making. This paper brought together three approaches for energy consumption accounting, i.e., energy flow analysis (EFA), input–output analysis (IOA) and ecological network analysis (ENA), and compared their different perspectives and the policy implications for urban energy use. Beijing was used to exemplify the different energy analysis processes, and the 42 economic sectors of the city were aggregated into seven components. It was determined that EFA quantifies both the primary and final energy consumption of the urban components by tracking the different types of fuel used by the urban economy. IOA accounts for the embodied energy consumption (direct and indirect) used to produce goods and services in the city, whereas the control analysis of ENA quantifies the specific embodied energy that is regulated by the activities within the city’s boundary. The network control analysis can also be applied to determining which economic sectors drive the energy consumption and to what extent these sectors are dependent on each other for energy. So-called “controlled energy” is a new concept that adds to the analysis of urban energy consumption, indicating the adjustable energy consumed by sectors. The integration of insights from all three accounting perspectives further our understanding of sustainable energy use in cities

  19. Binding Energy calculation of GSK-3 protein of Human against some anti-diabetic compounds of Momordica charantia linn (Bitter melon).

    Science.gov (United States)

    Hazarika, Ridip; Parida, Pratap; Neog, Bijoy; Yadav, Raj Narain Singh

    2012-01-01

    Diabetes is one of the major life threatening diseases worldwide. It creates major health problems in urban India. Glycogen Synthase Kinase-3 (GSK-3) protein of human is known for phosphorylating and inactivating glycogen synthase which also acts as a negative regulator in the hormonal control of glucose homeostasis. In traditional medicine, Momordica charantia is used as antidiabetic plant because of its hypoglycemic effect. Hence to block the active site of the GSK-3 protein three anti-diabetic compounds namely, charantin, momordenol & momordicilin were taken from Momordica charantia for docking study and calculation of binding energy. The aim of present investigation is to find the binding energy of three major insulin-like active compounds against glycogen synthase kinase-3 (GSK-3), one of the key proteins involved in carbohydrate metabolism, with the help of molecular docking using ExomeTM Horizon suite. The study recorded minimum binding energy by momordicilin in comparison to the others.

  20. Energy

    International Nuclear Information System (INIS)

    Meister, F.

    2001-01-01

    This chapter of the environmental control report deals with the environmental impact of energy production, energy conversion, atomic energy and renewable energy. The development of the energy consumption in Austria for the years 1993 to 1999 is given for the different energy types. The development of the use of renewable energy sources in Austria is given, different domestic heat-systems are compared, life cycles and environmental balance are outlined. (a.n.)

  1. Binding of sodium dodecyl sulfate with linear and branched polyethyleneimines in aqueous solution at different pH values.

    Science.gov (United States)

    Wang, Hao; Wang, Yilin; Yan, Haike; Zhang, Jin; Thomas, Robert K

    2006-02-14

    Isothermal titration microcalorimetry (ITC), conductivity, and turbidity measurements have been carried out to study the interaction of sodium dodecyl sulfate (SDS) with polyethyleneimines (PEI) including linear PEI and branched PEI at different pH values of 3, 7, and 10. In all cases, the polymers show a remarkable affinity toward SDS. At pH 3, the polymer PEI is a strong polycation, and the binding is dominated by electrostatic 1:1 charge neutralization with the anionic surfactant. At pH 7, the electrostatic attraction between SDS and PEI is weak, and the hydrophobic interaction becomes stronger. At the natural pH of 10, PEI is essentially nonionic and binds SDS in the form of polymer-bound surfactant aggregates. The charge neutralization concentration (C1) of SDS for the PEI-SDS complex can be derived from the curves of variation of the enthalpy, conductivity, and turbidity with SDS concentration. There is good agreement between the results from the three methods and all show a decrease with increasing pH. The total interaction enthalpies (deltaH(total)) of PEI with SDS are obtained from the observed enthalpy curves and the difference enthalpy (deltaH*) between the total enthalpy of branched PEI with SDS, and the total enthalpy of linear PEI with SDS can be derived from the obtained deltaH(total). The difference deltaH* increases dramatically as pH increases, which indicates that the interactions are different for linear PEI and branched PEI at high pH values. A schematic map of the different states of aggregation is presented.

  2. ENERGY EFFICIENCY OF DIFFERENT WAYS OF CENTRAL HEATING

    Directory of Open Access Journals (Sweden)

    A. E. Piir

    2015-01-01

    Full Text Available  The article shows the calculation comparison of fuel for producing of heat-line water with a help of different technological installations, transforming (converting high-grade heat from burning process of fuel or in the process of non-reversible heat exchange with coolant (heating agent, or with a help of heat engines, which allow to decrease losses of working efficiency and thus to reduce the use of fuel. There were considered five types of plants beginning from the  simplest  one  up  to  the  most  complex  in  two  variants,  when  the  heat  exchangers and machines are perfect (ideal and when equipment has the known degree of efficiency (perfection:1 water-heat boiler station, working on organic fuel;2 electrical boiler station, obtaining energy on power transmission lines from condensing power station;3 line heater of TPP, obtaining steam from heating turbine;4 line heater CPP, powered by steam from pressure reducing unit;5 heat pump, producing energy on power supply lines from TPP.In this article were investigated three ideal reversible ways of transformation of   high- grade heat into low-grade heat with a help of decreasing and increasing and combined (suggested by the authors heat transformers and their thermodynamic equivalence was shown in this article. And there were suggested universal installation for electric energy generation, cold and heat of two grades for heat-water supply and the heating process on the base of gascompressors   gas turbines. These results are so important (actual for power engineers of the countries with  increasing consumption  of organic  fuel and  its enhancement in  value and realizing programs of energy saving .The analysis shows, that the quality of produced low-grade heat per unit of used high-grade heat for ideal plants (installations is: electrical boiler unit – 0.7;  water boiler unit – 1.0; for heat pump, heating turbine, combined heat transformers   – 4

  3. Photodetachment of Isolated Bicarbonate Anion: Electron Binding Energy of HCO3-

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xue B.; Xantheas, Sotiris S.

    2011-04-29

    We report the first direct photodetachment photoelectron spectroscopy of HCO3 in the gas phase under low temperature conditions. The observed photoelectron spectra are complicated due to excitations of manifolds in both vibrational and electronic states. A long and single vibrational progression with a frequency of 530 ± 20 cm-1 is partially resolved in the threshold of the T=20 K, 266 nm spectrum. The adiabatic electron detachment energy (ADE) of HCO3, or in other words the electron affinity (EA) of neutral HCO3, is experimentally determined from the (0-0) transition to be 3.680 ± 0.015 eV. High-level ab initio calculations at the CCSD(T) level of theory produce an anharmonic frequency of 546 cm-1 for HCO3 and a value of 3.62 eV for the (0,0) transition, both in excellent agreement with the experimentally determined values.

  4. The Sigma-2 Receptor and Progesterone Receptor Membrane Component 1 are Different Binding Sites Derived From Independent Genes

    Directory of Open Access Journals (Sweden)

    Uyen B. Chu

    2015-11-01

    Full Text Available The sigma-2 receptor (S2R is a potential therapeutic target for cancer and neuronal diseases. However, the identity of the S2R has remained a matter of debate. Historically, the S2R has been defined as (1 a binding site with high affinity to 1,3-di-o-tolylguanidine (DTG and haloperidol but not to the selective sigma-1 receptor ligand (+-pentazocine, and (2 a protein of 18–21 kDa, as shown by specific photolabeling with [3H]-Azido-DTG and [125I]-iodoazido-fenpropimorph ([125I]-IAF. Recently, the progesterone receptor membrane component 1 (PGRMC1, a 25 kDa protein, was reported to be the S2R (Nature Communications, 2011, 2:380. To confirm this identification, we created PGRMC1 knockout NSC34 cell lines using the CRISPR/Cas9 technology. We found that in NSC34 cells devoid of or overexpressing PGRMC1, the maximum [3H]-DTG binding to the S2R (Bmax as well as the DTG-protectable [125I]-IAF photolabeling of the S2R were similar to those of wild-type control cells. Furthermore, the affinities of DTG and haloperidol for PGRMC1 (KI = 472 μM and 350 μM, respectively, as determined in competition with [3H]-progesterone, were more than 3 orders of magnitude lower than those reported for the S2R (20–80 nM. These results clarify that PGRMC1 and the S2R are distinct binding sites expressed by different genes.

  5. A strategy different from France's: German energy policy

    International Nuclear Information System (INIS)

    Linkohr, R.

    2013-01-01

    Shortly after the Fukushima accident, the German chancellor, Angela Merkel, announced a new course for the country's energy policy: nuclear power is to be fully abandoned by 2022, owing to a massive recourse to renewable sources of energy. The proclaimed goal is for renewable energy to make up 35% of the country's energy mix by 2035 and even 80% by 2050. This energy transition, though benefiting from a consensus, has run up against several difficulties: an unadapted electric power grid, the excessively high costs of investment, and exorbitant electricity rates for consumers.... Till now, this energy policy's basis principles have not come under question, but questioning are arising about the pace and cost of this transformation. (author)

  6. VP24-Karyopherin Alpha Binding Affinities Differ between Ebolavirus Species, Influencing Interferon Inhibition and VP24 Stability

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Toni M.; Edwards, Megan R.; Diederichs, Audrey; Alinger, Joshua B.; Leung, Daisy W.; Amarasinghe, Gaya K.; Basler, Christopher F.; Lyles, Douglas S.

    2016-12-14

    ABSTRACT

    Zaire ebolavirus(EBOV),Bundibugyo ebolavirus(BDBV), andReston ebolavirus(RESTV) belong to the same genus but exhibit different virulence properties. VP24 protein, a structural protein present in all family members, blocks interferon (IFN) signaling and likely contributes to virulence. Inhibition of IFN signaling by EBOV VP24 (eVP24) involves its interaction with the NPI-1 subfamily of karyopherin alpha (KPNA) nuclear transporters. Here, we evaluated eVP24, BDBV VP24 (bVP24), and RESTV VP24 (rVP24) interactions with three NPI-1 subfamily KPNAs (KPNA1, KPNA5, and KPNA6). Using purified proteins, we demonstrated that each VP24 binds to each of the three NPI-1 KPNAs. bVP24, however, exhibited approximately 10-fold-lower KPNA binding affinity than either eVP24 or rVP24. Cell-based assays also indicate that bVP24 exhibits decreased KPNA interaction, decreased suppression of IFN induced gene expression, and a decreased half-life in transfected cells compared to eVP24 or rVP24. Amino acid sequence alignments between bVP24 and eVP24 also identified residues within and surrounding the previously defined eVP24-KPNA5 binding interface that decrease eVP24-KPNA affinity or bVP24-KPNA affinity. VP24 mutations that lead to reduced KPNA binding affinity also decrease IFN inhibition and shorten VP24 half-lives. These data identify novel functional differences in VP24-KPNA interaction and reveal a novel impact of the VP24-KPNA interaction on VP24 stability.

    IMPORTANCEThe interaction of Ebola virus (EBOV) VP24 protein with host karyopherin alpha (KPNA) proteins blocks type I interferon (IFN) signaling, which is a central component of the host innate immune response to viral infection. Here, we quantitatively compared the

  7. Comparative study of different waste biomass for energy application.

    Science.gov (United States)

    Motghare, Kalyani A; Rathod, Ajit P; Wasewar, Kailas L; Labhsetwar, Nitin K

    2016-01-01

    Biomass is available in many varieties, consisting of crops as well as its residues from agriculture, forestry, and the agro-industry. These different biomass find their way as freely available fuel in rural areas but are also responsible for air pollution. Emissions from such solid fuel combustion to indoor, regional and global air pollution largely depend on fuel types, combustion device, fuel properties, fuel moisture, amount of air supply for combustion and also on climatic conditions. In both economic and environment point of view, gasification constitutes an attractive alternative for the use of biomass as a fuel, than the combustion process. A large number of studies have been reported on a variety of biomass and agriculture residues for their possible use as renewable fuels. Considering the area specific agriculture residues and biomass availability and related transportation cost, it is important to explore various local biomass for their suitability as a fuel. Maharashtra (India) is the mainstay for the agriculture and therefore, produces a significant amount of waste biomass. The aim of the present research work is to analyze different local biomass wastes for their proximate analysis and calorific value to assess their potential as fuel. The biomass explored include cotton waste, leaf, soybean waste, wheat straw, rice straw, coconut coir, forest residues, etc. mainly due to their abundance. The calorific value and the proximate analysis of the different components of the biomass helped in assessing its potential for utilization in different industries. It is observed that ash content of these biomass species is quite low, while the volatile matter content is high as compared to Indian Coal. This may be appropriate for briquetting and thus can be used as a domestic fuel in biomass based gasifier cook stoves. Utilizing these biomass species as fuel in improved cook-stove and domestic gasifier cook-stoves would be a perspective step in the rural energy and

  8. 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.

  9. Inferring Parametric Energy Consumption Functions at Different Software Levels

    DEFF Research Database (Denmark)

    Liqat, Umer; Georgiou, Kyriakos; Kerrison, Steve

    2016-01-01

    the development of a translation from LLVM IR to an intermediate representation and its integration with existing components, a translation from ISA to the same representation, a resource analyzer, an ISA-level energy model, and a mapping from this model to LLVM IR. The approach has been applied to programs....... This paper provides insights into the trade-off of precision versus analyzability at these levels.......The static estimation of the energy consumed by program executions is an important challenge, which has applications in program optimization and verification, and is instrumental in energy-aware software development. Our objective is to estimate such energy consumption in the form of functions...

  10. Study on Folate Binding Domain of Dihydrofolate Reductase in Different Plant species and Human beings

    OpenAIRE

    Samanta, Aveek; Datta, Animesh Kumar; Datta, Siraj

    2014-01-01

    Data base (NCBI and TIGR) searches are made to retrieve protein sequences of different plant species namely Medicago truncatula, Pisum sativum, Ricinus communis, Arabidopsis thaliana, Vitis vinifera, Glycine max, Daucus carota, Oryza sativa Japonica Group, Arabidopsis lyrata subsp. lyrata, Brachypodium distachyon, Oryza sativa Indica Group, Zea mays and careful alignment of derived sequences shows 95% or higher identity. Similarly, DHFR sequence of human being is also retrieved from NCBI. A p...

  11. Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin

    International Nuclear Information System (INIS)

    Soloviov, Maksym; Meuwly, Markus

    2015-01-01

    Multidimensional potential energy surfaces based on reproducing kernel-interpolation are employed to explore the energetics and dynamics of free and bound nitric oxide in myoglobin (Mb). Combining a force field description for the majority of degrees of freedom and the higher-accuracy representation for the NO ligand and the Fe out-of-plane motion allows for a simulation approach akin to a mixed quantum mechanics/molecular mechanics treatment. However, the kernel-representation can be evaluated at conventional force-field speed. With the explicit inclusion of the Fe-out-of-plane (Fe-oop) coordinate, the dynamics and structural equilibrium after photodissociation of the ligand are correctly described compared to experiment. Experimentally, the Fe-oop coordinate plays an important role for the ligand dynamics. This is also found here where the isomerization dynamics between the Fe–ON and Fe–NO state is significantly affected whether or not this co-ordinate is explicitly included. Although the Fe–ON conformation is metastable when considering only the bound 2 A state, it may disappear once the 4 A state is included. This explains the absence of the Fe–ON state in previous experimental investigations of MbNO

  12. Physical adsorption vs. chemical binding of undecylenic acid on porous silicon surface: a comparative study of differently functionalized materials

    Energy Technology Data Exchange (ETDEWEB)

    Salonen, J.; Lehto, V.P. [University of Turku (Finland). Department of Physics; Chirvony, V.; Matveeva, E. [Nanophotonics Technology Center, Technical University of Valencia (Spain); Pastor, E.

    2009-07-15

    To imply miscibility to porous silicon (PSi) used for biomedical purposes a number of functionalization methods are employed. In order to distinguish between a non-specific surfactant-like interaction (physical sorption) and chemical binding of unsaturated chemicals (undecylenic acid, UD) to H-terminated PSi surface we studied the two differently treated materials. Differential scanning calorimetry (DSC) and thermogravimetry (TGA), BET and FTIR measurements were performed with the PSi powder samples (n+ doped). Changes in surface area, weight loss, calorific effect and chemical composition that accompanied the thermal treatment have shown that the physisorbed UD molecules undergo a chemical process (binding) with the Si-H{sub x} surface groups at about 150 C in both, N{sub 2} inert atmosphere and in a synthetic air, oxidative atmosphere. Controlled conversion of physically sorbed molecules to the chemically attached ones is discussed with respect to methods of surface modification of PSi materials for increasing their biocompatibility. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  13. Energy poor or fuel poor: What are the differences?

    International Nuclear Information System (INIS)

    Li, Kang; Lloyd, Bob; Liang, Xiao-Jie; Wei, Yi-Ming

    2014-01-01

    Energy poverty and fuel poverty are descriptors of problems of households' energy consumption, they are both distinct problems and have been addressed by many researchers, organizations and governments. Cross use of the terms of energy poverty and fuel poverty in published papers is common. As an accurate descriptor is the presupposition of research and policy development, especially for those who just started to pay attention to this issue, this paper compares the definitions, research priorities, status quo, and problems of these two concepts, and summarizes the relationship between them. The paper suggests that only when the research targets are households who are living in a cold climate and have difficulty in getting access to electricity or modern cooking facilities, and in supplying indoor heating with appropriate cost, the concepts of energy poverty and fuel poverty have the chance to be broadened and mutually integrated. - Highlights: • Address energy poverty and fuel poverty simultaneously. • Compare energy poverty and fuel poverty from 4 perspectives. • Summarize the relationship between energy poverty and fuel poverty. • Divide energy poor and fuel poor into three categories

  14. Protein and energy utilization by cockerels fed four different ...

    African Journals Online (AJOL)

    Protein and energy efficiency were significantly (p<0.05) improved in birds fed diet 3 and diet 4. These results are due to the consumption of higher levels of protein and energy by cockerels fed diet 3 and diet 4 coupled with the birds ability to better utilize these nutrients compared to those fed diet 1 and diet 2 respectively.

  15. Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2

    Science.gov (United States)

    Athanasiou, Christina; Vasilakaki, Sofia; Dellis, Dimitris; Cournia, Zoe

    2018-01-01

    Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design data resource (D3R) organizes challenges against blinded experimental data to prospectively test computational methodologies as an opportunity for improved methods and algorithms to emerge. We participated in Grand Challenge 2 to predict the crystallographic poses of 36 Farnesoid X Receptor (FXR)-bound ligands and the relative binding affinities for two designated subsets of 18 and 15 FXR-bound ligands. Here, we present our methodology for pose and affinity predictions and its evaluation after the release of the experimental data. For predicting the crystallographic poses, we used docking and physics-based pose prediction methods guided by the binding poses of native ligands. For FXR ligands with known chemotypes in the PDB, we accurately predicted their binding modes, while for those with unknown chemotypes the predictions were more challenging. Our group ranked #1st (based on the median RMSD) out of 46 groups, which submitted complete entries for the binding pose prediction challenge. For the relative binding affinity prediction challenge, we performed free energy perturbation (FEP) calculations coupled with molecular dynamics (MD) simulations. FEP/MD calculations displayed a high success rate in identifying compounds with better or worse binding affinity than the reference (parent) compound. Our studies suggest that when ligands with chemical precedent are available in the literature, binding pose predictions using docking and physics-based methods are reliable; however, predictions are challenging for ligands with completely unknown chemotypes. We also show that FEP/MD calculations hold predictive value and can nowadays be used in a high throughput mode in a lead optimization project provided that crystal structures of

  16. Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2.

    Science.gov (United States)

    Athanasiou, Christina; Vasilakaki, Sofia; Dellis, Dimitris; Cournia, Zoe

    2018-01-01

    Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design data resource (D3R) organizes challenges against blinded experimental data to prospectively test computational methodologies as an opportunity for improved methods and algorithms to emerge. We participated in Grand Challenge 2 to predict the crystallographic poses of 36 Farnesoid X Receptor (FXR)-bound ligands and the relative binding affinities for two designated subsets of 18 and 15 FXR-bound ligands. Here, we present our methodology for pose and affinity predictions and its evaluation after the release of the experimental data. For predicting the crystallographic poses, we used docking and physics-based pose prediction methods guided by the binding poses of native ligands. For FXR ligands with known chemotypes in the PDB, we accurately predicted their binding modes, while for those with unknown chemotypes the predictions were more challenging. Our group ranked #1st (based on the median RMSD) out of 46 groups, which submitted complete entries for the binding pose prediction challenge. For the relative binding affinity prediction challenge, we performed free energy perturbation (FEP) calculations coupled with molecular dynamics (MD) simulations. FEP/MD calculations displayed a high success rate in identifying compounds with better or worse binding affinity than the reference (parent) compound. Our studies suggest that when ligands with chemical precedent are available in the literature, binding pose predictions using docking and physics-based methods are reliable; however, predictions are challenging for ligands with completely unknown chemotypes. We also show that FEP/MD calculations hold predictive value and can nowadays be used in a high throughput mode in a lead optimization project provided that crystal structures of

  17. Characterization of Protein and Peptide Binding to Nanogels Formed by Differently Charged Chitosan Derivatives

    Directory of Open Access Journals (Sweden)

    Anastasia Zubareva

    2013-07-01

    Full Text Available Chitosan (Chi is a natural biodegradable cationic polymer with remarkable potency as a vehicle for drug or vaccine delivery. Chi possesses multiple groups, which can be used both for Chi derivatization and for particle formation. The aim of this work was to produce stable nanosized range Chi gels (nanogels, NGs with different charge and to study the driving forces of complex formation between Chi NGs and proteins or peptides. Positively charged NGs of 150 nm in diameter were prepared from hexanoyl chitosan (HC by the ionotropic gelation method while negatively charged NGs of 190 nm were obtained from succinoyl Chi (SC by a Ca2+ coacervation approach. NGs were loaded with a panel of proteins or peptides with different weights and charges. We show that NGs preferentially formed complexes with oppositely charged molecules, especially peptides, as was demonstrated by gel-electrophoresis, confocal microscopy and HPLC. Complex formation was accompanied by a change in zeta-potential and decrease in size. We concluded that complex formation between Chi NGs and peptide/proteins is mediated mostly by electrostatic interactions.

  18. Energy Expenditure of Trotting Gait Under Different Gait Parameters

    Science.gov (United States)

    Chen, Xian-Bao; Gao, Feng

    2017-07-01

    Robots driven by batteries are clean, quiet, and can work indoors or in space. However, the battery endurance is a great problem. A new gait parameter design energy saving strategy to extend the working hours of the quadruped robot is proposed. A dynamic model of the robot is established to estimate and analyze the energy expenditures during trotting. Given a trotting speed, optimal stride frequency and stride length can minimize the energy expenditure. However, the relationship between the speed and the optimal gait parameters is nonlinear, which is difficult for practical application. Therefore, a simplified gait parameter design method for energy saving is proposed. A critical trotting speed of the quadruped robot is found and can be used to decide the gait parameters. When the robot is travelling lower than this speed, it is better to keep a constant stride length and change the cycle period. When the robot is travelling higher than this speed, it is better to keep a constant cycle period and change the stride length. Simulations and experiments on the quadruped robot show that by using the proposed gait parameter design approach, the energy expenditure can be reduced by about 54% compared with the 100 mm stride length under 500 mm/s speed. In general, an energy expenditure model based on the gait parameter of the quadruped robot is built and the trotting gait parameters design approach for energy saving is proposed.

  19. Quantification of the health hazards associated with different energy sources

    International Nuclear Information System (INIS)

    Reissland, J.A.; Kendall, G.M.; Greenhalgh, J.R.

    1982-01-01

    Comparisons of health hazards which may result from the operation of different types of electrical power-producing systems are a necessary input to the decision-making process of planning future supplies. Although other factors have played a dominant role in the past and will continue to be a major influence, much greater attention is now devoted to a consideration of detriment to health associated with large-scale industrial development. The paper considers only this health aspect of the comparison and concentrates on one aspect of that, namely on how the impact on health of workers and public can be expressed to represent the detriment. Two measures are discussed: the number of deaths and the effective loss of life, both evaluated per GW(e).a. The latter is extended along the same lines as in the ICRP publication 'Problems Involved in Developing an Index of Harm'. The index of harm is a measure of hazard to a worker in a particular industry; the analogous quantity here is a measure of hazard of operating a 1-GW(e) power plant. For illustration, the hazards of coal-fired and nuclear power stations are compared although certain factors are omitted from both cycles which it will be essential to include if the method is extended to bring wind, wave and solar energy sources into the comparison. Inevitably some contributions are very difficult to quantify and it may be more realistic to consider these qualitatively rather than attempt to fold them in with artificial numerical values. The procedure described for the inclusion of quantifiable factors seems to be a reasonable basis for comparison but it is not suggested that any such procedure is adequate by itself. Clearly comparisons should be made on several distinct bases. (author)

  20. Renewable energies in Slovakia and objectives for 2020 - development of the different sectors

    International Nuclear Information System (INIS)

    Queval, Benjamin; Makhloufi, Rachid; Libercan, Adam

    2011-10-01

    After a presentation of the Slovakian general context (geography, policy, energy consumption, production, sources and policy), this report presents the Slovakian renewable energy development program (actors, regulation, and foreseen development scenario), and proposes an overview of the current situation and perspectives for the different concerned sectors: photovoltaic, biomass, bio-fuels, geothermal energy, wind energy, hydraulic energy

  1. Alternatives - talk about energy differently. Radioactive waste a societal issue

    International Nuclear Information System (INIS)

    2004-01-01

    ''Alternatives'' is an information magazine proposed by the Areva Group, a world nuclear energy leader. It is devoted to the public information on topics of the Group activities. This issue deals with the fusion technology, the strengths and weaknesses of interconnected networks, the undersea tidal power farms, the danish paradox which has the highest levels of CO 2 emissions despite the use of wind energy, the international community renewed commitment to renewable energy, the hydrogen, the low speed wind turbines and the future miniature fuel cells. A special interest is given to the radioactive wastes management. (A.L.B.)

  2. Binding of ouabain and marinobufagenin leads to different structural changes in Na,K-ATPase and depends on the enzyme conformation.

    Science.gov (United States)

    Klimanova, Elizaveta A; Petrushanko, Irina Yu; Mitkevich, Vladimir A; Anashkina, Anastasia A; Orlov, Sergey N; Makarov, Alexander A; Lopina, Olga D

    2015-09-14

    Ion pump, Na,K-ATPase specifically binds cardiotonic steroids (CTS), which leads to inhibition of the enzyme activity and activation of signaling network in the cell. We have studied interaction of Na,K-ATPase with CTS of two different types - marinobufagenin and ouabain. We have shown that both CTS inhibit activity of Na,K-ATPase with the same Ki values, but binding of ouabain is sensitive to the conformation of Na,K-ATPase while binding of marinobufagenin is not. Furthermore, binding of ouabain and marinobufagenin results in different structural changes in Na,K-ATPase. Our data allow to explain the diversity of effects on the receptor function of Na,K-ATPase caused by different types of CTS. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  3. Evaluation of different weather files on energy analysis of buildings

    Energy Technology Data Exchange (ETDEWEB)

    Michopoulos, Apostolos; Voulgari, Vassiliki; Papakostas, Konstantinos; Kyriakis, Nikolas [Process Equipment Design Laboratory, Mechanical Engineering Department, Aristotle University of Thessaloniki -- POB 487 -- 541 24 Thessaloniki (Greece)

    2012-07-01

    The building energy demand simulation tools consist the compass of the roadmap towards the energy efficient building. Apart from the software itself, the result of the simulation strongly depends on the degree the data used represent the actual situation, among which the climate data of the area are a key factor. In this work, the energy demand of a large building complex is estimated, using the widely accepted EnergyPlus building simulation software in combination with two, also widely accepted, weather files. The simulation results for heating are compared with the actual fuel consumption of a three-year operation period. The comparison reveals that the weather file and the size of the simulation domain significantly affect the simulation representativeness.

  4. Altered levels of laminin receptor mRNA in various human carcinoma cells that have different abilities to bind laminin

    DEFF Research Database (Denmark)

    Wewer, U M; Liotta, L A; Jaye, M

    1986-01-01

    The human laminin receptor was purified and molecularly cloned to investigate its biosynthetic regulation. Laminin receptor from normal and neoplastic tissue was preparatively affinity purified to homogeneity based on the high affinity of the receptor for laminin. The apparent molecular weight...... of the receptor from different carcinoma sources and from normal placental tissue is in the range of 68-72 kDa. Isoelectric focusing and two-dimensional gel electrophoresis indicated that the receptor protein consists of one major polypeptide chain with a pI value of 6.4 +/- 0.2. Laminin receptor cDNA clones were...... isolated after screening a human endothelial lambda gt11 cDNA library with a monoclonal antibody directed against a domain of the laminin receptor involved in ligand binding. Definitive identification of the cDNA clones was based on comparison of cDNA sequence with the amino acid sequence of a cyanogen...

  5. Identification of light-harvesting chlorophyll a/b-binding protein genes of Zostera marina L. and their expression under different environmental conditions

    Science.gov (United States)

    Kong, Fanna; Zhou, Yang; Sun, Peipei; Cao, Min; Li, Hong; Mao, Yunxiang

    2016-02-01

    Photosynthesis includes the collection of light and the transfer of solar energy using light-harvesting chlorophyll a/b-binding (LHC) proteins. In high plants, the LHC gene family includes LHCA and LHCB sub-families, which encode proteins constituting the light-harvesting complex of photosystems I and II. Zostera marina L. is a monocotyledonous angiosperm and inhabits submerged marine environments rather than land environments. We characterized the Lhca and Lhcb gene families of Z. marina from the expressed sequence tags (EST) database. In total, 13 unigenes were annotated as ZmLhc, 6 in Lhca family and 7 in ZmLhcb family. ZmLHCA and ZmLHCB contained the conservative LHC motifs and amino acid residues binding chlorophyll. The average similarity among mature ZmLHCA and ZmLHCB was 48.91% and 48.66%, respectively, which indicated a high degree of divergence within ZmLHChc gene family. The reconstructed phylogenetic tree showed that the tree topology and phylogenetic relationship were similar to those reported in other high plants, suggesting that the Lhc genes were highly conservative and the classification of ZmLhc genes was consistent with the evolutionary position of Z. marina. Real-time reverse transcription (RT) PCR analysis showed that different members of ZmLhca and ZmLhcb responded to a stress in different expression patterns. Salinity, temperature, light intensity and light quality may affect the expression of most ZmLhca and ZmLhcb genes. Inorganic carbon concentration and acidity had no obvious effect on ZmLhca and ZmLhcb gene expression, except for ZmLhca6.

  6. EROI of crystalline silicon photovoltaics : Variations under different assumptions regarding manufacturing energy inputs and energy output

    OpenAIRE

    Lundin, Johan

    2013-01-01

    Installed photovoltaic nameplate power have been growing rapidly around the worldin the last few years. But how much energy is returned to society (i.e. net energy) by this technology, and which factors contribute the most to the amount of energy returned? The objective of this thesis was to examine the importance of certain inputs and outputs along the solar panel production chain and their effect on the energy return on (energy) investment (EROI) for crystalline wafer-based photovoltaics. A...

  7. ‘maskBAD’ – a package to detect and remove Affymetrix probes with binding affinity differences

    Directory of Open Access Journals (Sweden)

    Dannemann Michael

    2012-04-01

    Full Text Available Abstract Background Hybridization differences caused by target sequence differences can be a confounding factor in analyzing gene expression on microarrays, lead to false positives and reduce power to detect real expression differences. We prepared an R Bioconductor compatible package to detect, characterize and remove such probes in Affymetrix 3’IVT and exon-based arrays on the basis of correlation of signal intensities from probes within probe sets. Results Using completely mouse genomes we determined type 1 (false negatives and type 2 (false positives errors with high accuracy and we show that our method routinely outperforms previous methods. When detecting 76.2% of known SNP/indels in mouse expression data, we obtain at most 5.5% false positives. At the same level of false positives, best previous method detected 72.6%. We also show that probes with differing binding affinity both hinder differential expression detection and introduce artifacts in cancer-healthy tissue comparison. Conclusions Detection and removal of such probes should be a routine step in Affymetrix data preprocessing. We prepared a user friendly R package, compatible with Bioconductor, that allows the filtering and improving of data from Affymetrix microarrays experiments.

  8. 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

    2017-02-08

    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.

  9. Storing energy for cooling demand management in tropical climates: A techno-economic comparison between different energy storage technologies

    International Nuclear Information System (INIS)

    Comodi, Gabriele; Carducci, Francesco; Sze, Jia Yin; Balamurugan, Nagarajan; Romagnoli, Alessandro

    2017-01-01

    This paper addresses the role of energy storage in cooling applications. Cold energy storage technologies addressed are: Li-Ion batteries (Li-Ion EES), sensible heat thermal energy storage (SHTES); phase change material (PCM TES), compressed air energy storage (CAES) and liquid air energy storage (LAES). Batteries and CAES are electrical storage systems which run the cooling systems; SHTES and PCM TES are thermal storage systems which directly store cold energy; LAES is assessed as a hybrid storage system which provides both electricity (for cooling) and cold energy. A hybrid quantitative-qualitative comparison is presented. Quantitative comparison was investigated for different sizes of daily cooling energy demand and three different tariff scenarios. A techno-economic analysis was performed to show the suitability of the different storage systems at different scales. Three parameters were used (Pay-back period, Savings-per-energy-unit and levelized-cost-of-energy) to analyze and compare the different scenarios. The qualitative analysis was based on five comparison criteria (Complexity, Technology Readiness Level, Sustainability, Flexibility and Safety). Results showed the importance of weighing the pros and cons of each technology to select a suitable cold energy storage system. Techno-economic analysis highlighted the fundamental role of tariff scenario: a greater difference between peak and off-peak electricity tariff leads to a shorter payback period of each technology. - Highlights: • Techno-economic evaluation of energy storage solutions for cooling applications. • Comparison between five energy storage (EES, SHTES, PCM, CAES, LAES) is performed. • Qualitative and quantitative performance parameters were used for the analysis. • LAES/PCM can be valid alternatives to more established technologies EES, SHTES, CAES. • Tariffs, price arbitrage and investment cost play a key role in energy storage spread.

  10. Radioiodinated ligands for the estrogen receptor: Effect of different 7-cyanoalkyl chains on the binding affinity of novel iodovinyl-6-dehydroestradiols

    International Nuclear Information System (INIS)

    Neto, Carina; Oliveira, Maria Cristina; Gano, Lurdes; Marques, Fernanda; Santos, Isabel; Morais, Goreti Ribeiro; Yasuda, Takumi; Thiemann, Thies; Botelho, Filomena; Oliveira, Carlos F.

    2009-01-01

    Three novel 17α-ethynyl-Δ 6,7 -estra-3,17β-diols and their 17α-[ 125 I]-iodovinyl derivatives, containing different C7-cyanoalkyl chains, were studied as potential radioligands for the estrogen receptor. The influence of the chain length on the biological behaviour of the compounds was assessed through in vitro ER binding assays of the ethynyl derivatives and breast cancer cell uptake studies of the 17α-[ 125 I]-iodovinyl-Δ 6,7 -estra-3,17β-diols. A difference in alkyl chain induced a decrease in ER binding affinities of substances, however, the receptor-binding affinities (RBA) of all compounds were lower than that of estradiol itself. In addition, a non-specific cell binding was observed which is in accordance with the encountered ethynyl RBA values suggesting that the uptake is not ER mediated

  11. Radioiodinated ligands for the estrogen receptor: Effect of different 7-cyanoalkyl chains on the binding affinity of novel iodovinyl-6-dehydroestradiols

    Energy Technology Data Exchange (ETDEWEB)

    Neto, Carina [Instituto Tecnologico e Nuclear, Estrada Nacional 10, 2686-953 Sacavem (Portugal); Centro de Investigacao em Meio Ambiente Genetica e Oncobiologia (CIMAGO) (Portugal); Oliveira, Maria Cristina [Instituto Tecnologico e Nuclear, Estrada Nacional 10, 2686-953 Sacavem (Portugal); Centro de Investigacao em Meio Ambiente Genetica e Oncobiologia (CIMAGO) (Portugal)], E-mail: cmelo@itn.pt; Gano, Lurdes; Marques, Fernanda; Santos, Isabel [Instituto Tecnologico e Nuclear, Estrada Nacional 10, 2686-953 Sacavem (Portugal); Centro de Investigacao em Meio Ambiente Genetica e Oncobiologia (CIMAGO) (Portugal); Morais, Goreti Ribeiro [Faculty of Pharmacy, University of Lisbon, Lisbon (Portugal); Yasuda, Takumi [Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Fukuoka (Japan); Thiemann, Thies [Centro de Investigacao em Meio Ambiente Genetica e Oncobiologia (CIMAGO) (Portugal); Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Fukuoka (Japan); Botelho, Filomena [Centro de Investigacao em Meio Ambiente Genetica e Oncobiologia (CIMAGO) (Portugal); Instituto de Biofisica/Biomatematica, IBILI, FMUC, Coimbra (Portugal); Oliveira, Carlos F. [Centro de Investigacao em Meio Ambiente Genetica e Oncobiologia (CIMAGO) (Portugal); Clinica Ginecologica, FMUC, Coimbra (Portugal)

    2009-02-15

    Three novel 17{alpha}-ethynyl-{delta}{sup 6,7}-estra-3,17{beta}-diols and their 17{alpha}-[{sup 125}I]-iodovinyl derivatives, containing different C7-cyanoalkyl chains, were studied as potential radioligands for the estrogen receptor. The influence of the chain length on the biological behaviour of the compounds was assessed through in vitro ER binding assays of the ethynyl derivatives and breast cancer cell uptake studies of the 17{alpha}-[{sup 125}I]-iodovinyl-{delta}{sup 6,7}-estra-3,17{beta}-diols. A difference in alkyl chain induced a decrease in ER binding affinities of substances, however, the receptor-binding affinities (RBA) of all compounds were lower than that of estradiol itself. In addition, a non-specific cell binding was observed which is in accordance with the encountered ethynyl RBA values suggesting that the uptake is not ER mediated.

  12. Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test

    Science.gov (United States)

    Pandey, Preeti; Srivastava, Rakesh; Bandyopadhyay, Pradipta

    2018-03-01

    The relative performance of MM-PBSA and MM-3D-RISM methods to estimate the binding free energy of protein-ligand complexes is investigated by applying these to three proteins (Dihydrofolate Reductase, Catechol-O-methyltransferase, and Stromelysin-1) differing in the number of metal ions they contain. None of the computational methods could distinguish all the ligands based on their calculated binding free energies (as compared to experimental values). The difference between the two comes from both polar and non-polar part of solvation. For charged ligand case, MM-PBSA and MM-3D-RISM give a qualitatively different result for the polar part of solvation.

  13. 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.

  14. Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of d-amino acid oxidase inhibitors

    Science.gov (United States)

    Orgován, Zoltán; Ferenczy, György G.; Steinbrecher, Thomas; Szilágyi, Bence; Bajusz, Dávid; Keserű, György M.

    2018-02-01

    Optimization of fragment size d-amino acid oxidase (DAAO) inhibitors was investigated using a combination of computational and experimental methods. Retrospective free energy perturbation (FEP) calculations were performed for benzo[d]isoxazole derivatives, a series of known inhibitors with two potential binding modes derived from X-ray structures of other DAAO inhibitors. The good agreement between experimental and computed binding free energies in only one of the hypothesized binding modes strongly support this bioactive conformation. Then, a series of 1-H-indazol-3-ol derivatives formerly not described as DAAO inhibitors was investigated. Binding geometries could be reliably identified by structural similarity to benzo[d]isoxazole and other well characterized series and FEP calculations were performed for several tautomers of the deprotonated and protonated compounds since all these forms are potentially present owing to the experimental pKa values of representative compounds in the series. Deprotonated compounds are proposed to be the most important bound species owing to the significantly better agreement between their calculated and measured affinities compared to the protonated forms. FEP calculations were also used for the prediction of the affinities of compounds not previously tested as DAAO inhibitors and for a comparative structure-activity relationship study of the benzo[d]isoxazole and indazole series. Selected indazole derivatives were synthesized and their measured binding affinity towards DAAO was in good agreement with FEP predictions.

  15. Age and sex differences in oxytocin and vasopressin V1a receptor binding densities in the rat brain: focus on the social decision-making network.

    Science.gov (United States)

    Smith, Caroline J W; Poehlmann, Max L; Li, Sara; Ratnaseelan, Aarane M; Bredewold, Remco; Veenema, Alexa H

    2017-03-01

    Oxytocin (OT) and vasopressin (AVP) regulate various social behaviors via activation of the OT receptor (OTR) and the AVP V1a receptor (V1aR) in the brain. Social behavior often differs across development and between the sexes, yet our understanding of age and sex differences in brain OTR and V1aR binding remains incomplete. Here, we provide an extensive analysis of OTR and V1aR binding density throughout the brain in juvenile and adult male and female rats, with a focus on regions within the social decision-making network. OTR and V1aR binding density were higher in juveniles than in adults in regions associated with reward and socio-spatial memory and higher in adults than in juveniles in key regions of the social decision-making network and in cortical regions. We discuss possible implications of these shifts in OTR and V1aR binding density for the age-specific regulation of social behavior. Furthermore, sex differences in OTR and V1aR binding density were less numerous than age differences. The direction of these sex differences was region-specific for OTR but consistently higher in females than in males for V1aR. Finally, almost all sex differences in OTR and V1aR binding density were already present in juveniles and occurred in regions with denser binding in adults compared to juveniles. Possible implications of these sex differences for the sex-specific regulation of behavior, as well potential underlying mechanisms, are discussed. Overall, these findings provide an important framework for testing age- and sex-specific roles of OTR and V1aR in the regulation of social behavior.

  16. The effects of different casting techniques on the hardness, energy ...

    African Journals Online (AJOL)

    The effect of casting technique on the impact strength, energy absorbance and hardness of sand cast Pb-Sb-Cu alloys was studied following casting of the alloys using three techniques. Cooling of the alloys after casting was carried out in water, air and furnace in order to vary the micro-structure of the alloys produced.

  17. Evaluation of energy consumption in different drying methods

    Energy Technology Data Exchange (ETDEWEB)

    Motevali, Ali; Minaei, Saeid; Khoshtagaza, Mohammad Hadi [Department of Agricultural Machinery Engineering, Agricultural Faculty, Tarbiat Modares University, Tehran 14115-111 (Iran, Islamic Republic of)

    2011-02-15

    This study was conducted to evaluate energy consumption in various drying systems including hot-air convection, use of microwave pretreatment with convection dryer, microwave drying, vacuum drying and infrared drying. Tests were conducted using pomegranate arils under various experimental conditions as follows. In convection dryer at six temperature levels (45, 50, 55, 60, 65 and 70 C) and three air velocity levels (0.5, 1 and 1.5 m/s) at three pretreatments of control, 100 W microwave pretreatment for 20 min and 200 W microwave pretreatment for 10 min. Experiments in the microwave dryer were done at three power levels of 100, 200 and 300 W and in vacuum dryer at five temperature levels (50, 60, 70, 80, and 90 C) under 250 kPa pressure. For infrared drying, there were four air velocity levels (0.3, 0.5, 0.7 and 1 m/s) and three illumination levels (0.22, 0.31 and 0.49 W/cm{sup 2}). Experimental results showed that minimum and maximum energy consumption in pomegranate drying were associated with microwave and vacuum dryers, respectively. The use of microwave pretreatment in drying pomegranate arils in hot air dryer decreased drying time and energy consumption in comparison with pure convection drying. In infrared drying, it was found that drying time increased with air velocity which resulted in increased energy consumption. (author)

  18. Dye solar cells: a different approach to solar energy

    CSIR Research Space (South Africa)

    Le Roux, Lukas J

    2008-11-01

    Full Text Available An attractive and cheaper alternative to siliconbased photovoltaic (PV) cells for the conversion of solar light into electrical energy is to utilise dyeadsorbed, large-band-gap metal oxide materials such as TiO2 to absorb the solar light...

  19. Fattening Performance of White Fulani Cattle Fed Different Energy ...

    African Journals Online (AJOL)

    Twenty White Fulani bulls with an average weight of 225kg were randomly allotted to four isonitrogenous diets formulated with maize offal, wheat offal, rice offal and sorghum panicle as the energy sources. Signal grass (Bracharia decumbens) hay was offered as the basal diet. A metabolism trial was conducted at the end of ...

  20. Energy supplementation of yearling steers at different stocking rates ...

    African Journals Online (AJOL)

    (supplementering met 0, 1,2 of 4 kg mieliemeel/dag), elkeen teen een van twee veebeladings fligte veebelading (LSR: 6 ... en 1 18.1 + 7 .4 kg oor die weiperiode van 124 dae teen supplementeringspeile van 0, l, 2 en 4 kg mieliemeel/os/dag, ... Keywords: Energy supplementation, growth rates, subtropical pastures.

  1. Computational Studies of Difference in Binding Modes of Peptide and Non-Peptide Inhibitors to MDM2/MDMX Based on Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Yuxin Zhang

    2012-02-01

    Full Text Available Inhibition of p53-MDM2/MDMX interaction is considered to be a promising strategy for anticancer drug design to activate wild-type p53 in tumors. We carry out molecular dynamics (MD simulations to study the binding mechanisms of peptide and non-peptide inhibitors to MDM2/MDMX. The rank of binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA method agrees with one of the experimental values. The results suggest that van der Waals energy drives two kinds of inhibitors to MDM2/MDMX. We also find that the peptide inhibitors can produce more interaction contacts with MDM2/MDMX than the non-peptide inhibitors. Binding mode predictions based on the inhibitor-residue interactions show that the π–π, CH–π and CH–CH interactions dominated by shape complimentarity, govern the binding of the inhibitors in the hydrophobic cleft of MDM2/MDMX. Our studies confirm the residue Tyr99 in MDMX can generate a steric clash with the inhibitors due to energy and structure. This finding may theoretically provide help to develop potent dual-specific or MDMX inhibitors.

  2. Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding.

    Science.gov (United States)

    Biela, Adam; Betz, Michael; Heine, Andreas; Klebe, Gerhard

    2012-08-01

    The binding of four congeneric peptide-like thermolysin inhibitors has been studied by high-resolution crystal structure analysis and isothermal titration calorimetry. The ligands differ only by a terminal carboxylate and/or methyl group. A surprising non-additivity of functional group contributions for the carboxylate and/or methyl groups is detected. Adding the methyl first and then the carboxylate group results in a small Gibbs free energy increase and minor enthalpy/entropy partitioning for the first modification, whereas the second involves a strong affinity increase combined with large enthalpy/entropy changes. However, first adding the carboxylate and then the methyl group yields reverse effects: the acidic group attachment now causes minor effects, whereas the added methyl group provokes large changes. As all crystal structures show virtually identical binding modes, affinity changes are related to rearrangements of the first solvation layer next to the S(2)' pocket. About 20-25 water molecules are visible next to the studied complexes. The added COO(-) groups perturb the local water network in both carboxylated complexes, and the attached methyl groups provide favorable interaction sites for water molecules. Apart from one example, a contiguously connected water network between protein and ligand functional groups is observed in all complexes. In the complex with the carboxylated ligand, which still lacks the terminal methyl group, the water network is unfavorably ruptured. This results in a surprising thermodynamic signature showing only a minor affinity increase upon COO(-) group attachment. Because the further added methyl group provides a favorable interaction site for water, the network can be reestablished, and a strong affinity increase with a large enthalpy/entropy signature is then detected. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Toxic metals (Ni2+, Pb2+, Hg2+) binding affinity of dissolved organic matter (DOM) derived from different ages municipal landfill leachate

    Science.gov (United States)

    Rikta, S. Y.; Tareq, Shafi M.; Uddin, M. Khabir

    2018-03-01

    Solid waste production is rapidly increasing in Bangladesh and landfill leachate is the consequence of the decomposition of this waste. These leachates contain heavy metals and significant amount of dissolved organic matter (DOM). DOM is known to have considerable role in heavy metals speciation. Hence, it is important to characterize DOM/leachate and evaluate toxic metals binding affinity of DOM. The objectives of this study were to characterize the DOM in landfill leachate through physico-chemical and optical analyses and to investigate the toxic metals (Ni2+, Pb2+ and Hg2+) binding affinity of three different ages (fresh sample L-1, young sample L-2 and mature sample L-3) DOM samples. Results suggested that leachate is a potential pollutant which contained very high organic pollutant load. Conditional stability constant (Log K) and percentages of fluorophores that correspond to metal binding (% f) values indicated that young DOM sample (L-2) had the highest binding affinity to all the three metals ions. In general, DOM samples showed the following order affinity to the metal ions; Ni2+ binding affinity: L-2 > L-3 > L-1, Pb2+ binding affinity: L-2 > L-3 > L-1 and Hg2+ binding affinity: L-2 > L-1 > L-3.

  4. Structural changes of mitochondrial creatine kinase upon binding of ADP, ATP, or Pi, observed by reaction-induced infrared difference spectra.

    Science.gov (United States)

    Granjon, T; Vacheron, M J; Vial, C; Buchet, R

    2001-03-06

    Structural modifications of rabbit heart mitochondrial creatine kinase induced by the binding of its nucleotide substrates and Pi were investigated. Reaction-induced difference spectra (RIDS), resulting from the difference between infrared spectra recorded before and after the photorelease of a caged ligand, allow us to detect very small variations in protein structure. Our results indicated that the protein secondary structure remained relatively stable during nucleotide binding. Indeed, this binding to creatine kinase affected only a few amino acids, and caused small peptide backbone deformations and alterations of the carbonyl side chains of aspartate or glutamate, reflecting modifications within preexisting elements rather than a net change in secondary structure. Nonetheless, MgADP and MgATP RIDS were distinct, whereas the MgPi RIDS presented some similarities with the MgATP one. The difference between MgADP and MgATP RIDS could reflect a distinct configuration of the two metal-nucleotide complexes inducing a different positioning and/or a distinct binding mode to the creatine kinase active site. Comparison of the MgATP and MgPi RIDS suggests that Pi binding took place at the same binding site as the gamma-phosphoryl group of ATP. Thus, the difference between MgADP and MgATP RIDS would mainly be due to the effect of the gamma-P of ATP. The differences observed when comparing the RIDS resulting from the binding of nucleotides to octameric mitochondrial creatine kinase or dimeric cytosolic isoform could reflect the distinct oligomerization states and physicochemical or kinetic properties of the two isoenzymes.

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

    International Nuclear Information System (INIS)

    Yesilgul, U.; Ungan, F.; Kasapoglu, E.; Sari, H.; Sökmen, I.

    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. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  6. Hyper-Binding across Time: Age Differences in the Effect of Temporal Proximity on Paired-Associate Learning

    Science.gov (United States)

    Campbell, Karen L.; Trelle, Alexandra; Hasher, Lynn

    2014-01-01

    Older adults show hyper- (or excessive) binding effects for simultaneously and sequentially presented distraction. Here, we addressed the potential role of hyper-binding in paired-associate learning. Older and younger adults learned a list of word pairs and then received an associative recognition task in which rearranged pairs were formed from…

  7. Investigation of the binding free energies of FDA approved drugs against subtype B and C-SA HIV PR: ONIOM approach.

    Science.gov (United States)

    Sanusi, Z K; Govender, T; Maguire, G E M; Maseko, S B; Lin, J; Kruger, H G; Honarparvar, B

    2017-09-01

    Human immune virus subtype C is the most widely spread HIV subtype in Sub-Sahara Africa and South Africa. A profound structural insight on finding potential lead compounds is therefore necessary for drug discovery. The focus of this study is to rationalize the nine Food and Drugs Administration (FDA) HIV antiviral drugs complexed to subtype B and C-SA PR using ONIOM approach. To achieve this, an integrated two-layered ONIOM model was used to optimize the geometrics of the FDA approved HIV-1 PR inhibitors for subtype B. In our hybrid ONIOM model, the HIV-1 PR inhibitors as well as the ASP 25/25' catalytic active residues were treated at high level quantum mechanics (QM) theory using B3LYP/6-31G(d), and the remaining HIV PR residues were considered using the AMBER force field. The experimental binding energies of the PR inhibitors were compared to the ONIOM calculated results. The theoretical binding free energies (?G bind ) for subtype B follow a similar trend to the experimental results, with one exemption. The computational model was less suitable for C-SA PR. Analysis of the results provided valuable information about the shortcomings of this approach. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide much improved binding energies for complex enzyme drug interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Consumer Attitudes About Renewable Energy. Trends and Regional Differences

    Energy Technology Data Exchange (ETDEWEB)

    Bird, Lori [Natural Marketing Institute, Harleysville, PA (United States); Sumner, Jenny [Natural Marketing Institute, Harleysville, PA (United States)

    2011-04-01

    The data in this report are taken from Natural Marketing Institute's (NMI's) Lifestyles of Health and Sustainability Consumer Trends Database. Created in 2002, the syndicated consumer database contains responses from 2,000 to 4,000 nationally representative U.S. adults (meaning the demographics of the sample are consistent with U.S. Census findings) each year. NMI used the database to analyze consumer attitudes and behavior related to renewable energy and to update previously conducted related research. Specifically, this report will explore consumer awareness, concerns, perceived benefits, knowledge of purchase options, and usage of renewable energy as well as provide regional comparisons and trends over time.

  9. Consumer Attitudes About Renewable Energy: Trends and Regional Differences

    Energy Technology Data Exchange (ETDEWEB)

    Natural Marketing Institute, Harleysville, Pennsylvania

    2011-04-01

    The data in this report are taken from Natural Marketing Institute's (NMI's) Lifestyles of Health and Sustainability Consumer Trends Database. Created in 2002, the syndicated consumer database contains responses from 2,000 to 4,000 nationally representative U.S. adults (meaning the demographics of the sample are consistent with U.S. Census findings) each year. NMI used the database to analyze consumer attitudes and behavior related to renewable energy and to update previously conducted related research. Specifically, this report will explore consumer awareness, concerns, perceived benefits, knowledge of purchase options, and usage of renewable energy as well as provide regional comparisons and trends over time.

  10. PcExl1 a novel acid expansin-like protein from the plant pathogen Pectobacterium carotovorum, binds cell walls differently to BsEXLX1.

    Directory of Open Access Journals (Sweden)

    Miguel Olarte-Lozano

    Full Text Available Microbial expansins act on plant cell walls similarly to plant expansins, albeit their loosening activity levels are tenfold lesser compared to plant expansins. We report the characterization of an expansin-like gene from the plant pathogen Pectobacterium carotovorum, named exl1. PcExl1 is an acidic protein that binds cellulose (Avicel, and weakens filter paper. The acidic nature of PcExl1 confers different binding properties when compared to Bacillus subtilis BsEXLX1, which is a basic protein. PcExl1 binding to wheat cell wall increased when acidic components were depleted, reaching a similar level to the binding to Avicel, indicating that cellulose is the target of PcExl1.

  11. PcExl1 a novel acid expansin-like protein from the plant pathogen Pectobacterium carotovorum, binds cell walls differently to BsEXLX1.

    Science.gov (United States)

    Olarte-Lozano, Miguel; Mendoza-Nuñez, Mario A; Pastor, Nina; Segovia, Lorenzo; Folch-Mallol, Jorge; Martínez-Anaya, Claudia

    2014-01-01

    Microbial expansins act on plant cell walls similarly to plant expansins, albeit their loosening activity levels are tenfold lesser compared to plant expansins. We report the characterization of an expansin-like gene from the plant pathogen Pectobacterium carotovorum, named exl1. PcExl1 is an acidic protein that binds cellulose (Avicel), and weakens filter paper. The acidic nature of PcExl1 confers different binding properties when compared to Bacillus subtilis BsEXLX1, which is a basic protein. PcExl1 binding to wheat cell wall increased when acidic components were depleted, reaching a similar level to the binding to Avicel, indicating that cellulose is the target of PcExl1.

  12. Effective energies and exposure determinations of two different energy X-ray beams incident on a personnel monitor

    International Nuclear Information System (INIS)

    Okuno, E.; Cruz, M.T. da

    1984-01-01

    The effective energy of one X or gamma ray beam can be determined by means of two thermoluminescent (TL) dosemeters mounted between suitable filters. However, it has been observed that personnel monitors exposed to two different energy ionizing radiations provide different effective energies depeding on the type of TL phosphor used. This fact could be a powerful tool for identifying exposures to radiation with quite different effective energies which are very common in practice. Two types of TL dosemeters were used : pellets of cold pressed natural fluoride and NaCl developed in our own laboratory, and LiF, TLD-100 from Harshaw Chemical Co.. Experimental results obtained with these combined dosemeters after irradiation with different sets of exposures and energy values of ionizing radiations are also presented. (Author) [pt

  13. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

    Energy Technology Data Exchange (ETDEWEB)

    MacArthur, Stewart; Li, Xiao-Yong; Li, Jingyi; Brown, James B.; Chu, Hou Cheng; Zeng, Lucy; Grondona, Brandi P.; Hechmer, Aaron; Simirenko, Lisa; Keranen, Soile V.E.; Knowles, David W.; Stapleton, Mark; Bickel, Peter; Biggin, Mark D.; Eisen, Michael B.

    2009-05-15

    BACKGROUND: We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in less conserved non-coding DNA, suggesting that many are likely non-functional. RESULTS: Here we show that an additional 15 transcription factors that regulate other aspects of embryo patterning show a similar quantitative continuum of function and binding to thousands of genomic regions in vivo. Collectively, the 21 regulators show a surprisingly high overlap in the regions they bind given that they belong to 11 DNA binding domain families, specify distinct developmental fates, and can act via different cis-regulatory modules. We demonstrate, however, that quantitative differences in relative levels of binding to shared targets correlate with the known biological and transcriptional regulatory specificities of these factors. CONCLUSIONS: It is likely that the overlap in binding of biochemically and functionally unrelated transcription factors arises from the high concentrations of these proteins in nuclei, which, coupled with their broad DNA binding specificities, directs them to regions of open chromatin. We suggest that most animal transcription factors will be found to show a similar broad overlapping pattern of binding in vivo, with specificity achieved by modulating the amount, rather than the identity, of bound factor.

  14. Combined e-beam lithography using different energies

    Czech Academy of Sciences Publication Activity Database

    Krátký, Stanislav; Kolařík, Vladimír; Horáček, Miroslav; Meluzín, Petr; Král, Stanislav

    2017-01-01

    Roč. 177, JUN (2017), s. 30-34 ISSN 0167-9317 R&D Projects: GA TA ČR TE01020233; GA MŠk(CZ) LO1212; GA MŠk ED0017/01/01 Institutional support: RVO:68081731 Keywords : grayscale e-beam lithography * mix and match process * absorbed energy density * resist sensitivity * micro-optical elements Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering OBOR OECD: Nano-processes (applications on nano-scale) Impact factor: 1.806, year: 2016

  15. The differences in heparin binding for the C-terminal basic-sequence-rich peptides of HPV-16 and HPV-18 capsid protein L1

    International Nuclear Information System (INIS)

    Sun Jian; Yu Jisheng; Yu Zhiwu; Zha Xiao; Wu Yuqing

    2012-01-01

    Graphial abstract: The differences in heparin binding for the C-terminal basic-sequence-rich peptides of HPV-16 and HPV-18 capsid protein L1. Highlights: ► Several driving forces contribute to the interaction between heparin and peptides. ► C-terminal of HPV L1 is a potential candidate for the attachment to host cells. ► The C-terminal peptides of HPV-16 and -18 L1 have different heparin-binding. ► The different heparin-binding provides an explanation for the distinct prevalences. - Abstract: The high-risk types of human papillomaviruses (HPV) HPV-16 and -18 are the predominant types associated with cervical cancer. HPV-16 and -18 account for about 50% and 20%, respectively, of cervical cancers worldwide. While the reason and molecular mechanism of the distinct prevalence and distributions between them remain poorly understood, the binding affinity of cell surface receptor with capsid proteins, especially L1, may be involved. We examined heparin binding with two synthetic peptides corresponding to the 14 amino acid C-terminal peptides of HPV-16 and -18 L1 with the goal of comparing the equivalent residues in different HPV types. Using isothermal titration calorimetry (ITC) and static right-angle light scattering (SLS), we determined the binding constant K, reaction enthalpy ΔH, and other thermodynamic parameters in the interaction. Especially, we assessed the role of specific residues in binding with heparin by comparing the NMR spectra of free and heparin-bound peptides.

  16. Electron flux models for different energies at geostationary orbit

    Science.gov (United States)

    Boynton, R. J.; Balikhin, M. A.; Sibeck, D. G.; Walker, S. N.; Billings, S. A.; Ganushkina, N.

    2016-10-01

    Forecast models were derived for energetic electrons at all energy ranges sampled by the third-generation Geostationary Operational Environmental Satellites (GOES). These models were based on Multi-Input Single-Output Nonlinear Autoregressive Moving Average with Exogenous inputs methodologies. The model inputs include the solar wind velocity, density and pressure, the fraction of time that the interplanetary magnetic field (IMF) was southward, the IMF contribution of a solar wind-magnetosphere coupling function proposed by Boynton et al. (2011b), and the Dst index. As such, this study has deduced five new 1 h resolution models for the low-energy electrons measured by GOES (30-50 keV, 50-100 keV, 100-200 keV, 200-350 keV, and 350-600 keV) and extended the existing >800 keV and >2 MeV Geostationary Earth Orbit electron fluxes models to forecast at a 1 h resolution. All of these models were shown to provide accurate forecasts, with prediction efficiencies ranging between 66.9% and 82.3%.

  17. Practical consequences of the assessment of different energy health risks

    International Nuclear Information System (INIS)

    Hamilton, L.D.

    1984-01-01

    Public authorities must make decisions about energy, and the risks of alternative strategies need to be calculated including health and environmental costs. Information from various sources must be organized into a logical framework for comparing impacts. This must include the widest practicable range of health and environmental damage - public health impact of pollution, role of accidents, disease and hazardous materials in the workplace, and odds for catastrophes. It must put each part of the energy cycle into perspective - giving particular attention to uncertainties in knowledge - to convey what is known, what is uncertain, and the importance of each factor in the overall picture. This paper gives examples of the use of health-impact assessment by decision-makers: (1) comparative risk assessment of the health effects of coal and nuclear fuel cycles used in nuclear power plant siting and licensing hearings, and (2) health risks of acid deposition and other air-transported pollutants, carried out as part of an assessment for the U.S. Congress Office of Technology Assessment. (author)

  18. Studies of the biogenic amine transporters. 1. Dopamine reuptake blockers inhibit [3H]mazindol binding to the dopamine transporter by a competitive mechanism: preliminary evidence for different binding domains.

    Science.gov (United States)

    Dersch, C M; Akunne, H C; Partilla, J S; Char, G U; de Costa, B R; Rice, K C; Carroll, F I; Rothman, R B

    1994-02-01

    The present study addressed the hypothesis that the DA transporter ligand, [3H]mazindol, labels multiple sites/states associated with the dopamine (DA) transporter in striatal membranes. Incubations with [3H]mazindol proceeded for 18-24 hr at 4 degrees C in 55.2 mM sodium phosphate buffer, pH 7.4, with a protease inhibitor cocktail. In order to obtain data suitable for quantitative curve fitting, it was necessary to repurify the [3H]mazindol by HPLC before a series of experiments. Under these conditions, we observed greater than 80% specific binding. The method of binding surface analysis was used to characterize the interaction of GBR12935, BTCP, mazindol, and CFT with binding site/sites labeled by [3H]mazindol. A one site model fit the data as well as the two site model: Bmax = 16911 fmol/mg protein, Kd of [3H]mazindol = 75 nM, Ki of GBR12935 = 8.1 nM, Ki of CFT = 50 nM and Ki of BTCP = 44 nM. The inhibitory mechanism (competitive or noncompetitive) of several drugs (GBR12935, CFT, BTCP, cocaine, cis-flupentixol, nomifensine, WIN35,065-2, bupropion, PCP, and benztropine) was determined. All drugs inhibited [3H]mazindol binding by a competitive mechanism. Although the ligand-selectivity of the [3H]mazindol binding site indicates that it is the uptake inhibitor recognition site of the classic DA transporter, the quantitative differences among the ligand-selectivities of different radioligands for the same site suggest that each radioligand labels different overlapping domains of the DA uptake inhibitor recognition site. It is likely that development of domain-selective drugs may further our understanding of the DA transporter.

  19. Glycoprotein profiles of macrophages at different stages of activation as revealed by lectin binding after electrophoretic separation.

    Science.gov (United States)

    Irimura, T; North, S M; Nicolson, G L

    1987-01-01

    Glycoprotein profiles of rat macrophages (M phi) at different stages of activation were studied by examining the reactivity of various lectins to the glycoproteins separated by polyacrylamide gel electrophoresis. Ricinus communis agglutinin 1 (RCA1) revealed several components including glycoproteins of Mr 160 kDa and 65 kDa prominent in resident M phi. A pokeweed mitogen (PWM) isolectin, Pa-4, recognizes branched poly(N-acetyllactosamine)-type carbohydrate chains, and revealed a significant increase in glycoproteins of Mr ranging from 70 kDa to 150 kDa on thioglycolate-elicited M phi. Increased reactivity of PWM to thioglycolate-elicited M phi was observed by direct binding of 125I-labeled Pa-4 to intact or glutaraldehyde-fixed M phi. Histochemical staining of formaldehyde-fixed M phi in vitro with biotinylated Pa-4 was consistent with the gel analysis, that is, resident M phi had no reactivity while thioglycolate-elicited M phi showed slight reactivity. Alveolar and intratumoral M phi bound more Pa-4 than resident or thioglycolate-elicited M phi. The PWM isolectin may therefore serve as a marker for an early stage of M phi activation.

  20. Differences in oestrogen receptors in malignant and normal breast tissue as identified by the binding of a new synthetic progestogen.

    Science.gov (United States)

    Iqbal, M. J.; Colletta, A. A.; Houmayoun-Valyani, S. D.; Baum, M.

    1986-01-01

    Oestrogen receptor protein (ER) was detected in 9 of 11 samples of malignant breast tissue and 8 of 9 samples of normal breast tissue. Levels of cytosolic ER (ERc) in malignant breast were 21-1102 fmol mg-1 soluble protein (Kd 1.8 X 10(-9)-3.1 X 10(-8) mol l-1) and those of nucleosolic ER (ERn), 13-526 fmol mg-1 soluble protein (Kd 2.1 X 10(-9)-1.4 X 10(-8) mol l-1). In normal breast tissue ERc levels were 33-640 fmol mg-1 soluble protein (Kd 1.3 X 10(-10)-3.2 X 10(-9) mol l-1), ERn was detected in only 2 samples, 8 and 87 fmol mg-1 soluble protein with Kd 3.2 X 10(-9) and 1.4 X 10(-9) l mol-1 respectively. 17 alpha-ethinyl-13 beta-ethyl-17 beta-hydroxy-4,15-gonadiene-3-one (gestodene), a new synthetic progestogen displaced 3H-oestradiol (3H-E2) from both ERc and ERn in malignant tissue but not in normal breast, or these receptors from endometrial tissue. In competition studies gestodene was approximately 3 times more effective in displacing 3H-E2 from ERc and ERn in malignant breast tissue than the natural ligand. Quantitation of ER by gestodene were ERc, 12-1134 fmol gestodene bound mg-1 soluble protein (Kd 1 X 10(-9)-8.1 X 10(-9) mol l-1); ERn, 17-531 fmol gestodene bound mg-1 soluble protein (Kd 1.6 X 10(-9)-1.1 X 10(-8) mol l-1). L-13-ethyl-17 alpha-ethinyl, 17 beta-hydroxy-gonen-3-one (levonorgestrel) showed no binding to ER in malignant breast, normal breast or endometrial tissue. In circulation both gestodene and levonorgestrel displaced E2 from sex hormone binding globulin more than any of the androgens tested. These results suggest that gestodene is a progestogen with oestrogenic and/or antioestrogenic properties and provide strong evidence for differences in ER from malignant and normal breast tissue. PMID:3756080

  1. Energy utilization under different dietary regime in sheep

    International Nuclear Information System (INIS)

    Nasr, M.A.H.

    1982-01-01

    The present system of ruminant nutrition in egypt depends upon the agroindustrial by - products, crop residues and limited quantities of green fodders. Any future development will come through introducing non-traditional materials in ruminant rations and through benefiting from the recent scientific developments occurred in our understanding to the ruminal and post-ruminal digestion. Four rations, were tested throughout the present investigation, these diets consisted of molasses as low-cost, readily fermentable source of energy and as a good carrier for urea, and rice straw . On this diet the supply of amino acids may not be sufficient for moderate production levels by the animals.Hence, amino acids shortage and imbalance, in such animals has had to be expected

  2. Different sensitivities to competitive inhibition of benzodiazepine receptor binding of {sup 11}C-iomazenil and {sup 11}C-flumazenil in rhesus monkey brain

    Energy Technology Data Exchange (ETDEWEB)

    Inoue, Osamu; Hosoi, Rie; Kobayashi, Kaoru [Osaka Univ., Suita (Japan). Medical School; Itoh, Takashi; Gee, A.; Suzuki, Kazutoshi

    2001-04-01

    The in vivo binding kinetics of {sup 11}C-iomazenil were compared with those of {sup 11}C-flumazenil binding in rhesus monkey brain. The monkey was anesthetized with ketamine and intravenously injected with either {sup 11}C-iomazenil or {sup 11}C-flumazenil in combination with the coadministration of different doses of non-radioactive flumazenil (0, 5 and 20 {mu}g/kg). The regional distribution of {sup 11}C-iomazenil in the brain was similar to that of {sup 11}C-flumazenil, but the sensitivity of {sup 11}C-iomazenil binding to competitive inhibition by non-radioactive flumazenil was much less than that of {sup 11}C-flumazenil binding. A significant reduction in {sup 11}C-flumazenil binding in the cerebral cortex was observed with 20 {mu}g/kg of flumazenil, whereas a relatively smaller inhibition of {sup 11}C-iomazenil binding in the same region was observed with the same dose of flumazenil. These results suggest that {sup 11}C-flumazenil may be a superior radiotracer for estimating benzodiazepine receptor occupancy in the intact brain. (author)

  3. Communication: regularizing binding energy distributions and thermodynamics of hydration: theory and application to water modeled with classical and ab initio simulations.

    Science.gov (United States)

    Weber, Valéry; Merchant, Safir; Asthagiri, D

    2011-11-14

    The high-energy tail of the distribution of solute-solvent interaction energies is poorly characterized for condensed systems, but this tail region is of principal interest in determining the excess free energy of the solute. We introduce external fields centered on the solute to modulate the short-range repulsive interaction between the solute and solvent. This regularizes the binding energy distribution and makes it easy to calculate the free energy of the solute with the field. Together with the work done to apply the field in the presence and absence of the solute, we calculate the excess chemical potential of the solute. We present the formal development of this idea and apply it to study liquid water. © 2011 American Institute of Physics

  4. Life-cycle energy implications of different residential settings: Recognizing buildings, travel, and public infrastructure

    International Nuclear Information System (INIS)

    Nichols, Brice G.; Kockelman, Kara M.

    2014-01-01

    The built environment can be used to influence travel demand, but very few studies consider the relative energy savings of such policies in context of a complex urban system. This analysis quantifies the day-to-day and embodied energy consumption of four different neighborhoods in Austin, Texas, to examine how built environment variations influence various sources of urban energy consumption. A microsimulation combines models for petroleum use (from driving) and residential and commercial power and natural gas use with rigorously measured building stock and infrastructure materials quantities (to arrive at embodied energy). Results indicate that the more suburban neighborhoods, with mostly detached single-family homes, consume up to 320% more embodied energy, 150% more operational energy, and about 160% more total life-cycle energy (per capita) than a densely developed neighborhood with mostly low-rise-apartments and duplexes. Across all neighborhoods, operational energy use comprised 83 to 92% of total energy use, and transportation sources (including personal vehicles and transit, plus street, parking structure, and sidewalk infrastructure) made up 44 to 47% of the life-cycle energy demands tallied. Energy elasticity calculations across the neighborhoods suggest that increased population density and reduced residential unit size offer greatest life-cycle energy savings per capita, by reducing both operational demands from driving and home energy use, and from less embodied energy from construction. These results provide measurable metrics for comparing different neighborhood styles and develop a framework to anticipate energy-savings from changes in the built environment versus household energy efficiency. - Highlights: • Total energy demands (operational and embodied) of 5 Austin settings were studied here. • Suburban settings consume much more energy than densely developed neighborhoods. • Transportation sources make up 44 to 47% of the total energy

  5. Variation of the Detergent-Binding Capacity and Phospholipid Content of Membrane Proteins When Purified in Different Detergents

    Science.gov (United States)

    Ilgü, Hüseyin; Jeckelmann, Jean-Marc; Gachet, María Salomé; Boggavarapu, Rajendra; Ucurum, Zöhre; Gertsch, Jürg; Fotiadis, Dimitrios

    2014-01-01

    Purified membrane proteins are ternary complexes consisting of protein, lipid, and detergent. Information about the amounts of detergent and endogenous phospholipid molecules bound to purified membrane proteins is largely lacking. In this systematic study, three model membrane proteins of different oligomeric states were purified in nine different detergents at commonly used concentrations and characterized biochemically and biophysically. Detergent-binding capacities and phospholipid contents of the model proteins were determined and compared. The insights on ternary complexes obtained from the experimental results, when put into a general context, are summarized as follows. 1), The amount of detergent and 2) the amount of endogenous phospholipids bound to purified membrane proteins are dependent on the size of the hydrophobic lipid-accessible protein surface areas and the physicochemical properties of the detergents used. 3), The size of the detergent and lipid belt surrounding the hydrophobic lipid-accessible surface of purified membrane proteins can be tuned by the appropriate choice of detergent. 4), The detergents n-nonyl-β-D-glucopyranoside and Cymal-5 have exceptional delipidating effects on ternary complexes. 5), The types of endogenous phospholipids bound to membrane proteins can vary depending on the detergent used for solubilization and purification. 6), Furthermore, we demonstrate that size-exclusion chromatography can be a suitable method for estimating the molecular mass of ternary complexes. The findings presented suggest a strategy to control and tune the numbers of detergent and endogenous phospholipid molecules bound to membrane proteins. These two parameters are potentially important for the successul crystallization of membrane proteins for structure determination by crystallographic approaches. PMID:24739165

  6. Variation of the detergent-binding capacity and phospholipid content of membrane proteins when purified in different detergents.

    Science.gov (United States)

    Ilgü, Hüseyin; Jeckelmann, Jean-Marc; Gachet, María Salomé; Boggavarapu, Rajendra; Ucurum, Zöhre; Gertsch, Jürg; Fotiadis, Dimitrios

    2014-04-15

    Purified membrane proteins are ternary complexes consisting of protein, lipid, and detergent. Information about the amounts of detergent and endogenous phospholipid molecules bound to purified membrane proteins is largely lacking. In this systematic study, three model membrane proteins of different oligomeric states were purified in nine different detergents at commonly used concentrations and characterized biochemically and biophysically. Detergent-binding capacities and phospholipid contents of the model proteins were determined and compared. The insights on ternary complexes obtained from the experimental results, when put into a general context, are summarized as follows. 1), The amount of detergent and 2) the amount of endogenous phospholipids bound to purified membrane proteins are dependent on the size of the hydrophobic lipid-accessible protein surface areas and the physicochemical properties of the detergents used. 3), The size of the detergent and lipid belt surrounding the hydrophobic lipid-accessible surface of purified membrane proteins can be tuned by the appropriate choice of detergent. 4), The detergents n-nonyl-β-D-glucopyranoside and Cymal-5 have exceptional delipidating effects on ternary complexes. 5), The types of endogenous phospholipids bound to membrane proteins can vary depending on the detergent used for solubilization and purification. 6), Furthermore, we demonstrate that size-exclusion chromatography can be a suitable method for estimating the molecular mass of ternary complexes. The findings presented suggest a strategy to control and tune the numbers of detergent and endogenous phospholipid molecules bound to membrane proteins. These two parameters are potentially important for the successul crystallization of membrane proteins for structure determination by crystallographic approaches. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  7. Metal removal and associated binding fraction transformation in contaminated river sediment washed by different types of agents.

    Directory of Open Access Journals (Sweden)

    Hong Wang

    Full Text Available In ex-situ washing, HCl, EDTA and H2O2 solutions can effectively extract heavy metals in river sediment. Nevertheless they often target different sediment components, possibly transforming metal species into more bioavailable and hence toxic ones. This study, in batch settings, investigated the influences of different types of washing agents (i.e. HCl, EDTA and H2O2 on metal (i.e. Cu and Zn removal from contaminated river sediment, destroy or dissolution of sediment components, and transformation of metal fractions during chemical washing treatment. Additionally, bioavailability of these metals left in the washed sediment was assessed. Results showed that HCl obtained the highest Cu and Zn removal through destroying the reducible, oxidizable and residual sediment components. Meanwhile, it transformed metal fractions to acid extractable one, resulting in an increase in metal bioavailability. Thus, the feasibility of washing with HCl for sediment remediation shall be reconsidered due to the caused high metal bioavailability. EDTA was capable of removing metals via direct complexation of labile metal species and indirect dissolution of reducible and oxidizable sediment components, where the transformation of corresponding metal binding fraction may occur. H2O2 obtained the lowest total Cu and Zn removal, but it preferentially removed the oxidizable metal species by oxidizing sulfides in the sediment. The bioavailable levels of Cu and Zn in the sediment washed by EDTA or H2O2 seemed not increase. To maintain a good balance between labile metal species removal and avoiding increase of metal bioavailability, EDTA and H2O2 are promising additives for metal removal by sediment washing.

  8. Differential Penicillin-Binding Protein 5 (PBP5) Levels in the Enterococcus faecium Clades with Different Levels of Ampicillin Resistance.

    Science.gov (United States)

    Montealegre, Maria Camila; Roh, Jung Hyeob; Rae, Meredith; Davlieva, Milya G; Singh, Kavindra V; Shamoo, Yousif; Murray, Barbara E

    2017-01-01

    Ampicillin resistance in Enterococcus faecium is a serious concern worldwide, complicating the treatment of E. faecium infections. Penicillin-binding protein 5 (PBP5) is considered the main ampicillin resistance determinant in E. faecium The three known E. faecium clades showed sequence variations in the pbp5 gene that are associated with their ampicillin resistance phenotype; however, these changes alone do not explain the array of resistance levels observed among E. faecium clinical strains. We aimed to determine if the levels of PBP5 are differentially regulated between the E. faecium clades, with the hypothesis that variations in PBP5 levels could help account for the spectrum of ampicillin MICs seen in E. faecium We studied pbp5 mRNA levels and PBP5 protein levels as well as the genetic environment upstream of pbp5 in 16 E. faecium strains that belong to the different E. faecium clades and for which the ampicillin MICs covered a wide range. Our results found that pbp5 and PBP5 levels are increased in subclade A1 and A2 ampicillin-resistant strains compared to those in clade B and subclade A2 ampicillin-susceptible strains. Furthermore, we found evidence of major clade-associated rearrangements in the region upstream of pbp5, including large DNA fragment insertions, deletions, and single nucleotide polymorphisms, that may be associated with the differential regulation of PBP5 levels between the E. faecium clades. Overall, these findings highlight the contribution of the clade background to the regulation of PBP5 abundance and point to differences in the region upstream of pbp5 as likely contributors to the differential expression of ampicillin resistance. Copyright © 2016 American Society for Microbiology.

  9. Dissociation kinetics of excited ions: PEPICO measurements of Os3(CO)12 — The 7-35 eV single ionization binding energy region

    Science.gov (United States)

    Schalk, Oliver; Josefsson, Ida; Geng, Ting; Richter, Robert; Sa'adeh, Hanan; Thomas, Richard D.; Mucke, Melanie

    2018-02-01

    In this article, we study the photoinduced dissociation pathways of a metallocarbonyl, Os3(CO)12, in particular the consecutive loss of CO groups. To do so, we performed photoelectron-photoion coincidence (PEPICO) measurements in the single ionization binding energy region from 7 to 35 eV using 45-eV photons. Zero-energy ion appearance energies for the dissociation steps were extracted by modeling the PEPICO data using the statistical adiabatic channel model. Upon ionization to the excited ionic states above 13 eV binding energy, non-statistical behavior was observed and assigned to prompt CO loss. Double ionization was found to be dominated by the knockout process with an onset of 20.9 ± 0.4 eV. The oscillator strength is significantly larger for energies above 26.6 ± 0.4 eV, corresponding to one electron being ejected from the Os3 center and one from the CO ligands. The cross section for double ionization was found to increase linearly up to 35 eV ionization energy, at which 40% of the generated ions are doubly charged.

  10. A Comparison between Different Methods of Estimating Anaerobic Energy Production

    Science.gov (United States)

    Andersson, Erik P.; McGawley, Kerry

    2018-01-01

    Purpose: The present study aimed to compare four methods of estimating anaerobic energy production during supramaximal exercise. Methods: Twenty-one junior cross-country skiers competing at a national and/or international level were tested on a treadmill during uphill (7°) diagonal-stride (DS) roller-skiing. After a 4-minute warm-up, a 4 × 4-min continuous submaximal protocol was performed followed by a 600-m time trial (TT). For the maximal accumulated O2 deficit (MAOD) method the V.O2-speed regression relationship was used to estimate the V.O2 demand during the TT, either including (4+Y, method 1) or excluding (4-Y, method 2) a fixed Y-intercept for baseline V.O2. The gross efficiency (GE) method (method 3) involved calculating metabolic rate during the TT by dividing power output by submaximal GE, which was then converted to a V.O2 demand. An alternative method based on submaximal energy cost (EC, method 4) was also used to estimate V.O2 demand during the TT. Results: The GE/EC remained constant across the submaximal stages and the supramaximal TT was performed in 185 ± 24 s. The GE and EC methods produced identical V.O2 demands and O2 deficits. The V.O2 demand was ~3% lower for the 4+Y method compared with the 4-Y and GE/EC methods, with corresponding O2 deficits of 56 ± 10, 62 ± 10, and 63 ± 10 mL·kg−1, respectively (P estimated O2 deficits were −6 ± 5 mL·kg−1 (4+Y vs. 4-Y, P estimated with GE/EC based on the average of four submaximal stages compared with the last stage was 1 ± 2 mL·kg−1, with a typical error of 3.2%. Conclusions: These findings demonstrate a disagreement in the O2 deficits estimated using current methods. In addition, the findings suggest that a valid estimate of the O2 deficit may be possible using data from only one submaximal stage in combination with the GE/EC method. PMID:29472871

  11. Effects of Consuming Preloads with Different Energy Density and Taste Quality on Energy Intake and Postprandial Blood Glucose

    Directory of Open Access Journals (Sweden)

    Siew Ling Tey

    2018-01-01

    Full Text Available Consumption of reduced energy dense foods and drink has the potential to reduce energy intake and postprandial blood glucose concentrations. In addition, the taste quality of a meal (e.g., sweet or savoury may play a role in satiation and food intake. The objective of this randomised crossover study was to examine whether energy density and taste quality has an impact on energy intake and postprandial blood glucose response. Using a preload design, participants were asked to consume a sweet (“Cheng Teng” or a savoury (broth preload soup in high energy density (HED; around 0.50 kcal/g; 250 kcal or low energy density (LED; around 0.12 kcal/g; 50 kcal in mid-morning and an ad libitum lunch was provided an hour after the preload. Participants recorded their food intake for the rest of the day after they left the study site. Energy compensation and postprandial blood glucose response were measured in 32 healthy lean males (mean age = 28.9 years, mean BMI = 22.1 kg/m2. There was a significant difference in ad libitum lunch intake between treatments (p = 0.012, with higher intake in sweet LED and savoury LED compared to sweet HED and savoury HED. Energy intake at subsequent meals and total daily energy intake did not differ between the four treatments (both p ≥ 0.214. Consumption of HED preloads resulted in a larger spike in postprandial blood glucose response compared with LED preloads, irrespective of taste quality (p < 0.001. Energy density rather than taste quality plays an important role in energy compensation and postprandial blood glucose response. This suggests that regular consumption of low energy-dense foods has the potential to reduce overall energy intake and to improve glycemic control.

  12. Binding energy of donor impurity states and optical absorption in the Tietz-Hua quantum well under an applied electric field

    Science.gov (United States)

    Al, E. B.; Kasapoglu, E.; Sakiroglu, S.; Duque, C. A.; Sökmen, I.

    2018-04-01

    For a quantum well which has the Tietz-Hua potential, the ground and some excited donor impurity binding energies and the total absorption coefficients, including linear and third order nonlinear terms for the transitions between the related impurity states with respect to the structure parameters and the impurity position as well as the electric field strength are investigated. The binding energies were obtained using the effective-mass approximation within a variational scheme and the optical transitions between any two impurity states were calculated by using the density matrix formalism and the perturbation expansion method. Our results show that the effects of the electric field and the structure parameters on the optical transitions are more pronounced. So we can adjust the red or blue shift in the peak position of the absorption coefficient by changing the strength of the electric field as well as the structure parameters.

  13. Energy equity: will the UN Sustainable Energy For All initiative make a difference

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, Emma

    2012-05-15

    Access to affordable modern energy services may not be a Millennium Development Goal (MDG) but without it, sustainable development, indeed the MDGs themselves, cannot be achieved. Yet energy access remains an area of great global inequity. On one hand, wealthy countries and communities consume vast amounts of often subsidised energy resources every day. On the other hand, 1-in-5 people lives with no access to grid electricity, and around 40 per cent of the world's population (nearly three billion people) lack the technologies to make cooking fuels clean, safe and efficient. Can the UN's Sustainable Energy for All initiative in 2012 redress the balance? Perhaps, but only if it puts improving the lives of the poorest and most vulnerable at the heart of its efforts.

  14. Simulation Study of the Energy Performance of Different Space Heating Methods in Plus-energy Housing

    DEFF Research Database (Denmark)

    Schøtt, Jacob; Andersen, Mads E.; Kazanci, Ongun Berk

    2016-01-01

    cases the heat source was a natural gas fired condensing boiler, and for the floor heating cases also an air-to-water heat pump was used to compare two heat sources. The systems were also compared in terms of auxiliary energy use for pumps and fans. The results show that the investigated floor heating...... from the low temperature heating potential since an increased floor covering requires higher average water temperatures in the floor loops and decreases the COP of the heat pump. The water-based heating systems required significantly less auxiliary energy input compared to the air-based heating system......Due to a shortage of energy resources, the focus on indoor environment and energy use in buildings is increasing which sets higher standards for the performance of HVAC systems in buildings. The variety of available heating systems for both residential buildings and office buildings is therefore...

  15. Binding Energies of the pi-Stacked Anisole Dimer: New Molecular Beam-Laser Spectroscopy Experiments and CCSD(T) Calculations

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Nachtigallová, Dana; Mazzoni, F.; Pasquini, M.; Pietraperzia, G.; Becucci, M.; Müller-Dethlefs, K.; Hobza, Pavel

    2015-01-01

    Roč. 21, č. 18 (2015), s. 6740-6746 ISSN 0947-6539 R&D Projects: GA ČR GBP208/12/G016 Grant - others:GA MŠk(CZ) ED2.1.00/03.0058 Program:ED Institutional support: RVO:61388963 Keywords : binding energy * noncovalent interactions * pi stacking * laser spectroscopy * CCSD(T) calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.771, year: 2015

  16. Cation-pi interactions with a model for the side chain of tryptophan: structures and absolute binding energies of alkali metal cation-indole complexes.

    Science.gov (United States)

    Ruan, Chunhai; Yang, Zhibo; Hallowita, Nuwan; Rodgers, M T

    2005-12-22

    Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.

  17. Thermodynamics for proton binding of phytate in KNO{sub 3(aq)} at different temperatures and ionic strengths

    Energy Technology Data Exchange (ETDEWEB)

    Bretti, Clemente; De Stefano, Concetta, E-mail: cdestefano@unime.it; Lando, Gabriele; Sammartano, Silvio

    2013-08-20

    Highlights: • Protonation data were modeled in a wide range of temperatures and ionic strengths. • Protonation values decrease with increasing ionic strength and temperature. • In KNO{sub 3} proton binding process is slightly exothermic, but less than in NaCl. • The major contribution for the proton association is entropic in nature. • Results are in agreement with previous findings for KCl and NaCl. - Abstract: Potentiometric measurements were performed in KNO{sub 3(aq)}, to determine the apparent protonation constants of phytate at different temperatures (278.15 ≤ T (K) ≤ 323.15) and ionic strengths (0.25 ≤ I (mol) dm{sup −3} ≤ 3.0) values. In general, the protonation constants decrease with increasing both temperature and ionic strength. The data reported were critically compared with previous results obtained in KCl and the values are in a good agreement, considering the experimental errors and slight differences between the activity coefficients of the various species in KCl and KNO{sub 3}. Experimental data were then modeled as a function of temperature and ionic strength using, with comparable results, two approaches: the extended Debye–Hückel equation and the specific ion interaction theory (SIT). The single specific ion interaction coefficients, ε, were also determined. The corresponding values are higher than those in Na{sup +} media. The protonation constants were also analyzed considering a simplified weak interaction model using an empirical equation that contains an additional term which takes into account the formation of weak complexes. The results obtained for the modeling of the protonation constants are in agreement with the literature findings. Thermodynamic protonation parameters were also obtained at different temperatures and ionic strengths. The proton association process is slightly exothermic and the enthalpic contribution is less negative than that in NaCl solution. As observed in other cases for phytate anion, the

  18. Energy utilization of light and heavy weaned piglets subjected to different dietary energy levels

    Directory of Open Access Journals (Sweden)

    Andréa Machado Leal Ribeiro

    Full Text Available ABSTRACT This study was conducted to evaluate the effects of dietary metabolisable energy (ME: 3.25, 3.40, 3.55, or 3.70 Mcal kg−1 and weaning weight (WW: light 4.0±0.7 kg, and heavy: 6.3±0.6 kg on productive response and energy utilization of weaned piglets. Sixty-four male piglets were housed in 32 metabolic cages (two animals per cage during the first 14 d postweaning. At day 15, only one animal per cage was kept until day 28. Body composition, energy, and nutrient deposition rates and energy utilization efficiency were measured through a comparative slaughter procedure. Piglets with light WW had a poorer feed conversion ratio and lower weight gain and feed intake when expressed per live weight. Increased ME led to greater daily fat deposition in the empty bodies (defined as weighted mean of the carcass + organs + blood, no intestinal content, while light WW piglets had a reduced protein deposition. Light WW piglets increased heat production with increased ME, but no effect was seen for the heavy WW piglets. By contrast, heavy WW piglets increased empty body gross energy as ME increased, while no influence was observed on light WW piglets. Increasing dietary energy levels did not contribute to the subsequent growth performance of piglets that were lighter at weaning. The lack of interaction between weaning weight and dietary ME content on growth performance does not support the hypothesis that light piglets at weaning do not exhibit compensatory growth because of limitations in energy intake.

  19. First-Principle Framework for Total Charging Energies in Electrocatalytic Materials and Charge-Responsive Molecular Binding at Gas-Surface Interfaces.

    Science.gov (United States)

    Tan, Xin; Tahini, Hassan A; Seal, Prasenjit; Smith, Sean C

    2016-05-04

    Heterogeneous charge-responsive molecular binding to electrocatalytic materials has been predicted in several recent works. This phenomenon offers the possibility of using voltage to manipulate the strength of the binding interaction with the target gas molecule and thereby circumvent thermochemistry constraints, which inhibit achieving both efficient binding and facile release of important targets such as CO2 and H2. Stability analysis of such charge-induced molecular adsorption has been beyond the reach of existing first-principle approaches. Here, we draw on concepts from semiconductor physics and density functional theory to develop a first principle theoretical approach that allows calculation of the change in total energy of the supercell due to charging. Coupled with the calculated adsorption energy of gas molecules at any given charge, this allows a complete description of the energetics of the charge-induced molecular adsorption process. Using CO2 molecular adsorption onto negatively charged h-BN (wide-gap semiconductor) and g-C4N3 (half metal) as example cases, our analysis reveals that - while adsorption is exothermic after charge is introduced - the overall adsorption processes are not intrinsically spontaneous due to the energetic cost of charging the materials. The energies needed to overcome the barriers of these processes are 2.10 and 0.43 eV for h-BN and g-C4N3, respectively. This first principle approach opens up new pathways for a more complete description of charge-induced and electrocatalytic processes.

  20. The role of extra-atomic relaxation in determining Si2p binding energy shifts at silicon/silicon oxide interfaces

    International Nuclear Information System (INIS)

    Zhang, K.Z.; Greeley, J.N.; Banaszak Holl, M.M.; McFeely, F.R.

    1997-01-01

    The observed binding energy shift for silicon oxide films grown on crystalline silicon varies as a function of film thickness. The physical basis of this shift has previously been ascribed to a variety of initial state effects (Si endash O ring size, strain, stoichiometry, and crystallinity), final state effects (a variety of screening mechanisms), and extrinsic effects (charging). By constructing a structurally homogeneous silicon oxide film on silicon, initial state effects have been minimized and the magnitude of final state stabilization as a function of film thickness has been directly measured. In addition, questions regarding the charging of thin silicon oxide films on silicon have been addressed. From these studies, it is concluded that initial state effects play a negligible role in the thickness-dependent binding energy shift. For the first ∼30 Angstrom of oxide film, the thickness-dependent binding energy shift can be attributed to final state effects in the form of image charge induced stabilization. Beyond about 30 Angstrom, charging of the film occurs. copyright 1997 American Institute of Physics

  1. Energy differently - Booklet supplement to 'Alternatives economiques' journal (no. 54, Feb. 2012)

    International Nuclear Information System (INIS)

    Anon.

    2012-01-01

    This booklet screens the different renewable energy sources and focusses on their ecological advantage and economical maturity aspects. The book is divided in five parts: 1 - the energy transition: energies of yesterday and tomorrow; France: the end of compulsive consumption?; NegaWatt: a transition scenario for France; 2 - consuming less energy: saving energy; will the building industry revolution take place?; electricity: the constantly seeking more attitude can be avoided; smart grids: can they generate energy saving?; is the electric-powered car really ecological?; waste sorting: more effort is needed; is Internet a source of energy saving?; does tele-working reduce pollution?; how to feed people without impacting environment?; should we stop purchasing imported goods?; how can we get rid of trucks?; Is the carbon compensation system useful?; is innovation capable to save us?; 3 - producing energy differently: renewable energies - the French backwardness; hydro-energy; marine energies; thermal solar energy; photovoltaic energy; solar concentration; terrestrial wind power; offshore wind power; geothermal energy; heat pumps; agro-fuels; biomass and wood fuels; biogas; cogeneration; CO 2 capture and sequestration; adapting the power grid to the renewable energies development; 4 - Initiatives: Enercoop, a 100% renewable power supplier; Le Mene (Brittany, France): towards a positive energy territory; local wind turbines: from Montdidier to Issoudun; the eco-districts revolution; interdependent funds for alternate energies; against fossil fuels extraction; Juneau (Alaska) moves to low-consumption; when solidarity and electricity go together: the example of Nicaragua; 5 - energy in debates: 'it is not too late'; a challenge for democracy; is France ready for nuclear phasing out?; reorganizing consumption; a turn to take today; understanding the photovoltaic crisis; how to finance renewable energy sources?; what impact on employment?; should we have to establish a

  2. Binding affinity and in vitro cytotoxicity of harmaline targeting different motifs of nucleic acids: An ultimate drug designing approach.

    Science.gov (United States)

    Bhattacharjee, Paromita; Ghosh, Tapas; Sarkar, Sarita; Pandya, Prateek; Bhadra, Kakali

    2017-12-15

    The work focuses towards interaction of harmaline, with nucleic acids of different motifs by multispectroscopic and calorimetric techniques. Findings of this study suggest that binding constant varied in the order single-stranded (ss) poly(A) > double-stranded calf thymus (CT) DNA > double-stranded poly(G)·poly(C) > clover leaf tRNA Phe . Prominent structural changes of ss poly(A), CT DNA, and poly(G)· poly(C) with concomitant induction of optical activity in the bound achiral alkaloid molecule was observed, while with tRNA Phe , very weak induced circular dichroism perturbation was seen. The interaction was predominantly exothermic, enthalpy driven, and entropy favored with CT DNA and poly(G)·poly(C), while it was entropy driven with poly(A) and tRNA Phe . Intercalated state of harmaline inside poly(A), CT DNA, and poly(G)·poly(C) was shown by viscometry, ferrocyanide quenching, and molecular docking. All these findings unequivocally pointed out preference of harmaline towards ss poly(A) inducing self-structure formation. Furthermore, harmaline administration caused a significant decrease in proliferation of HeLa and HepG 2 cells with GI 50 of 28μM and 11.2μM, respectively. Nucleic acid fragmentation, cellular ultramorphological changes, decreased mitochondrial membrane potential, upregulation of p53 and caspase 3, generation of reactive oxygen species, and a significant increase in the G 2 /M population made HepG 2 more prone to apoptosis than are HeLa cells. Copyright © 2017 John Wiley & Sons, Ltd.

  3. DCE-MRI using small-molecular and albumin-binding contrast agents in experimental carcinomas with different stromal content

    Energy Technology Data Exchange (ETDEWEB)

    Farace, Paolo; Merigo, Flavia; Fiorini, Silvia; Nicolato, Elena; Tambalo, Stefano; Daducci, Alessandro [Department of Morphological-Biomedical Sciences, Section of Anatomy and Histology, University of Verona, Verona (Italy); Degrassi, Anna [Nerviano Medical Sciences Institute, Milan (Italy); Sbarbati, Andrea [Department of Morphological-Biomedical Sciences, Section of Anatomy and Histology, University of Verona, Verona (Italy); Rubello, Domenico, E-mail: domenico.rubello@libero.it [Department of Radiology, Nuclear Medicine, Medical Physics, Services of Radiology and Nuclear Medicine, ' S. Maria della Misericordia' Hospital, Viale Tre Martiri 140, 45100 Rovigo (Italy); Marzola, Pasquina [Department of Morphological-Biomedical Sciences, Section of Anatomy and Histology, University of Verona, Verona (Italy)

    2011-04-15

    Objectives: To compare DCE-MRI experiments performed using a standard small-molecular (Gd-DTPA) and an albumin-binding (MS-325) contrast agent in two carcinoma models with different stromal content. Materials and methods: DU-145 or BXPC-3 cancer cells were subcutaneously injected into nude mice. DCE-MRI was performed by a bolus injection of Gd-DTPA or MS-325 about 2 weeks after inoculation. For quantitative analysis a volume of interest was manually drawn over each tumor. To address the heterogeneous enhancement, each tumor volume was then divided into the 20% most-enhancing and the remaining 80% least-enhancing fractions. Mean tumor enhancement was calculated over these selected tumor volumes and compared between tumor groups and contrast agents. Maps of differential enhancement, peak enhancement and time-to-peak were used for visual evaluation. CD31 and VEGF immunohistochemistry were performed in excised tumors. Results: In the 80% least-enhancing volume, at late time points of the dynamic scan, the mean enhancement elicited by MS-325 was higher in BXPC-3 than in DU-145 tumors. In the 20% most-enhancing volume, using either contrast agents, significant difference between the two tumors types were observed only early, while at later time points of the dynamic scan the difference were obscured by the faster washout observed in the BXPC-3 tumors. Enhancement maps confirmed that BXPC-3 tumors were characterized by marked washout rate using either contrast agent, particularly in the higher enhancing peripheral rim. With MS-325 this washout pattern appeared to be specific to the BXPC-3 carcinomas, since it was not observed in the DU-145 tumors. Finally, in both tumor types, MS-325 produced significantly higher enhancement than Gd-DTPA in the late phase of the dynamic scan. Ex vivo analysis confirmed the marked presence of aberrant infiltrative stroma in BXPC-3 tumors, in which tumor vessels were embedded. In all tumors the central portion was less viable and less

  4. Household Energy Consumption Behaviour for Different Demographic Regions in Thailand from 2000 to 2010

    Directory of Open Access Journals (Sweden)

    Tharinya Supasa

    2017-12-01

    Full Text Available Since 1995, the residential sector has been a fast-growing energy consumption sector in Thailand. This sector contributes dramatically to the growth of Thailand’s electricity and oil demand. Our study analysed Thailand’s residential energy consumption characteristics and the seven underlying factors affecting the growth in energy use of five demographic regions using an energy input–output method. Embodied energy decomposition revealed that direct energy consumption accounted for approximately 30% of total residential energy use, whereas indirect energy consumption was at 70%. During the studied period, the growth in indirect energy use for all household groups was primarily the result of higher consumption of ‘commerce’, ‘air transport’, ‘manufacturing’, ‘food and beverages’ and ‘agriculture’ products. Moreover, each influencing driver contributes differently to each household’s growth in energy demand. The number of households was the leading factor that dominated the increases in residential energy use in the Greater Bangkok and Central regions. Growth in residential energy consumption in the Northern, Northeastern and Southern regions was strongly dominated by changes in income per capita. Consumption structure and using energy-efficient products had a moderate impact on all regions’ energy consumption. Thus, our findings provide additional energy-saving strategies to restrain further growth in residential energy demand.

  5. An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles

    Science.gov (United States)

    Xu, Beisi; Yang, Yuedong; Liang, Haojun; Zhou, Yaoqi

    2009-01-01

    How to make an accurate representation of protein-DNA interactions by an energy function is a long-standing unsolved problem in structural biology. Here, we modified a statistical potential based on the distance-scaled, finite ideal-gas reference state (DFIRE) so that it is optimized for protein-DNA interactions. The changes include a volume-fraction correction to account for unmixable atom types in proteins and DNA in addition to the usage of a low-count correction, residue/base-specific atom types, and a shorter cutoff distance for protein-DNA interactions. The new statistical energy functions are tested in threading and docking decoy discriminations and prediction of protein-DNA binding affinities and transcription-factor binding profiles. Results indicate that new proposed energy functions are among the best in existing energy functions for protein-DNA interactions. The new energy functions are available as a web-server called DDNA 2.0 at http://sparks.informatics.iupui.edu. The server version was trained by the entire 212 protein-DNA complexes. PMID:19274740

  6. Differences in human skin between the epidermal growth factor receptor distribution detected by EGF binding and monoclonal antibody recognition

    DEFF Research Database (Denmark)

    Green, M R; Couchman, J R

    1985-01-01

    Two methods have been used to examine epidermal growth factor (EGF) receptor distribution in human scalp and foreskin. The first employed [125I]EGF viable explants and autoradiography to determine the EGF binding pattern while the second used a monoclonal antibody to the human EGF receptor to map...... the distribution on frozen skin sections of an extracellular epitope on the EGF receptor. The [125I]EGF binding experiments showed accessible, unoccupied EGF receptors to be present on the epidermal basal cells (with reduced binding to spinous cells), the basal cells of the hair shaft and sebaceous gland......, the eccrine sweat glands, capillary system, and the hair follicle outer root sheath, generally similar in pattern to that previously reported for full-thickness rat skin and human epidermis. The same areas also bound EGF-R1 but in addition the monoclonal antibody recognized a cone of melanin containing...

  7. Socio-Demographic Differences in Energy Drink Consumption and Reasons for Consumption among US College Students

    Science.gov (United States)

    Poulos, Natalie S.; Pasch, Keryn E.

    2016-01-01

    Background: Energy drink consumption has become increasingly prevalent among US college students, yet little is known about current rates of consumption and reasons for consumption among current energy drink users, particularly differences related to gender and race/ethnicity. Objectives: To better understand energy drink consumption alone and…

  8. Differences in human skin between the epidermal growth factor receptor distribution detected by EGF binding and monoclonal antibody recognition

    DEFF Research Database (Denmark)

    Green, M R; Couchman, J R

    1985-01-01

    the distribution on frozen skin sections of an extracellular epitope on the EGF receptor. The [125I]EGF binding experiments showed accessible, unoccupied EGF receptors to be present on the epidermal basal cells (with reduced binding to spinous cells), the basal cells of the hair shaft and sebaceous gland...... presumptive cortex cells, excluding the medulla, lying around and above the upper dermal papilla of anagen hair follicles, epithelial cells around the lower dermal papilla region, and in some tissue samples the cell margins of the viable differentiating layers of the epidermis. In a control study, to clarify...

  9. 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.

  10. Protection against Schistosoma mansoni infection using a Fasciola hepatica-derived fatty acid binding protein from different delivery systems.

    Science.gov (United States)

    Vicente, Belén; López-Abán, Julio; Rojas-Caraballo, Jose; del Olmo, Esther; Fernández-Soto, Pedro; Muro, Antonio

    2016-04-18

    Schistosomiasis is a water-borne disease afflicting over 261 million people in many areas of the developing countries with high morbidity and mortality. The control relies mainly on treatment with praziquantel. Fatty acid binding proteins (FABP) have demonstrated high levels of immune-protection against trematode infections. This study reports the immunoprotection induced by cross-reacting Fasciola hepatica FABP, native (nFh12) and recombinantly expressed using two different expression systems Escherichia coli (rFh15) and baculovirus (rFh15b) against Schistosoma mansoni infection. BALB/c mice were vaccinated with native nFh12 or recombinant rFh15 and rFh15 FABP from F. hepatica formulated in adjuvant adaptation (ADAD) system with natural or chemical synthesised immunomodulators (PAL and AA0029) and then challenged with 150 cercariae of S. mansoni. Parasite burden, hepatic lesions and antibody response were studied in vaccination trials. Furthermore differences between rFh15 and rFh15b immunological responses (cytokine production, splenocyte population and antibody levels) were studied. Vaccination with nFh12 induced significant reductions in worm burden (83%), eggs in tissues (82-92%) and hepatic lesions (85%) compared to infected controls using PAL. Vaccination with rFh15 showed lower total worm burden (56-64%), eggs in the liver (21-61%), eggs in the gut (30-77%) and hepatic damage (67-69%) using PAL and AA0029 as immunomodulators. In contrast, mice vaccinated with rFh15b showed only reductions in eggs trapped in the liver and intestine (53 and 60%, respectively), and hepatic lesions (45%). We observed a significant rise in TNFα, IL-6, IL-2, IL-4 and high antibody response (IgG, IgG1, IgG2a, IgM and IgE) in mice immunised with either rFh15 or rFh15b. Moreover, mice immunised with rFh15b showed an increase in IFNγ and a decrease in B220 cells compared to untreated mice, and less production of IgG1 and IgM than in mice immunised by rFh15. Higher level of

  11. Derivation of the Crick-Wyman equation for allosteric proteins defining the difference between the number of binding sites and the Hill coefficient.

    Science.gov (United States)

    Poitevin, Frédéric; Edelstein, Stuart J

    2013-05-13

    In response to a 100-word footnote in the 1965 article by Monod, Wyman, and Changeux, a detailed manuscript signed by Francis Crick and Jeffries Wyman with 6000 words and 30 equations entitled "A Footnote on Allostery" circulated in 1965 among a limited group of scientists interested in allosteric interactions. This interesting and provocative document is published in this special issue for the first time. An intriguing equation in their text relates the difference between n (the number of ligand binding sites) and n' (the Hill coefficient) to the ratio of the saturation functions Y¯, for oligomers with n-1 and n binding sites. A compact derivation of this equation was not provided by Crick and Wyman, but one is presented here based on a definition of Y¯ involving the binding polynomial and its first derivative. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. Variations in insulin responsiveness in rat fat cells are due to metabolic differences rather than insulin binding

    DEFF Research Database (Denmark)

    Hansen, Finn Mølgård; Nilsson, Poul; Sonne, Ole

    1983-01-01

    -insulin to fat cells. Insulin binding was not correlated to the plasma insulin level which however was reflected in the lipoprotein lipase activity in the adipose tissue. In conclusion, these results indicate that variations in insulin responsiveness in fat cells are due to alterations in cellular metabolism...

  13. Phase Partitioning of GM1 and Its Bodipy-Labeled Analog Determine Their Different Binding to Cholera Toxin

    DEFF Research Database (Denmark)

    Rissanen, Sami; Grzybek, Michal; Orłowski, Adam

    2017-01-01

    membrane vesicles and giant unilamellar vesicles, specific binding of Cholera Toxin (CTxB) to GM1 glycolipids is a commonly used strategy to label raft domains or Lo membrane environments. However, these studies often use acyl-chain labeled bodipy-GM1 (bdGM1), whose headgroup accessibility and membrane...

  14. Comparison [(3)H]-flumazenil binding parameters in rat cortical membrane using different separation methods, filtration and centrifugation.

    Science.gov (United States)

    Ahmadi, Fatemeh; Faizi, Mehrdad; Tabatabai, Sayyed Abbas; Beiki, Davood; Shahhosseini, Soraya

    2013-10-01

    Radioligand receptor binding assays are a common method to evaluate the affinity of newly synthesized benzodiazepine ligands for the receptor. [(3)H]-flumazenil is an antagonist of benzodiazepine receptors and is generally used as a radioligand. In this study, the binding parameters of [(3)H]-flumazenil to rat cortical membranes were evaluated using two separation methods: filtration with GF/C filters and centrifugation. Additionally, the effects of vacuum pressure, exposure time to the cocktail, and geometry on the filtration method were studied. The binding parameters of [(3)H]-flumazenil (Kd and Bmax) were determined through saturation studies using two methods. The results from this study showed that the filtration method is time consuming and requires more steps to be completed. Because filtration causes partial elution of bound [(3)H]-flumazenil into the liquid scintillation cocktail, the results are not reproducible, which result in inaccurate estimation of the binding parameters. The centrifugation method in contrast to filtration is straightforward and produces reproducible as well as reliable results, all of the steps are performed in a single polypropylene tube, which eliminates the loss of tissue and avoids other systematic errors associated with transfer and handling. © 2013.

  15. Renewable Energy and Efficiency Modeling Analysis Partnership (REMAP): An Analysis of How Different Energy Models Addressed a Common High Renewable Energy Penetration Scenario in 2025

    Energy Technology Data Exchange (ETDEWEB)

    Blair, N.; Jenkin, T.; Milford, J.; Short, W.; Sullivan, P.; Evans, D.; Lieberman, E.; Goldstein, G.; Wright, E.; Jayaraman, K. R.; Venkatesh, B.; Kleiman, G.; Namovicz, C.; Smith, B.; Palmer, K.; Wiser, R.; Wood, F.

    2009-09-01

    Energy system modeling can be intentionally or unintentionally misused by decision-makers. This report describes how both can be minimized through careful use of models and thorough understanding of their underlying approaches and assumptions. The analysis summarized here assesses the impact that model and data choices have on forecasting energy systems by comparing seven different electric-sector models. This analysis was coordinated by the Renewable Energy and Efficiency Modeling Analysis Partnership (REMAP), a collaboration among governmental, academic, and nongovernmental participants.

  16. Accurate calculation of conformational free energy differences in explicit water: the confinement-solvation free energy approach.

    Science.gov (United States)

    Esque, Jeremy; Cecchini, Marco

    2015-04-23

    The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent.

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

    Science.gov (United States)

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

    2008-01-01

    We revisit the reactivity of trapped pure gold (Au(n)+, n cluster cations (Ag(m)Au(n)+, m + n adsorption sites, associated vibrational frequencies) of CO to the noble metal as a function of cluster size and composition. Starting from results for pure gold cluster cations for which an overall decrease of CO binding energy with increasing cluster size was experimentally observed--from about 1.09 +/- 0.1 eV (for n = 6) to below 0.65 +/- 0.1 eV (for n > 26) we demonstrate that metal--CO bond energies correlate with the total electron density and with the energy of the lowest unoccupied molecular orbital (LUMO) on the bare metal cluster cation as obtained by density functional theory (DFT) computations. This is a consequence of the predominantly sigma-donating character of the CO-M bond. Further support for this concept is found by contrasting the predictions of binding energies to the experimental results for small alloy cluster cations (Ag(m)Au(n)+, 4 adsorption sites and pre-screen favorable isomers.

  18. Inhibitor and peptide binding to calmodulin characterized by high pressure Fourier transform infrared spectroscopy and Förster resonance energy transfer.

    Science.gov (United States)

    Cinar, Süleyman; Czeslik, Claus

    2018-03-17

    We compare the binding of an inhibitor with that of a natural peptide to Ca 2+ saturated calmodulin (holo-CaM). As inhibitor we have chosen trifluoperazine (TFP) that is inducing a huge conformational change of holo-CaM from the open dumbbell-shaped to the closed globular conformation upon binding. On the other hand, melittin is used as model peptide, which is a well-known natural binding partner of holo-CaM. The experiments are carried out as a function of pressure to reveal the contribution of volume or packing effects to the stability of the calmodulin-ligand complexes. From high-pressure Fourier transform infrared (FTIR) spectroscopy, we find that the holo-CaM/TFP complex has a much higher pressure stability than the holo-CaM/melittin complex. Although the analysis of the secondary structure of holo-CaM (without and with ligand) indicates no major changes up to several kbar, pressure-induced exposure of α-helices to water is most pronounced for holo-CaM without ligand, followed by holo-CaM/melittin and then holo-CaM/TFP. Moreover, structural pressure resistance of the holo-CaM/TFP complex in comparison with the holo-CaM/melittin complex is also clearly visible by higher Ca 2+ affinity. Förster resonance energy transfer (FRET) from the Tyr residues of holo-CaM to the Trp residue of melittin even suggests some partial dissociation of the complex under pressure which points to void volumes at the protein-ligand interface and to electrostatic binding. Thus, all results of this study show that the inhibitor TFP binds to holo-CaM with higher packing density than the peptide melittin enabling a favorable volume contribution to the inhibitor efficiency. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Differences and similarities of energy innovation systems – comparison of five technology areas in Denmark

    DEFF Research Database (Denmark)

    Borup, Mads

    2016-01-01

    This paper presents a study of the energy innovation systems concerning five technology areas in Denmark: biomass energy, wind power, solar cells, fuel cells & hydrogen and energy efficiency technology. The study shows that the characteristics of the innovation systems differ significantly between...... the areas amongst other things concerning actor landscapes, market formations, and patterns of learning and interaction. This is despite the common context of Danish society and Danish energy systems, policy and institutions. An increase in maturity has appeared in some of the areas over the latest decades......, including the significance of the international dimension and the relationships to the established energy sector and incumbents....

  20. Modelling energy costs for different operational strategies of a large water resource recovery facility.

    Science.gov (United States)

    Póvoa, P; Oehmen, A; Inocêncio, P; Matos, J S; Frazão, A

    2017-05-01

    The main objective of this paper is to demonstrate the importance of applying dynamic modelling and real energy prices on a full scale water resource recovery facility (WRRF) for the evaluation of control strategies in terms of energy costs with aeration. The Activated Sludge Model No. 1 (ASM1) was coupled with real energy pricing and a power consumption model and applied as a dynamic simulation case study. The model calibration is based on the STOWA protocol. The case study investigates the importance of providing real energy pricing comparing (i) real energy pricing, (ii) weighted arithmetic mean energy pricing and (iii) arithmetic mean energy pricing. The operational strategies evaluated were (i) old versus new air diffusers, (ii) different DO set-points and (iii) implementation of a carbon removal controller based on nitrate sensor readings. The application in a full scale WRRF of the ASM1 model coupled with real energy costs was successful. Dynamic modelling with real energy pricing instead of constant energy pricing enables the wastewater utility to optimize energy consumption according to the real energy price structure. Specific energy cost allows the identification of time periods with potential for linking WRRF with the electric grid to optimize the treatment costs, satisfying operational goals.

  1. Variations in insulin responsiveness in rat fat cells are due to metabolic differences rather than insulin binding

    DEFF Research Database (Denmark)

    Hansen, Finn Mølgård; Nilsson, Poul; Sonne, Ole

    1983-01-01

    to fat cells. Insulin binding was not correlated to the plasma insulin level which however was reflected in the lipoprotein lipase activity in the adipose tissue. In conclusion, these results indicate that variations in insulin responsiveness in fat cells are due to alterations in cellular metabolism......Insulin resistance was studied by comparing insulin response and insulin binding in four groups of rats. Glucose metabolism in isolated fat cells from male Wistar rats weighing 340 g was less responsive to a supramaximal dose of insulin than glucose metabolism in fat cells from rats weighing 200 g....... Induction of streptozotocin-diabetes in rats weighing 200 g resulted in a marked decrease in the insulin responsiveness of fat cells. Ventromedial hypothalamic lesions of 340 g rats had the opposite effect and restored the insulin responsiveness of fat cells. The responsiveness in the four groups...

  2. Comparison of gas-solid chromatography and MM2 force field molecular binding energies for greenhouse gases on a carbonaceous surface.

    Science.gov (United States)

    Rybolt, Thomas R; Bivona, Kevin T; Thomas, Howard E; O'Dell, Casey M

    2009-10-01

    Gas-solid chromatography was used to determine B(2s) (gas-solid virial coefficient) values for eight molecular adsorbates interacting with a carbon powder (Carbopack B, Supelco). B(2s) values were determined by multiple size variant injections within the temperature range of 313-553 K. The molecular adsorbates included: carbon dioxide (CO(2)); tetrafluoromethane (CF(4)); hexafluoroethane (C(2)F(6)); 1,1-difluoroethane (C(2)H(4)F(2)); 1-chloro-1,1-difluoroethane (C(2)H(3)ClF(2)); dichlorodifluoromethane (CCl(2)F(2)); trichlorofluoromethane (CCl(3)F); and 1,1,1-trichloroethane (C(2)H(3)Cl(3)). Two of these molecules are of special interest because they are "super greenhouse gases". The global warming potential, GWP, for CF(4) is 6500 and for C(2)F(6) is 9200 relative to the reference value of 1 for CO(2). The GWP index considers both radiative blocking and molecular lifetime. For these and other industrial greenhouse gases, adsorptive trapping on a carbonaceous solid, which depends on molecule-surface binding energy, could avoid atmospheric release. The temperature variations of the gas-solid virial coefficients in conjunction with van't Hoff plots were used to find the experimental adsorption energy or binding energy values (E(*)) for each adsorbate. A molecular mechanics based, rough-surface model was used to calculate the molecule-surface binding energy (Ecal(*)) using augmented MM2 parameters. The surface model consisted of parallel graphene layers with two separated nanostructures each containing 17 benzene rings arranged in linear strips. The separation of the parallel nanostructures had been optimized in a prior study to appropriately represent molecule-surface interactions for Carbopack B. Linear regressions of E(*) versus Ecal(*) for the current data set of eight molecules and the same surface model gave E(*)=0.926 Ecal(*) and r(2)=0.956. A combined set of the current and prior Carbopack B adsorbates studied (linear alkanes, branched alkanes, cyclic alkanes

  3. A New Nonlinear Regression Approach That Allows Detection of Inter-Individual Differences in Single-Point Radioligand Binding Studies

    Science.gov (United States)

    2000-08-01

    Georgetown U. Med. Ctr., 3900 Reservoir Rd., Washington, DC 20007; 2Applied Mathematics Program, Johns Hopkins University, 9601 Medical Center Dr., Rockville...TERMS Nonlinear regresion , Monte-Carlo 15. NUMBER OF PAGES randomization, Scheffe’s test, radioligand binding 16. PRICE CODE 24 17. SECURITY 18...appropriate for this situation. Indeed, here it is necessary to formulate this problem as a multiple linear regression model expressed with the aid of

  4. The Staphylococcus aureus extracellular matrix protein (Emp) has a fibrous structure and binds to different extracellular matrices.

    Science.gov (United States)

    Geraci, Jennifer; Neubauer, Svetlana; Pöllath, Christine; Hansen, Uwe; Rizzo, Fabio; Krafft, Christoph; Westermann, Martin; Hussain, Muzaffar; Peters, Georg; Pletz, Mathias W; Löffler, Bettina; Makarewicz, Oliwia; Tuchscherr, Lorena

    2017-10-20

    The extracellular matrix protein Emp of Staphylococcus aureus is a secreted adhesin that mediates interactions between the bacterial surface and extracellular host structures. However, its structure and role in staphylococcal pathogenesis remain unknown. Using multidisciplinary approaches, including circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy, transmission electron (TEM) and immunogold transmission electron microscopy, functional ELISA assays and in silico techniques, we characterized the Emp protein. We demonstrated that Emp and its truncated forms bind to suprastructures in human skin, cartilage or bone, among which binding activity seems to be higher for skin compounds. The binding domain is located in the C-terminal part of the protein. CD spectroscopy revealed high contents of β-sheets (39.58%) and natively disordered structures (41.2%), and TEM suggested a fibrous structure consisting of Emp polymers. The N-terminus seems to be essential for polymerization. Due to the uncommonly high histidine content, we suggest that Emp represents a novel type of histidine-rich protein sharing structural similarities to leucine-rich repeats proteins as predicted by the I-TASSER algorithm. These new findings suggest a role of Emp in infections of deeper tissue and open new possibilities for the development of novel therapeutic strategies.

  5. Comparison of EAS simulation results using CORSIKA code for different high-energy interaction models

    International Nuclear Information System (INIS)

    Thakuria, Chabin; Boruah, K.

    2011-01-01

    Interpretation of EAS characteristics for primary energy above the energy attained by man made accelerator is dominated by model predictions and detailed simulations. Differences and uncertainties in these hadronic interaction models play crucial role in the prediction of EAS characteristics. A comparative study for muon numbers to primary energy ratio and depth of shower maximum for different hadronic interaction models available in monte-carlo simulation code CORSIKA viz. QGSJET01, QGSJET-II, DPMJET, EPOS, SYBILL, and VENUS for two primaries (viz. proton and iron) in the energy range 10 14 eV to 10 17 eV is presented in this work.

  6. Sex Differences in Energy Metabolism Need to Be Considered with Lifestyle Modifications in Humans

    Directory of Open Access Journals (Sweden)

    Betty N. Wu

    2011-01-01

    Full Text Available Women have a higher proportion of body fat compared to men. However, women consume fewer kilojoules per kilogram lean mass and burn fat more preferentially during exercise compared with men. During gestation, women store even greater amounts of fat that cannot be solely attributed to increased energy intake. These observations suggest that the relationship between kilojoules consumed and kilojoules utilised is different in men and women. The reason for these sex differences in energy metabolism is not known; however, it may relate to sex steroids, differences in insulin resistance, or metabolic effects of other hormones such as leptin. When considering lifestyle modifications, sex differences in energy metabolism should be considered. Moreover, elucidating the regulatory role of hormones in energy homeostasis is important for understanding the pathogenesis of obesity and perhaps in the future may lead to ways to reduce body fat with less energy restriction.

  7. An Origin of Cooperative Oxygen Binding of Human Adult Hemoglobin: Different Roles of the α and β Subunits in the α2β2 Tetramer.

    Science.gov (United States)

    Nagatomo, Shigenori; Nagai, Yukifumi; Aki, Yayoi; Sakurai, Hiroshi; Imai, Kiyohiro; Mizusawa, Naoki; Ogura, Takashi; Kitagawa, Teizo; Nagai, Masako

    2015-01-01

    Human hemoglobin (Hb), which is an α2β2 tetramer and binds four O2 molecules, changes its O2-affinity from low to high as an increase of bound O2, that is characterized by 'cooperativity'. This property is indispensable for its function of O2 transfer from a lung to tissues and is accounted for in terms of T/R quaternary structure change, assuming the presence of a strain on the Fe-histidine (His) bond in the T state caused by the formation of hydrogen bonds at the subunit interfaces. However, the difference between the α and β subunits has been neglected. To investigate the different roles of the Fe-His(F8) bonds in the α and β subunits, we investigated cavity mutant Hbs in which the Fe-His(F8) in either α or β subunits was replaced by Fe-imidazole and F8-glycine. Thus, in cavity mutant Hbs, the movement of Fe upon O2-binding is detached from the movement of the F-helix, which is supposed to play a role of communication. Recombinant Hb (rHb)(αH87G), in which only the Fe-His in the α subunits is replaced by Fe-imidazole, showed a biphasic O2-binding with no cooperativity, indicating the coexistence of two independent hemes with different O2-affinities. In contrast, rHb(βH92G), in which only the Fe-His in the β subunits is replaced by Fe-imidazole, gave a simple high-affinity O2-binding curve with no cooperativity. Resonance Raman, 1H NMR, and near-UV circular dichroism measurements revealed that the quaternary structure change did not occur upon O2-binding to rHb(αH87G), but it did partially occur with O2-binding to rHb(βH92G). The quaternary structure of rHb(αH87G) appears to be frozen in T while its tertiary structure is changeable. Thus, the absence of the Fe-His bond in the α subunit inhibits the T to R quaternary structure change upon O2-binding, but its absence in the β subunit simply enhances the O2-affinity of α subunit.

  8. An Origin of Cooperative Oxygen Binding of Human Adult Hemoglobin: Different Roles of the α and β Subunits in the α2β2 Tetramer

    Science.gov (United States)

    Sakurai, Hiroshi; Imai, Kiyohiro; Mizusawa, Naoki; Ogura, Takashi

    2015-01-01

    Human hemoglobin (Hb), which is an α2β2 tetramer and binds four O2 molecules, changes its O2-affinity from low to high as an increase of bound O2, that is characterized by ‘cooperativity’. This property is indispensable for its function of O2 transfer from a lung to tissues and is accounted for in terms of T/R quaternary structure change, assuming the presence of a strain on the Fe-histidine (His) bond in the T state caused by the formation of hydrogen bonds at the subunit interfaces. However, the difference between the α and β subunits has been neglected. To investigate the different roles of the Fe-His(F8) bonds in the α and β subunits, we investigated cavity mutant Hbs in which the Fe-His(F8) in either α or β subunits was replaced by Fe-imidazole and F8-glycine. Thus, in cavity mutant Hbs, the movement of Fe upon O2-binding is detached from the movement of the F-helix, which is supposed to play a role of communication. Recombinant Hb (rHb)(αH87G), in which only the Fe-His in the α subunits is replaced by Fe-imidazole, showed a biphasic O2-binding with no cooperativity, indicating the coexistence of two independent hemes with different O2-affinities. In contrast, rHb(βH92G), in which only the Fe-His in the β subunits is replaced by Fe-imidazole, gave a simple high-affinity O2-binding curve with no cooperativity. Resonance Raman, 1H NMR, and near-UV circular dichroism measurements revealed that the quaternary structure change did not occur upon O2-binding to rHb(αH87G), but it did partially occur with O2-binding to rHb(βH92G). The quaternary structure of rHb(αH87G) appears to be frozen in T while its tertiary structure is changeable. Thus, the absence of the Fe-His bond in the α subunit inhibits the T to R quaternary structure change upon O2-binding, but its absence in the β subunit simply enhances the O2-affinity of α subunit. PMID:26244770

  9. Can Ethnic Background Differences in Children's Body Composition Be Explained by Differences in Energy Balance-Related Behaviors? A Mediation Analysis within the Energy-Project

    NARCIS (Netherlands)

    Fernandez Alvira, J.M.; te Velde, S.J.; Jimenez-Pavon, D.; Manios, Y.; Singh, A.S.; Moreno, L.A.; Brug, J.

    2013-01-01

    Background:In affluent countries, children from non-native ethnicity have in general less favourable body composition indicators and energy balance-related behaviors (EBRBs) than children from native ethnicity. However, differences between countries have been reported.Methodology/Principal

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

    Directory of Open Access Journals (Sweden)

    Dimitrios Spiliotopoulos

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

  11. Motif III in superfamily 2 "helicases" helps convert the binding energy of ATP into a high-affinity RNA binding site in the yeast DEAD-box protein Ded1.

    Science.gov (United States)

    Banroques, Josette; Doère, Monique; Dreyfus, Marc; Linder, Patrick; Tanner, N Kyle

    2010-03-05

    Motif III in the putative helicases of superfamily 2 is highly conserved in both its sequence and its structural context. It typically consists of the sequence alcohol-alanine-alcohol (S/T-A-S/T). Historically, it was thought to link ATPase activity with a "helicase" strand displacement activity that disrupts RNA or DNA duplexes. DEAD-box proteins constitute the largest family of superfamily 2; they are RNA-dependent ATPases and ATP-dependent RNA binding proteins that, in some cases, are able to disrupt short RNA duplexes. We made mutations of motif III (S-A-T) in the yeast DEAD-box protein Ded1 and analyzed in vivo phenotypes and in vitro properties. Moreover, we made a tertiary model of Ded1 based on the solved structure of Vasa. We used Ded1 because it has relatively high ATPase and RNA binding activities; it is able to displace moderately stable duplexes at a large excess of substrate. We find that the alanine and the threonine in the second and third positions of motif III are more important than the serine, but that mutations of all three residues have strong phenotypes. We purified the wild-type and various mutants expressed in Escherichia coli. We found that motif III mutations affect the RNA-dependent hydrolysis of ATP (k(cat)), but not the affinity for ATP (K(m)). Moreover, mutations alter and reduce the affinity for single-stranded RNA and subsequently reduce the ability to disrupt duplexes. We obtained intragenic suppressors of the S-A-C mutant that compensate for the mutation by enhancing the affinity for ATP and RNA. We conclude that motif III and the binding energy of gamma-PO(4) of ATP are used to coordinate motifs I, II, and VI and the two RecA-like domains to create a high-affinity single-stranded RNA binding site. It also may help activate the beta,gamma-phosphoanhydride bond of ATP. (c) 2009 Elsevier Ltd. All rights reserved.

  12. Age dependent accumulation patterns of advanced glycation end product receptor (RAGE) ligands and binding intensities between RAGE and its ligands differ in the liver, kidney, and skeletal muscle.

    Science.gov (United States)

    Son, Myeongjoo; Chung, Wook-Jin; Oh, Seyeon; Ahn, Hyosang; Choi, Chang Hu; Hong, Suntaek; Park, Kook Yang; Son, Kuk Hui; Byun, Kyunghee

    2017-01-01

    Much evidence indicates receptor for advanced glycation end products (RAGE) related inflammation play essential roles during aging. However, the majority of studies have focused on advanced glycation end products (AGEs) and not on other RAGE ligands. In the present study, the authors evaluated whether the accumulation of RAGE ligands and binding intensities between RAGE and its ligands differ in kidney, liver, and skeletal muscle during aging. In C57BL/6 N mice aged 12 weeks, 12 months, and 22 months, ligands accumulation, binding intensities between RAGE and its ligands, activated macrophage infiltration, M1/M2 macrophage expression, glyoxalase-1expression, and signal pathways related to inflammation were evaluated. The RAGE ligands age-associated accumulation patterns were found to be organ dependent. Binding intensities between RAGE and its ligands in kidney and liver increased with age, but those in skeletal muscle were unchanged. Infiltration of activated macrophages in kidney and liver increased with age, but infiltration in the skeletal muscle was unchanged. M1 expression increased and M2 and glyoxalase-1 expression decreased with age in kidney and liver, but their expressions in skeletal muscle were not changed. These findings indicate patterns of RAGE ligands accumulation, RAGE/ligands binding intensities, or inflammation markers changes during aging are organs dependent.

  13. The ligand specificities of the insulin receptor and the insulin-like growth factor I receptor reside in different regions of a common binding site

    Energy Technology Data Exchange (ETDEWEB)

    Kjeldsen, T.; Andersen, A.S.; Wiberg, F.C.; Rasmussen, J.S.; Schaeffer, L.; Balschmidt, P.; Moller, K.B.; Moller, N.P.H. (Novo Nordisk, Bagsvaerd (Denmark))

    1991-05-15

    To identify the region(s) of the insulin receptor and the insulin-like growth factor I (IGF-I) receptor responsible for ligand specificity (high-affinity binding), expression vectors encoding soluble chimeric insulin/IGF-I receptors were prepared. The chimeric receptors were expressed in mammalian cells and partially purified. Binding studies revealed that a construct comprising an IGF-I receptor in which the 68 N-terminal amino acids of the insulin receptor {alpha}-subunit had replaced the equivalent IGF-I receptor segment displayed a markedly increased affinity for insulin. In contrast, the corresponding IGF-I receptor sequence is not critical for high-affinity IGF-I binding. It is shown that part of the cysteine-rich domain determines IGF-I specificity. The authors have previously shown that exchanging exons 1, 2, and 3 of the insulin receptor with the corresponding IGF-I receptor sequence results in loss of high affinity for insulin and gain of high affinity for IGF-I. Consequently, it is suggested that the ligand specificities of the two receptors (i.e., the sequences that discriminate between insulin and IGF-I) reside in different regions of a binding site with common features present in both receptors.

  14. Comparison of the Fibronectin-Binding Protein FNE from Streptococcus equi Subspecies equi with FNZ from S. equi Subspecies zooepidemicus Reveals a Major and Conserved Difference

    Science.gov (United States)

    Lindmark, Hans; Nilsson, Martin; Guss, Bengt

    2001-01-01

    The gene fnz from Streptococcus equi subspecies zooepidemicus encodes a cell surface protein that binds fibronectin (Fn). Fifty tested isolates of S. equi subspecies equi all contain DNA sequences with similarity to fnz. This work describes the cloning and sequencing of a gene, designated fne, with similarity to fnz from two S. equi subspecies equi isolates. The DNA sequences were found to be identical in the two strains, and sequence comparison of the fne and fnz genes revealed only minor differences. However, one base deletion was found in the middle of the fne gene and eight base pairs downstream of the altered reading frame there is a stop codon. An Fn-binding protein was purified from the growth medium of a subspecies equi culture. Determination of the NH2-terminal amino acid sequence and molecular mass, as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, revealed that the purified protein is the gene product of the 5′-terminal half of fne. Fn-binding activity has earlier only been found in the COOH-terminal half of FNZ. By the use of a purified recombinant protein containing the NH2 half of FNZ, we provide here evidence that this half of the protein also harbors an Fn-binding domain. PMID:11292736

  15. Characterization of water binding and germination traits of magnetically exposed maize (Zea mays L.) seeds equilibrated at different relative humidities at two temperatures.

    Science.gov (United States)

    Vashisth, Ananta; Nagarajan, Shantha

    2009-04-01

    A study was undertaken to characterize the water sorption properties and enhancement in germination and seedling vigour of maize (Zea mays L.) seeds exposed to static magnetic fields of 100 mT and 200 mT for 2 and 1 h, respectively. Water sorption isotherms were constructed for magnetically- exposed and unexposed seeds by equilibrating over different saturated salt solutions at 25 and 35 degrees C. The germination and vigour parameters were evaluated for magnetically-exposed and unexposed seeds, equilibrated over the wide range of relative humidities (RHs) at 25 and 35 degrees C. Moisture content increased with increase in RH and decreased with increase in equilibrium temperature. The germination and vigour reduced at high and very low humidities. Magnetically-exposed seeds maintained higher germination and vigour at both temperatures and all RHs, indicating the better quality of magnetically-exposed seeds. The leachate conductivity of magnetically-exposed seeds was lower than unexposed seeds at all RHs, suggesting better membrane integrity in magnetically-exposed seeds. Analysis of the isotherms using D'Arcy-Watt equation revealed that irrespective of the temperature, in magnetically-treated seeds weak binding sites were more and strong and multi-molecular binding sites were less compared to the unexposed seeds. Total binding sites were more in unexposed control seeds. The modification of binding properties of seed water and increased seed membrane integrity in magnetically-exposed seeds might have enhanced the germination traits and early seedling growth of maize.

  16. Multi-region optimal deployment of renewable energy considering different interregional transmission scenarios

    International Nuclear Information System (INIS)

    Wang, Ge; Zhang, Qi; Mclellan, Benjamin C.; Li, Hailong

    2016-01-01

    Renewable energy is expected to play much more important role in future low-carbon energy system, however, renewable energy has problems with regard to load-following and regional imbalance. This study aims to plan the deployment of intermittent renewable energy in multiple regions considering the impacts of regional natural conditions and generation capacity mix as well as interregional transmission capacity using a multi-region dynamic optimization model. The model was developed to find optimized development paths toward future smart electricity systems with high level penetration of intermittent renewable energy considering regional differences and interregional transmission at national scale. As a case study, the model was applied to plan power generation in nine interconnected regions in Japan out to 2030. Four scenarios were proposed with different supporting policies for the interregional power transmission infrastructures and different nuclear power phase-out scenarios. The analysis results show that (i) the government's support for power transmission infrastructures is vital important to develop more intermittent renewable energy in appropriate regions and utilize renewable energy more efficiently; (ii) nuclear and renewable can complement rather than replace each other if enough interregional transmission capacity is provided. - Highlights: • Plan the optimal deployment of intermittent renewable energy in multiple regions. • A multi-region dynamic optimization model was developed. • The impacts of natural conditions and interregional transmission are studied. • The government's support for transmission is vital important for renewable energy. • Nuclear and renewable can complement rather than replace each other.

  17. Energies and wave functions of an off-centre donor in hemispherical quantum dot: Two-dimensional finite difference approach and ritz variational principle

    Energy Technology Data Exchange (ETDEWEB)

    Nakra Mohajer, Soukaina; El Harouny, El Hassan [Laboratoire de Physique de la Matière Condensée, Département de Physique, Faculté des Sciences, Université Abdelmalek Essaadi, B.P. 2121 M’Hannech II, 93030 Tétouan (Morocco); Ibral, Asmaa [Equipe d’Optique et Electronique du Solide, Département de Physique, Faculté des Sciences, Université Chouaïb Doukkali, B. P. 20 El Jadida Principale, El Jadida (Morocco); Laboratoire d’Instrumentation, Mesure et Contrôle, Département de Physique, Faculté des Sciences, Université Chouaïb Doukkali, B. P. 20 El Jadida Principale, El Jadida (Morocco); El Khamkhami, Jamal [Laboratoire de Physique de la Matière Condensée, Département de Physique, Faculté des Sciences, Université Abdelmalek Essaadi, B.P. 2121 M’Hannech II, 93030 Tétouan (Morocco); and others

    2016-09-15

    Eigenvalues equation solutions of a hydrogen-like donor impurity, confined in a hemispherical quantum dot deposited on a wetting layer and capped by an insulating matrix, are determined in the framework of the effective mass approximation. Conduction band alignments at interfaces between quantum dot and surrounding materials are described by infinite height barriers. Ground and excited states energies and wave functions are determined analytically and via one-dimensional finite difference approach in case of an on-center donor. Donor impurity is then moved from center to pole of hemispherical quantum dot and eigenvalues equation is solved via Ritz variational principle, using a trial wave function where Coulomb attraction between electron and ionized donor is taken into account, and by two-dimensional finite difference approach. Numerical codes developed enable access to variations of donor total energy, binding energy, Coulomb correlation parameter, spatial extension and radial probability density with respect to hemisphere radius and impurity position inside the quantum dot.

  18. Energies and wave functions of an off-centre donor in hemispherical quantum dot: Two-dimensional finite difference approach and ritz variational principle

    International Nuclear Information System (INIS)

    Nakra Mohajer, Soukaina; El Harouny, El Hassan; Ibral, Asmaa; El Khamkhami, Jamal

    2016-01-01

    Eigenvalues equation solutions of a hydrogen-like donor impurity, confined in a hemispherical quantum dot deposited on a wetting layer and capped by an insulating matrix, are determined in the framework of the effective mass approximation. Conduction band alignments at interfaces between quantum dot and surrounding materials are described by infinite height barriers. Ground and excited states energies and wave functions are determined analytically and via one-dimensional finite difference approach in case of an on-center donor. Donor impurity is then moved from center to pole of hemispherical quantum dot and eigenvalues equation is solved via Ritz variational principle, using a trial wave function where Coulomb attraction between electron and ionized donor is taken into account, and by two-dimensional finite difference approach. Numerical codes developed enable access to variations of donor total energy, binding energy, Coulomb correlation parameter, spatial extension and radial probability density with respect to hemisphere radius and impurity position inside the quantum dot.

  19. Assessing energy and thermal comfort of different low-energy cooling concepts for non-residential buildings

    International Nuclear Information System (INIS)

    Salvalai, Graziano; Pfafferott, Jens; Sesana, Marta Maria

    2013-01-01

    Highlights: • Impact of five cooling technologies are simulated in six European climate zones with Trnsys 17. • The ventilation strategies reduce the cooling energy need even in South Europe climate. • Constant ventilation controller can lead to a poor cooling performance. • Comparing radiant strategies with air conditioning scenario, the energy saving is predicted to within 5–35%. - Abstract: Energy consumption for cooling is growing dramatically. In the last years, electricity peak consumption grew significantly, switching from winter to summer in many EU countries. This is endangering the stability of electricity grids. This article outlines a comprehensive analysis of an office building performances in terms of energy consumption and thermal comfort (in accordance with static – ISO 7730:2005 – and adaptive thermal comfort criteria – EN 15251:2007 –) related to different cooling concepts in six different European climate zones. The work is based on a series of dynamic simulations carried out in the Trnsys 17 environment for a typical office building. The simulation study was accomplished for five cooling technologies: natural ventilation (NV), mechanical night ventilation (MV), fan-coils (FC), suspended ceiling panels (SCP), and concrete core conditioning (CCC) applied in Stockholm, Hamburg, Stuttgart, Milan, Rome, and Palermo. Under this premise, the authors propose a methodology for the evaluation of the cooling concepts taking into account both, thermal comfort and energy consumption

  20. [Optimal energy supply in different age groups of critically ill children on mechanical ventilation].

    Science.gov (United States)

    Li, X H; Ji, J; Qian, S Y

    2018-01-02

    Objective: To analyze the resting energy expenditure and optimal energy supply in different age groups of critically ill children on mechanical ventilation in pediatric intensive care unit (PICU). Methods: Patients on mechanical ventilation hospitalized in PICU of Beijing Children's Hospital from March 2015 to March 2016 were enrolled prospectively. Resting energy expenditure of patients was calculated by US Med Graphic company critical care management (CCM) energy metabolism test system after mechanical ventilation. Patients were divided into three groups:10 years. The relationship between the measured and predictive resting energy expenditure was analyzed with correlation analysis; while the metabolism status and the optimal energy supply in different age groups were analyzed with chi square test and variance analysis. Results: A total of 102 patients were enrolled, the measured resting energy expenditure all correlated with predictive resting energy expenditure in different age groups (10 years ( r= 0.5, P= 0.0) ) . A total of 40 cases in group, including: 14 cases of low metabolism (35%), 14 cases of normal metabolism (35%), and 12 cases of high metabolism (30%); 45 cases in 3-10 years group, including: 22 cases of low metabolism (49%), 19 cases of normal metabolism (42%), 4 cases of high metabolism (9%); 17 cases in > 10 years group, including: 12 cases of low metabolism (71%), 4 cases of normal metabolism (23%), 1 case of high metabolism (6%). Metabolism status showed significant differences between different age groups ( χ (2)=11.30, P age groups ( F= 46.57, Pgroup, (184±53) kJ/ (kg⋅d) in 3-10 years group, and (120±30) kJ/ (kg⋅d) in > 10 years group. Conclusion: The resting energy metabolism of the critically ill children on mechanical ventilation is negatively related to the age. The actual energy requirement should be calculated according to different ages.

  1. Assessing the technical efficiency of energy use in different barberry production systems

    NARCIS (Netherlands)

    Mousavi-Avval, Seyed Hashem; Mohammadi, Ali; Rafiee, Shahin; Tabatabaeefar, Ahmad

    The main objectives of this study were to analyze the technical and scale efficiencies of farmers and to identify the wasteful uses of energy in different farm sizes of barberry production in Iran. For these purposes the data envelopment analysis approach was applied to the data of energy use for

  2. A research on environmental rating systems considering building energy performances in different climatic regions of Turkey

    NARCIS (Netherlands)

    Akiner, Ilknur; Akıner, Muhammed E.; Tijhuis, Wilco

    2015-01-01

    Turkey’s diverse regions lead to complex issues in sustainability. We studied to cities in different areas of the country to examine the effects of local climate on energy use in energy-efficient buildings. Erzurum is the coldest city; Antalya lies in the Mediterranean region and has the highest

  3. Climate impacts on extreme energy consumption of different types of buildings.

    Directory of Open Access Journals (Sweden)

    Mingcai Li

    Full Text Available Exploring changes of building energy consumption and its relationships with climate can provide basis for energy-saving and carbon emission reduction. Heating and cooling energy consumption of different types of buildings during 1981-2010 in Tianjin city, was simulated by using TRNSYS software. Daily or hourly extreme energy consumption was determined by percentile methods, and the climate impact on extreme energy consumption was analyzed. The results showed that days of extreme heating consumption showed apparent decrease during the recent 30 years for residential and large venue buildings, whereas days of extreme cooling consumption increased in large venue building. No significant variations were found for the days of extreme energy consumption for commercial building, although a decreasing trend in extreme heating energy consumption. Daily extreme energy consumption for large venue building had no relationship with climate parameters, whereas extreme energy consumption for commercial and residential buildings was related to various climate parameters. Further multiple regression analysis suggested heating energy consumption for commercial building was affected by maximum temperature, dry bulb temperature, solar radiation and minimum temperature, which together can explain 71.5 % of the variation of the daily extreme heating energy consumption. The daily extreme cooling energy consumption for commercial building was only related to the wet bulb temperature (R2= 0.382. The daily extreme heating energy consumption for residential building was affected by 4 climate parameters, but the dry bulb temperature had the main impact. The impacts of climate on hourly extreme heating energy consumption has a 1-3 hour delay in all three types of buildings, but no delay was found in the impacts of climate on hourly extreme cooling energy consumption for the selected buildings.

  4. Climate impacts on extreme energy consumption of different types of buildings.

    Science.gov (United States)

    Li, Mingcai; Shi, Jun; Guo, Jun; Cao, Jingfu; Niu, Jide; Xiong, Mingming

    2015-01-01

    Exploring changes of building energy consumption and its relationships with climate can provide basis for energy-saving and carbon emission reduction. Heating and cooling energy consumption of different types of buildings during 1981-2010 in Tianjin city, was simulated by using TRNSYS software. Daily or hourly extreme energy consumption was determined by percentile methods, and the climate impact on extreme energy consumption was analyzed. The results showed that days of extreme heating consumption showed apparent decrease during the recent 30 years for residential and large venue buildings, whereas days of extreme cooling consumption increased in large venue building. No significant variations were found for the days of extreme energy consumption for commercial building, although a decreasing trend in extreme heating energy consumption. Daily extreme energy consumption for large venue building had no relationship with climate parameters, whereas extreme energy consumption for commercial and residential buildings was related to various climate parameters. Further multiple regression analysis suggested heating energy consumption for commercial building was affected by maximum temperature, dry bulb temperature, solar radiation and minimum temperature, which together can explain 71.5 % of the variation of the daily extreme heating energy consumption. The daily extreme cooling energy consumption for commercial building was only related to the wet bulb temperature (R2= 0.382). The daily extreme heating energy consumption for residential building was affected by 4 climate parameters, but the dry bulb temperature had the main impact. The impacts of climate on hourly extreme heating energy consumption has a 1-3 hour delay in all three types of buildings, but no delay was found in the impacts of climate on hourly extreme cooling energy consumption for the selected buildings.

  5. Analytical framework for analyzing the energy conversion efficiency of different hybrid electric vehicle topologies

    International Nuclear Information System (INIS)

    Katrasnik, Tomaz

    2009-01-01

    Energy consumption and exhaust emissions of hybrid electric vehicles (HEVs) strongly depend on the HEV topology, power ratios of the components and applied control strategy. There are many available patterns of combining the power flows to meet load requirements making it difficult to analyze and evaluate a newly designed HEV. In order to enhance design of HEVs, the paper provides a stand alone analytical framework for evaluating energy conversion phenomena of different HEV topologies. Analytical analysis is based on the energy balance equations and considers the complete energy path in the HEVs from the energy sources to the wheels and to other energy sinks. The analytical framework enables structuring large amount of data in physically meaningful energy flows and associated energy losses, and therefore provides insightful information for HEV optimization. It therefore enables identification of most suitable HEV topology and of most suitable power ratios of the components, since it reveals and quantifies the instruments that could lead to improved energy conversion efficiency of particular HEV. The analytical framework is also applicable for correcting the energy consumption of the HEV to the value corresponding to balanced energy content of the electric storage devices.

  6. Thermodynamic Characterization of New Positive Allosteric Modulators Binding to the Glutamate Receptor A2 Ligand-Binding Domain

    DEFF Research Database (Denmark)

    Nørholm, Ann-Beth; Francotte, Pierre; Goffin, Eric

    2014-01-01

    ,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxides. Measurements of ligand binding by isothermal titration calorimetry (ITC) showed similar binding affinities for the modulator series at the GluA2 LBD but differences in the thermodynamic driving forces. Binding of 5c (7-F) and 6 (no-F) is enthalpy driven......, and combined with the shorter total simulation time, we found the OSP method to be more effective for this setup. Furthermore, from the molecular dynamics simulations, we extracted the enthalpies and entropies, and along with the ITC data, this suggested that the differences in binding free energies...

  7. 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

  8. Different binding modes of Cu and Pb vs. Cd, Ni, and Zn with the trihydroxamate siderophore desferrioxamine B at seawater ionic strength

    Energy Technology Data Exchange (ETDEWEB)

    Schijf, Johan; Christenson, Emily A.; Potter, Kailee J.

    2015-07-01

    The solution speciation in seawater of divalent trace metals (Cd, Cu, Ni, Pb, Zn) is dominated by strong, ostensibly metal-specific organic ligands that may play important roles in microbial metal acquisition and/or detoxification processes. We compare the effective stabilities of these metal-organic complexes to the stabilities of their complexes with a model siderophore, desferrioxamine B (DFOB). While metal-DFOB complexation has been studied in various dilute but often moderately coordinating media, for the purpose of this investigation we measured the stability constants in a non-coordinating background electrolyte at seawater ionic strength (0.7 M NaClO4). Potentiometric titrations of single metals (M) were performed in the presence of ligand (L) at different M:L molar ratios, whereupon the stability constants of multiple complexes were simultaneously determined by non-linear regression of the titration curves with FITEQL, using the optimal binding mode for each metal. Cadmium, Ni, and Zn, like trivalent Fe, sequentially form a bi-, tetra-, and hexadentate complex with DFOB as pH increases, consistent with their coordination number of 6 and regular octahedral geometry. Copper has a Jahn-Teller-distorted square-bipyramidal geometry whereas the geometry of Pb is cryptic, involving a range of bond lengths. Supported by a thermodynamic argument, our data suggest that this impedes binding of the third hydroxamate group and that the hexadentate Cu-DFOB and Pb-DFOB complex identified in earlier reports may instead be a deprotonated tetradentate complex. Absence of the hexadentate complex promotes the formation of a dinuclear (bidentate-tetradentate) complex, M2HL2+, albeit not for Pb in 0.7 M NaCl, evidently due to extensive complexation with chloride. Stabilities of the hexadentate Ni-DFOB, Zn-DFOB, and the tetradentate Pb-DFOB complex are nearly equal, yet about 2 orders of magnitude higher and 4 orders of magnitude lower than those of the hexadentate Cd-DFOB and

  9. C0 and C1 N-terminal Ig domains of myosin binding protein C exert different effects on thin filament activation.

    Science.gov (United States)

    Harris, Samantha P; Belknap, Betty; Van Sciver, Robert E; White, Howard D; Galkin, Vitold E

    2016-02-09

    Mutations in genes encoding myosin, the molecular motor that powers cardiac muscle contraction, and its accessory protein, cardiac myosin binding protein C (cMyBP-C), are the two most common causes of hypertrophic cardiomyopathy (HCM). Recent studies established that the N-terminal domains (NTDs) of cMyBP-C (e.g., C0, C1, M, and C2) can bind to and activate or inhibit the thin filament (TF). However, the molecular mechanism(s) by which NTDs modulate interaction of myosin with the TF remains unknown and the contribution of each individual NTD to TF activation/inhibition is unclear. Here we used an integrated structure-function approach using cryoelectron microscopy, biochemical kinetics, and force measurements to reveal how the first two Ig-like domains of cMyPB-C (C0 and C1) interact with the TF. Results demonstrate that despite being structural homologs, C0 and C1 exhibit different patterns of binding on the surface of F-actin. Importantly, C1 but not C0 binds in a position to activate the TF by shifting tropomyosin (Tm) to the "open" structural state. We further show that C1 directly interacts with Tm and traps Tm in the open position on the surface of F-actin. Both C0 and C1 compete with myosin subfragment 1 for binding to F-actin and effectively inhibit actomyosin interactions when present at high ratios of NTDs to F-actin. Finally, we show that in contracting sarcomeres, the activating effect of C1 is apparent only once low levels of Ca(2+) have been achieved. We suggest that Ca(2+) modulates the interaction of cMyBP-C with the TF in the sarcomere.

  10. Energy landscape differences