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Sample records for binding energies obtained

  1. Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

    Science.gov (United States)

    Olsson, Martin A; Söderhjelm, Pär; Ryde, Ulf

    2016-06-30

    In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi-empirical PM6-DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free-energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  2. 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.

  3. 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.

  4. Obtaining evapotranspiration and surface energy fluxes with ...

    African Journals Online (AJOL)

    In this study, SEBAL (Surface Energy Balance Algorithm for Land), a remote sensing based evapotranspiration model, has been applied with Landsat ETM+ sensor for the estimation of actual ... The land uses in this study area consists of irrigated agriculture, rain-fed agriculture and livestock grazing. The obtained results ...

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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....

  10. 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.

  11. 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

  12. Comparison of estimates of feed energy obtained from ostriches with ...

    African Journals Online (AJOL)

    Unknown

    Comparison of estimates of feed energy obtained from ostriches with estimates obtained from ... balanced diets different in fibre content, and therefore also different in energy content, with energy values obtained ... Ostriches had significantly (P ≤ 0.01) higher ME values than both pigs and ruminants for all three types of.

  13. 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.

  14. 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.

  15. 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.

  16. 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

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

    Science.gov (United States)

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

    2015-06-09

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

  18. Apparatus for obtaining electric energy in speed highways

    International Nuclear Information System (INIS)

    Khalatyan, P.R.; Khalatyan, R.P.; Khalatyan, E.P.

    2012-01-01

    The problems of obtaining electricity by means of moving motor-transport are examined. An apparatus installed in the distributive zone of intensive traffic speed highways is proposed. Part of air mass movement of kinetic energy is transformed from the movement of automobiles into electricity

  19. Obtaining cellulose binding and hydrolyzing activity of a family 11 hybrid xylanase by fusion with xylan binding domain.

    Science.gov (United States)

    Liu, Ming-Qi; Dai, Xian-Jun; Liu, Guang-Fu; Wang, Qian

    2013-03-01

    The xylan binding domain (XBD) and linker sequences (LS) from thermostable and thermophilic Thermomonospora fusca xylanase A (TfxA) was fused to the carboxyl-terminus of a family 11 hybrid xylanase ATx. The constructed chimera (ATxX) was successfully expressed in Pichia pastoris, partially purified to homogeneity, and then characterized in detail. After 96-h 0.25% methanol induction, the xylanase and cellulose activity of ATxX from pPATxX1 transformant culture medium supernatant were 452.1 U/mg and 19.3 U/mg, respectively. SDS-PAGE analysis revealed that the molecular mass of ATxX was about 33.01 kDa. 3.7% ATxX was bound after incubation with 1% microcrystal cellulose at 25 °C for 3 h, while the ATx did not show cellulose binding-hydrolyzing ability. These results suggested that ATx obtained cellulose binding and hydrolyzing ability by fusing with XBD and LS. Enzymatic studies showed that the temperature and pH optimum of the ATxX xylanase activity were 60 °C and pH 5.0, respectively, which were the same as that of ATx. The temperature and pH optimum of the ATxX cellulase activity were 60 °C and pH 6.0, respectively. The major hydrolytic products released by ATxX from birchwood xylan were xylotriose and xylohexaose. Xylooligosaccharides from xylobiose to xylohexaose could be hydrolyzed by ATxX. Mode of action analysis showed that the chimeric ATxX was an endo-acting enzyme. The XBD and LS plays an important role in the binding and hydrolyzing of xylanase to insoluble substrates. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. 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...

  1. 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.

  2. 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...

  3. 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 ...

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

    CERN Document Server

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

    2001-01-01

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

  5. 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

  6. 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).

  7. 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...

  8. 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.

  9. PbSe nanocubes obtained by high-energy milling

    Energy Technology Data Exchange (ETDEWEB)

    Rojas-Chavez, H., E-mail: hrojasc@ipn.mx [Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada - IPN (Mexico); Reyes-Carmona, F. [Facultad de Quimica - UNAM (Mexico); Achimovicova, M. [Slovak Academy of Sciences, Institute of Geotechnics (Slovakia); Daneu, N. [Jozef Stefan Institute, Department for Nanostructured Materials (Slovenia); Jaramillo-Vigueras, D. [Centro de Investigacion e Innovacion Tecnologica - IPN (Mexico)

    2012-06-15

    In this study, PbSe nanocubes were obtained by high-energy milling, and their optical properties were investigated by measuring the UV-VIS-IR spectra in the range of 200-2,000 nm. The optical absorption of all samples showed a strong UV emission band at 1.45 eV. Previously, to obtain only PbSe nanocubes, an intermediate phase was identified, PbSeO{sub 3}. Although both PbSeO{sub 3} and PbSe were traced through this study, a major effort is devoted to characterize the latter. To trace how chemical transitions evolve from precursors to PbSe, X-ray diffraction and Rietveld refinement were carried out. Therefore, the following parameters were evaluated as a function of milling time: phase percentages, area-to-volume ratio, average crystallite dimensions, specific surface area, and morphology changes. To corroborate previous findings, nitrogen adsorption and transmission electron microscopy techniques were used. All the set experimental results unambiguously confirm that crystallites show a cubic morphology, with its average crystallite size distribution being around 24 nm.

  10. Cellulose Nanocrystals Obtained from Rice By-Products and Their Binding Potential to Metallic Ions

    Directory of Open Access Journals (Sweden)

    Vanessa L. Albernaz

    2015-01-01

    Full Text Available The present study aimed to develop and optimize a method to obtain cellulose nanocrystals from the agricultural by-products rice husk and straw and to evaluate their electrostructural modifications in the presence of metallic ions. First, different particle formation conditions and routes were tested and analyzed by spectrophotometry, dynamic light scattering (DLS, and Zeta potential measurements. Then, electrostructural effects of ions Na(I, Cd(II, and Al(III on the optimized nanoparticles were analyzed by atomic force microscopy (AFM, scanning electron microscopy (SEM, and electrical conductivity (EC assessments. The produced cellulose nanocrystals adopted a rod-like shape. AFM height distribution and EC data indicated that the nanocrystals have more affinity in binding with Na(I > Al(III > Cd(II. These data suggest that the use of these cellulose nanocrystals in the bioremediation field is promising, both in metal sorption from wastewater and as an alternative for water desalination.

  11. The technique of obtaining single-energy γ-rays in calibrating energy response of detector

    International Nuclear Information System (INIS)

    Li Rurong; Peng Taiping; Hu Mengchun; Li Zhongbao

    2004-01-01

    This paper introduces the principle of transforming γ-rays from 60 Co into a series of single-energy γ-rays and stresses the technique of shielding radiation-interfere and reducing energy-dispersion. The Single-energy γ-rays of any energy in the range of 0.36-1.02 MeV may be obtained by means of this technique. (authors)

  12. Development of Methods for Obtaining Position Image and Chemical Binding Information from Flow Experiments of Porous Media

    Energy Technology Data Exchange (ETDEWEB)

    Haugan, Are

    1998-12-01

    Existing oil reservoirs might be more fully exploited if the properties of the flow of oil and water in porous media were better known. In laboratory experiments it is important to collect as much information as possible to make a descriptive model of the system, including position imaging and chemical binding information. This thesis develops nuclear methods for obtaining position image and chemical binding information from flow experiments of porous media. A combined positron emission tomography and single photon emission computed tomography system to obtain position images, and a time-differential perturbed angular correlation system to obtain chemical binding information, have been built and thoroughly tested. 68 refs., 123 figs., 14 tabs.

  13. 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.

  14. 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.

  15. 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

  16. 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).

  17. Subtleties in obtaining the electrostatic energy of continuous distributions

    International Nuclear Information System (INIS)

    Bezerra, M; Souza, Reinaldo de Melo e; Kort-Kamp, W J M; Farina, C

    2014-01-01

    The mathematical steps that generalize the expression for the electrostatic energy of a set of point charges to the corresponding expression for a continuous charge distribution involve a few subtleties that are not usually discussed in standard introductory or advanced electromagnetic textbooks. In this paper, we point out such subtleties and discuss how to deal with them in cases of volume and surface charge distributions. We also show explicitly that it is not possible to define electrostatic energy for a linear charge distribution, since this energy would be divergent. Finally, we use dimensional analysis to recover our results in a simpler and more elegant form. (paper)

  18. Subtleties in obtaining the electrostatic energy of continuous distributions

    Science.gov (United States)

    Bezerra, M.; Souza, Reinaldo de Melo e.; Kort-Kamp, W. J. M.; Farina, C.

    2014-11-01

    The mathematical steps that generalize the expression for the electrostatic energy of a set of point charges to the corresponding expression for a continuous charge distribution involve a few subtleties that are not usually discussed in standard introductory or advanced electromagnetic textbooks. In this paper, we point out such subtleties and discuss how to deal with them in cases of volume and surface charge distributions. We also show explicitly that it is not possible to define electrostatic energy for a linear charge distribution, since this energy would be divergent. Finally, we use dimensional analysis to recover our results in a simpler and more elegant form.

  19. 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/.

  20. 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.

  1. Novel ZnO-binding peptides obtained by the screening of a phage display peptide library

    Energy Technology Data Exchange (ETDEWEB)

    Golec, Piotr [Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Molecular Biology (affiliated with the University of Gdansk) (Poland); Karczewska-Golec, Joanna [University of Gdansk and Medical University of Gdansk, Laboratory of Molecular Bacteriology, Intercollegiate Faculty of Biotechnology (Poland); Los, Marcin; Wegrzyn, Grzegorz, E-mail: wegrzyn@biotech.univ.gda.pl [University of Gdansk, Department of Molecular Biology (Poland)

    2012-11-15

    Zinc oxide (ZnO) is a semiconductor compound with a potential for wide use in various applications, including biomaterials and biosensors, particularly as nanoparticles (the size range of ZnO nanoparticles is from 2 to 100 nm, with an average of about 35 nm). Here, we report isolation of novel ZnO-binding peptides, by screening of a phage display library. Interestingly, amino acid sequences of the ZnO-binding peptides reported in this paper and those described previously are significantly different. This suggests that there is a high variability in sequences of peptides which can bind particular inorganic molecules, indicating that different approaches may lead to discovery of different peptides of generally the same activity (e.g., binding of ZnO) but having various detailed properties, perhaps crucial under specific conditions of different applications.

  2. 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.

  3. Activation energy for mullitization of gel fibres obtained from ...

    Indian Academy of Sciences (India)

    and aluminum nitrate was optimized to obtain spinnable precursor sol for synthesis of fibres. Thermogravimetry– ... (XRD) analyses were used to characterize properties of the gel and ceramic fibres. The precursor gel completely .... The polymer chains of M–O–M and M–OH–M were present while the condensation ...

  4. Nanocrystalline titanium characteristics obtained through cryogenic and high energy milling

    International Nuclear Information System (INIS)

    Rojas, P; Zuniga, A; Lavernia, E.J

    2008-01-01

    The microstructure and changes in chemical composition of Ti powders produced by cryogenic milling (modified Atritor) and by high energy milling (Spex mill) were investigated. The effect of high energy milling and cryomilling parameters, such as milling time and ball to powder ratio (BPR), on the particle size, grain size, chemistry, and structure of Ti powders were investigated using x-ray diffraction, scanning electron microscopy, and transmission electron microscopy. The experimental results show that Ti powders with a grain size of approximately 20 nm (nanocrystalline) can be produced using the cryomilling technique. The average particle size increased initially with milling time from the original 55 μm to a maximum value of 125 after milling for 2 hours, and then decreased to 44μm after milling for 8 hours. Both the average particle size and the grain size decreased as the BPR increased. The results using Spex mill show that the particle size and grain size both decreased as the milling time increased. The oxygen, nitrogen and iron content of the powders increased with the milling time (au)

  5. 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

  6. 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...

  7. 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…

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  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. 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.

  16. 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.

  17. Binding of alpha-fetoprotein by immobilized monoclonal antibodies during episodes of zero-gravity obtained by parabolic flight

    Science.gov (United States)

    Spooner, Brian S.; Guikema, James A.; Barnes, Grady

    1990-01-01

    Alpha-fetoprotein (AFP), a single-chain polypeptide which is synthesized by the liver and yolk sac of the human fetus, provided a model ligand for assessing the effects of microgravity on ligand binding to surface-immobilized model receptor molecules. Monoclonal antibodies, used as receptors for AFP, were immobilized by covalent attachment to latex microparticles. Zero gravity environment was obtained by parabolic flight aboard NASA 930, a modified KC-135 aircraft. Buring the onset of an episode of zero gravity, ligand and receptor were mixed. Timed incubation (20 s) was terminated by centrifugation, the supernatant removed, and microparticies were assessed for bound AFP by immunochemical methods. The extent of binding was not influenced by microgravity, when compared with 1-G controls, which suggests that aberrant cellular activities observed in microgravity are not the simple expression of altered macromolecular interactions.

  18. 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.

  19. 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.

  20. 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

  1. Receptor binding sites for substance P in surgical specimens obtained from patients with ulcerative colitis and Crohn disease

    Energy Technology Data Exchange (ETDEWEB)

    Mantyh, C.R.; Gates, T.S.; Zimmerman, R.P.; Welton, M.L.; Passaro, E.P. Jr.; Vigna, S.R.; Maggio, J.E.; Kruger, L.; Mantyh, P.W.

    1988-05-01

    Several lines of evidence indicate that tachykinin neuropeptides (substance P (SP), substance K (SK), and neuromedin K (NK)) play a role in regulating the inflammatory and immune responses. To test this hypothesis in a human inflammatory disease, quantitative receptor autoradiography was used to examine possible abnormalities in tachykinin binding sites in surgical specimens from patients with inflammatory bowel disease. In all cases, specimens were processed for quantitative receptor autoradiography by using /sup 125/I-labeled Bolton-Hunter conjugates of NK, SK, and SP. In colon tissue obtained from ulcerative colitis and Crohn disease patients, very high concentrations of SP receptor binding sites are expressed by arterioles and venules located in the submucosa, muscalairs mucosa, external circular muscle, external longitudinal muscle, and serosa, in contrast to control patients. These results demonstrate that receptor binding sites for SP, but not SK or NK, are ectopically expressed in high concentrations by cells involved in mediating inflammatory and immune responses. These data suggest that SP may be involved in the pathophysiology of inflammatory bowel disease and might provide some insight into the interaction between the nervous system and the regulation of inflammation and the immune response in human inflammatory disease.

  2. 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.

  3. 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.

  4. 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.

  5. Energy saving in greenhouses can be obtained by energy balance-controlled screens

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, N. E. (Univ. of Aarhus, Faculty of Agricultural Sciences, Dept. of Horticulture, Aarslev (Denmark)), e-mail: niels.andersson@agrsci.dk

    2011-03-15

    The energy screens in two greenhouses, one clad with double acrylic and one with single glass, were controlled by an energy balance model. The parameters in the model were heat transmission coefficients, air temperature in the greenhouse and outdoors, irradiance and a single constant for the solar energy efficiency. The energy consumption, screen movements and daily light integral were compared with a glass greenhouse in which the energy screens were controlled by irradiance. In the greenhouse with light-controlled screens the set point for opening and closing of the screens was 5 Wm-2. The energy-saving screens controlled by the energy balance model opened later and closed earlier than in the greenhouse with light-controlled screens. When using the energy balance model the energy saving was 14% for the glass greenhouse and 41% for the double acrylic greenhouse compared with the glass greenhouse with light-controlled screens. The air temperature was on average similar in the three greenhouses, but when the screens were controlled by energy balance the daily light integral was approximately 10% lower and the number of hours the screens were closed was prolonged with 35% for the glass-covered greenhouse and 25% for the double acrylic-covered greenhouse compared with the greenhouse with light-controlled screens. Energy peaks in connection with operation of the screens were not reduced. During the experiment Begonia elatior, Dendranthema grandiflora (Chrysanthemum), Hedera helix, Helianthus annuus, Gerbera jamesonii and Kalanchoe blossfeldiana were grown in the greenhouses. There was a trend in prolongation of the production time when the plants were grown in the glass greenhouse with energy balance control of the screens. A lower number of flowers or inflorescences were observed for some of the plant species produced in the greenhouses with energy balance-controlled screens

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

    Science.gov (United States)

    Qi, Chong

    2012-10-01

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

  8. Hypernuclear interactions and the binding energies of and hypernuclei

    Energy Technology Data Exchange (ETDEWEB)

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

    1988-01-01

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

  9. 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

  10. Probabilities and energies to obtain the counting efficiency of electron-capture nuclides, KLMN model

    International Nuclear Information System (INIS)

    Casas Galiano, G.; Grau Malonda, A.

    1994-01-01

    An intelligent computer program has been developed to obtain the mathematical formulae to compute the probabilities and reduced energies of the different atomic rearrangement pathways following electron-capture decay. Creation and annihilation operators for Auger and X processes have been introduced. Taking into account the symmetries associated with each process, 262 different pathways were obtained. This model allows us to obtain the influence of the M-electron-capture in the counting efficiency when the atomic number of the nuclide is high

  11. 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

  12. 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

  13. 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.

  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. 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.

  17. 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.

  18. 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.

  19. Characteristics of Biochar Obtained by Hydrothermal Carbonization of Cellulose for Renewable Energy

    OpenAIRE

    Daegi Kim; Kunio Yoshikawa; Ki Young Park

    2015-01-01

    The effect of hydrothermal carbonization on the properties of cellulose present in lignocellulosic biomass was investigated for converting it into a renewable energy resource with high energy recovery efficiency. The biochar obtained from cellulose subjected to hydrothermal carbonization showed a significant increase in its carbon content and a calorific value. 13C NMR spectroscopy showed that when raw cellulose was subjected to hydrothermal carbonization above 220 °C, the resulting biochar h...

  20. 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...

  1. 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.

  2. Probabilities and energies to obtain the counting efficiency of electron-capture nuclides. KLMN model

    International Nuclear Information System (INIS)

    Galiano, G.; Grau, A.

    1994-01-01

    An intelligent computer program has been developed to obtain the mathematical formulae to compute the probabilities and reduced energies of the different atomic rearrangement pathways following electron-capture decay. Creation and annihilation operators for Auger and X processes have been introduced. Taking into account the symmetries associated with each process, 262 different pathways were obtained. This model allows us to obtain the influence of the M-electro capture in the counting efficiency when the atomic number of the nuclide is high. (Author)

  3. 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

  4. Characterization of Al2O3-Co ceramic composite obtained by high energy mill

    International Nuclear Information System (INIS)

    Souza, J.L.; Assis, R.B. de; Carlos, E.M.; Oliveira, T.P.; Costa, F.A. da

    2014-01-01

    This work aims to characterize the ceramic composite Al 2 O3-Co obtained by high energy grinding. The composites were obtained by milling Al 2 O 3 and Co in a high energy mill at a speed of 400 rpm, in proportions of 5 to 20% Cobalt (Co). Ceramic composites with 5 and 20% cobalt were sintered at 1200 and 1300 ° C, with a 60-minute plateau and a heating rate of 10 ° C / min. The samples were characterized by X-ray diffraction (XRD), thermogravimetry and differential scanning calorimetry (TG / DSC) and scanning electron microscopy (SEM). The results show the significant effect of cobalt percentage and high energy grinding on the final properties of the Al 2 O 3 - Co ceramic composite, presenting satisfactory values for the composite with a 20% cobalt percentage, showing to be a promising material for application in cutting tools

  5. Energy distribution of the particles obtained after irradiation of carbon nanotubes with carbon projectiles

    Energy Technology Data Exchange (ETDEWEB)

    Denton, Cristian D. [Departament de Física Aplicada, Universitat d’Alacant, Apartat 99, E-03690 Alacant (Spain); Moreno-Marín, Juan Carlos; Heredia-Avalos, Santiago [Departament de Física, Enginyeria de Sistemes i Teoria de la Senyal, Universitat d’Alacant, Apartat 99, E-03690 Alacant (Spain)

    2015-06-01

    The idea of using carbon nanotubes (CNTs) as masks against irradiation has recently emerged, because of the region of a given material covered by a CNT can be protected from the effects of irradiation, creating nanowires. In this case, it is interesting to know in detail the number of generated recoils and their energy. In order to obtain these data, we simulate the irradiation of CNTs with carbon ions using a molecular dynamics code. To describe the interaction between carbon ions we use the Brenner potential joined smoothly to the Universal ZBL potential at short distances. We have analyzed the energy distributions of the carbon atoms emerging from the CNT for single projectile irradiation with incident energies from 30 eV to 5 keV. Our results show that the number and the energy of the recoil carbon atoms emerging from the CNT increases with the projectile incident energy. In average, each projectile with incident energy of 1 keV produces ∼3.6 recoils, which have a mean energy of 150 eV, while projectiles with 5 keV produce ∼7 recoils with a mean energy of 400 eV.

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

    Directory of Open Access Journals (Sweden)

    M Olivia Kim

    2015-10-01

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

  7. Correlation between measured energy expenditure and clinically obtained variables in trauma and sepsis patients.

    Science.gov (United States)

    Frankenfield, D C; Omert, L A; Badellino, M M; Wiles, C E; Bagley, S M; Goodarzi, S; Siegel, J H

    1994-01-01

    Indirect calorimetry is the preferred method for determining caloric requirements of patients, but availability of the device is limited by high cost. A study was therefore conducted to determine whether clinically obtainable variables could be used to predict metabolic rate. Patients with severe trauma or sepsis who required mechanical ventilation were measured by an open-circuit indirect calorimeter. Several clinical variables were obtained simultaneously. Measurements were repeated every 12 hours for up to 10 days. Twenty-six trauma and 30 sepsis patients were measured 423 times. Mean resting energy expenditure was 36 +/- 7 kcal/kg (trauma) vs 45 +/- 8 kcal/kg (sepsis) (p types.

  8. On modified finite difference method to obtain the electron energy distribution functions in Langmuir probes

    Science.gov (United States)

    Kang, Hyun-Ju; Choi, Hyeok; Kim, Jae-Hyun; Lee, Se-Hun; Yoo, Tae-Ho; Chung, Chin-Wook

    2016-06-01

    A modified central difference method (MCDM) is proposed to obtain the electron energy distribution functions (EEDFs) in single Langmuir probes. Numerical calculation of the EEDF with MCDM is simple and has less noise. This method provides the second derivatives at a given point as the weighted average of second order central difference derivatives calculated at different voltage intervals, weighting each by the square of the interval. In this paper, the EEDFs obtained from MCDM are compared to those calculated via the averaged central difference method. It is found that MCDM effectively suppresses the noises in the EEDF, while the same number of points are used to calculate of the second derivative.

  9. On modified finite difference method to obtain the electron energy distribution functions in Langmuir probes

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Hyun-Ju; Chung, Chin-Wook, E-mail: joykang@hanyang.ac.kr [Department of Electrical Engineering, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 133-791 (Korea, Republic of); Choi, Hyeok; Kim, Jae-Hyun; Lee, Se-Hun; Yoo, Tae-Ho [Seoul Science High School, 63, Hyehwa-ro, Jongno-gu, Seoul 110-530 (Korea, Republic of)

    2016-06-15

    A modified central difference method (MCDM) is proposed to obtain the electron energy distribution functions (EEDFs) in single Langmuir probes. Numerical calculation of the EEDF with MCDM is simple and has less noise. This method provides the second derivatives at a given point as the weighted average of second order central difference derivatives calculated at different voltage intervals, weighting each by the square of the interval. In this paper, the EEDFs obtained from MCDM are compared to those calculated via the averaged central difference method. It is found that MCDM effectively suppresses the noises in the EEDF, while the same number of points are used to calculate of the second derivative.

  10. 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...

  11. Masses and proton separation energies obtained from Qa and Qp measurements

    International Nuclear Information System (INIS)

    Davids, C. N.; Woods, P. J.; Batchelder, J. C.; Bingham, C. R.; Blumenthal, D. J.; Brown, L. T.; Carpenter, L. F.; Henderson, D. J.; Janssens, R. V. F.; Penttila, H. T.; Seweryniak, D.

    2000-01-01

    For many nuclei beyond the proton drip line in the Z>72, N>82 region, both proton and a emission are energetically allowed. In the case of some proton emitters, there are α-decay chains emanating from both parent and daughter nuclei. This means that if the mass excess of one member of an α-decay chain is known, then the mass excesses for all members of both chains can be obtained. In addition, proton separation energies may be derived for nuclei in the α-decay chain of the proton emitter. The method of time- and space-correlations also allows the identification of isomeric states in these nuclei. As an example, a large number of mass excesses and proton separation energies for ground and metastable states have been derived from Q a and Q p values obtained from the proton emitters 165,166,167 Ir, 171 Au, 177 Tl, and their daughters

  12. Bespoke Bias for Obtaining Free Energy Differences within Variationally Enhanced Sampling.

    Science.gov (United States)

    McCarty, James; Valsson, Omar; Parrinello, Michele

    2016-05-10

    Obtaining efficient sampling of multiple metastable states through molecular dynamics and hence determining free energy differences is central for understanding many important phenomena. Here we present a new biasing strategy, which employs the recent variationally enhanced sampling approach (Valsson and Parrinello Phys. Rev. Lett. 2014, 113, 090601). The bias is constructed from an intuitive model of the local free energy surface describing fluctuations around metastable minima and depends on only a few parameters which are determined variationally such that efficient sampling between states is obtained. The bias constructed in this manner largely reduces the need of finding a set of collective variables that completely spans the conformational space of interest, as they only need to be a locally valid descriptor of the system about its local minimum. We introduce the method and demonstrate its power on two representative examples.

  13. Obtaining energy from waste; La obtencion de energia a partir de residuos

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Zayas, J.; Villarrubia Lopez, M.

    2008-07-01

    During the April 2008 Environmental Management seminar, dedicated to how obtaining of energy from waste, supported by Gas Natural, a book La Recuperation energia eco-efficient de los residues. Potential in Spain was presented, and multiple offers were exposed to use in Spain the waste with energetic purposes, especially in Catalonia. One example to take advantage of the waste was a practical case: waste conversion in synthesis gas by plasma. (Author)

  14. An efficient and accurate method to obtain the energy-dependent Green function for general potentials

    International Nuclear Information System (INIS)

    Kramer, T; Heller, E J; Parrott, R E

    2008-01-01

    Time-dependent quantum mechanics provides an intuitive picture of particle propagation in external fields. Semiclassical methods link the classical trajectories of particles with their quantum mechanical propagation. Many analytical results and a variety of numerical methods have been developed to solve the time-dependent Schroedinger equation. The time-dependent methods work for nearly arbitrarily shaped potentials, including sources and sinks via complex-valued potentials. Many quantities are measured at fixed energy, which is seemingly not well suited for a time-dependent formulation. Very few methods exist to obtain the energy-dependent Green function for complicated potentials without resorting to ensemble averages or using certain lead-in arrangements. Here, we demonstrate in detail a time-dependent approach, which can accurately and effectively construct the energy-dependent Green function for very general potentials. The applications of the method are numerous, including chemical, mesoscopic, and atomic physics

  15. 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.

  16. Simulation of motions of the plasma in a fusion reactor for obtaining of future energy

    International Nuclear Information System (INIS)

    Zhumabekov, Askhat

    2017-01-01

    According to the most conservative estimates, by the middle of the XXI century in the world energy consumption will double. This will be a consequence of the global economic development, population growth and other geopolitical and economic factors. Energy consumption in the world is growing much faster than its production and industrial use of new advanced technologies in the energy sector, for objective reasons, will not begin until 2030. This paper discusses how to obtain and develop nuclear energy on the experience of the National Nuclear Center. Implemented model for the problem of plasma confinement, and also presents the main achievements of modern construction and Megaproject National Nuclear Center in Kurchatov, the Republic of Kazakhstan. Spend a social survey in the East Kazakhstan region on the theme: “Prospects for the development of nuclear energy in Kazakhstan” and the citizens’ opinion. Narration new priorities for May 22, 2015 in Ust-Kamenogorsk in the industrial park “Altai” based on the competition of innovation projects green technology in the international exhibition “OSKEMEN EXPO – 2015”, with the participation of the regional authorities of the Republic of Kazakhstan, representatives of JSC NC “Astana Expo” and delegations from Japan, Russia, Canada, USA, South Korea. (paper)

  17. Simulation of motions of the plasma in a fusion reactor for obtaining of future energy

    Science.gov (United States)

    Zhumabekov, Askhat

    2017-01-01

    According to the most conservative estimates, by the middle of the XXI century in the world energy consumption will double. This will be a consequence of the global economic development, population growth and other geopolitical and economic factors. Energy consumption in the world is growing much faster than its production and industrial use of new advanced technologies in the energy sector, for objective reasons, will not begin until 2030. This paper discusses how to obtain and develop nuclear energy on the experience of the National Nuclear Center. Implemented model for the problem of plasma confinement, and also presents the main achievements of modern construction and Megaproject National Nuclear Center in Kurchatov, the Republic of Kazakhstan. Spend a social survey in the East Kazakhstan region on the theme: “Prospects for the development of nuclear energy in Kazakhstan” and the citizens’ opinion. Narration new priorities for May 22, 2015 in Ust-Kamenogorsk in the industrial park “Altai” based on the competition of innovation projects green technology in the international exhibition “OSKEMEN EXPO - 2015”, with the participation of the regional authorities of the Republic of Kazakhstan, representatives of JSC NC “Astana Expo” and delegations from Japan, Russia, Canada, USA, South Korea.

  18. 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

  19. 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.

  20. 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.

  1. 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 ...

  2. 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 ...

  3. 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.

  4. Report of test and research results on atomic energy obtained in national institutes in fiscal 1985

    International Nuclear Information System (INIS)

    1986-01-01

    As for the test and research on the utilization of atomic energy in national institutes, the budget was appropriated for the first time in fiscal year 1956, and since then, the many valuable results of research have been obtained so far in the diversified fields of nuclear fusion, safety research, the irradiation of foods, medicine and others, thus the test and research accomplished the large role for promoting the utilization of atomic energy in Japan. In this report, the gists of the results of the test and research on the utilization of atomic energy carried out by national institutes in fiscal year 1985 are collected. No.1 of this report was published in 1960, and this is No.26. It is desired to increase the understanding about the recent trend and the results of the test and research on atomic energy utilization with this book. The researches on nuclear fusion, engineering safety and environmental radioactivity safety, the irradiation of foods, the countermeasures against cancer, fertilized soil, the quality improvement of brewing and farm products, the protection of farm products and the improvement of breeding, diagnosis and medical treatment, pharmaceuticals, environmental hygiene, the application to physiology and pathology, radiochemistry, radiation measurement, process analysis, nuclear reactor materials, nuclear powered ships, civil engineering, radioactivation analysis and injury prevention are reported. (Kako, I.)

  5. 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.

  6. Binding ability of a HHP-tagged protein towards Ni{sup 2+} studied by paramagnetic NMR relaxation: The possibility of obtaining long-range structure information

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, Malene Ringkjo bing [University of Copenhagen, H.C. Orsted Institute, Department of Chemistry (Denmark); Lauritzen, Conni; Dahl, Soren Weis; Pedersen, John [Unizyme Laboratories A/S (Denmark); Led, Jens J. [University of Copenhagen, H.C. Orsted Institute, Department of Chemistry (Denmark)

    2004-06-15

    The binding ability of a protein with a metal binding tag towards Ni{sup 2+} was investigated by longitudinal paramagnetic NMR relaxation, and the possibility of obtaining long-range structure information from the paramagnetic relaxation was explored. A protein with a well-defined solution structure (Escherichia coli thioredoxin) was used as the model system, and the peptide His-His-Pro (HHP) fused to the N-terminus of the protein was used as the metal binding tag. It was found that the tag forms a stable dimer complex with the paramagnetic Ni{sup 2+} ion, where each metal ion binds two HHP-tagged protein molecules. However, it was also found that additional sites in the protein compete with the HHP-tag for the binding of the metal ion. These binding sites were identified as the side chain carboxylate groups of the aspartic and glutamic acid residues. Yet, the carboxylate groups bind the Ni{sup 2+} ions considerably weaker than the HHP-tag, and only protons spatially close to the carboxylate sites are affected by the Ni{sup 2+} ions bound to these groups. As for the protons that are unaffected by the carboxylate-bound Nisupb2+bsup> ions, it was found that the long-range distances derived from the paramagnetic relaxation enhancements are in good agreement with the solution structure of thioredoxin. Specifically, the obtained long-range paramagnetic distance constraints revealed that the dimer complex is asymmetric with different orientations of the two protein molecules relative to the Ni{sup 2+} ion. Abbreviations: NOE - nuclear Overhauser enhancement; E. coli - Escherichia coli; Trx - thioredoxin; IMAC - immobilized metal ion affinity chromatography; HT-DPPI - Polyhistidine-tagged dipeptidyl peptidase I; IPTG - isopropyl-1-thio-galactopyranoside; IR - inversion recovery; RMSD - root mean square deviation.

  7. 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-.

  8. 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.

  9. 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.

  10. Polymer binding to carbon nanotubes in aqueous dispersions: residence time on the nanotube surface as obtained by NMR diffusometry.

    Science.gov (United States)

    Frise, Anton E; Pagès, Guilhem; Shtein, Michael; Pri Bar, Ilan; Regev, Oren; Furó, István

    2012-03-08

    The binding of block copolymer Pluronic F-127 in aqueous dispersions of single- (SWCNT) and multiwalled (MWCNT) carbon nanotubes has been studied by pulsed-field-gradient (PFG) (1)H NMR spectroscopy. We show that a major fraction of polymers exist as a free species while a minor fraction is bound to the carbon nanotubes (CNT). The polymers exchange between these two states with residence times on the nanotube surface of 24 ± 5 ms for SWCNT and of 54 ± 11 ms for MWCNT. The CNT concentration in the solution was determined by improved thermal gravimetric analysis (TGA) indicating that the concentration of SWCNT dispersed by F-127 was significantly higher than that for MWCNT. For SWCNT, the area per adsorbed Pluronic F-127 molecule is estimated to be about 40 nm(2).

  11. DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Silvis Remko

    2008-12-01

    Full Text Available Abstract Background A typical step in the analysis of gene expression data is the determination of clusters of genes that exhibit similar expression patterns. Researchers are confronted with the seemingly arbitrary choice between numerous algorithms to perform cluster analysis. Results We developed an exploratory application that benchmarks the results of clustering methods using functional annotations. In addition, a de novo DNA motif discovery algorithm is integrated in our program which identifies overrepresented DNA binding sites in the upstream DNA sequences of genes from the clusters that are indicative of sites of transcriptional control. The performance of our program was evaluated by comparing the original results of a time course experiment with the findings of our application. Conclusion DISCLOSE assists researchers in the prokaryotic research community in systematically evaluating results of the application of a range of clustering algorithms to transcriptome data. Different performance measures allow to quickly and comprehensively determine the best suited clustering approach for a given dataset.

  12. 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.

  13. 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 ...

  14. Scope and limitations of high energy electron scattering in obtaining relevant structural information about atoms and molecules

    International Nuclear Information System (INIS)

    Ketkar, S.N.

    1984-01-01

    During the course of this work experiments were undertaken to measure the scattering cross-sections for high energy electrons scattering from various target systems. The experiments can be broadly classified into two categories, one dealing with rather small systems and the other dealing with large systems (at least in the view of physicists). Although the experimental aspects, in so much as the experimental measurement of the intensities of the scattered electron is concerned, is the same for both the cases the motivation for performing the experiment is totally different. In the first case, simple atomic and molecular target systems, namely He, H 2 and D 2 , are used. For such systems, good theoretical framework is available and critical comparisons of experimental cross sections are made with theoretical predictions. Attention is focussed mainly at small momentum transfer (up to 10A -1 ), and correlation and binding effects are studied. In the second case, somewhat larger molecular systems, namely naphthalene, anthraquinone, anthracene and dichromium tetraacetate are used. For such systems attention is focused at large momentum transfer (from 10 to 25 A -1 ) to obtain structural information about the molecules

  15. Microstructural analysis of sinterized aluminum powder obtained by the high energy milling of beverage cans

    International Nuclear Information System (INIS)

    Souza, Jose Raelson Pereira de; Peres, Mauricio Mhirdaui

    2016-01-01

    The objective is the study of the effect of high energy milling on the sintering of aluminum from beverage cans. The selected aluminum cans were cut and subjected to high energy milling under a common atmosphere (in the air). In milling, three grams of aluminum was used to maintain the ratio of 10/1 between the mass of the beads and the material. The milling time was varied in 1h, 1.5h and 2h, keeping the other variables constant. The particle size distribution was measured by laser granulometry, for further compaction and sintering at a temperature of 600 ° C for 2 h. The samples were characterized by scanning electron microscopy (SEM). The granulometric analysis of the powders found that higher milling times produced finer particles. Powders with granulometry of less than 45 μm were obtained at 1 h, 1.5 h and 2 h times. The times of 1.5h and 2h promoted finer particles with better distribution of size. The SEM analyzes showed little variation in the shape of the particles as a function of the variation of the grinding times, presenting irregularities in the platelet geometry. The sintering time and temperature were effective in the densification of the powder particles, which were influenced by the average particle size

  16. 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

  17. 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.

  18. Optimization of synthesis and peptization steps to obtain iron oxide nanoparticles with high energy dissipation rates

    Energy Technology Data Exchange (ETDEWEB)

    Mérida, Fernando [Deparment of Chemical Engineering, University of Puerto Rico, Mayagüez, P.O. Box 9046, Mayagüez, PR 00680 (United States); Chiu-Lam, Andreina [Department of Chemical Engineering, University of Florida, P.O. Box 116005, Gainesville, FL 32611-6005 (United States); Bohórquez, Ana C. [J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, FL 32611-6131 (United States); Maldonado-Camargo, Lorena [Department of Chemical Engineering, University of Florida, P.O. Box 116005, Gainesville, FL 32611-6005 (United States); Pérez, María-Eglée; Pericchi, Luis [Department of Mathematics, University of Puerto Rico, Río Piedras, P.O. Box 70377, San Juan, PR 00936-8377 (United States); Torres-Lugo, Madeline [Deparment of Chemical Engineering, University of Puerto Rico, Mayagüez, P.O. Box 9046, Mayagüez, PR 00680 (United States); Rinaldi, Carlos, E-mail: carlos.rinaldi@bme.ufl.edu [Department of Chemical Engineering, University of Florida, P.O. Box 116005, Gainesville, FL 32611-6005 (United States); J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, FL 32611-6131 (United States)

    2015-11-15

    Magnetic Fluid Hyperthermia (MFH) uses heat generated by magnetic nanoparticles exposed to alternating magnetic fields to cause a temperature increase in tumors to the hyperthermia range (43–47 °C), inducing apoptotic cancer cell death. As with all cancer nanomedicines, one of the most significant challenges with MFH is achieving high nanoparticle accumulation at the tumor site. This motivates development of synthesis strategies that maximize the rate of energy dissipation of iron oxide magnetic nanoparticles, preferable due to their intrinsic biocompatibility. This has led to development of synthesis strategies that, although attractive from the point of view of chemical elegance, may not be suitable for scale-up to quantities necessary for clinical use. On the other hand, to date the aqueous co-precipitation synthesis, which readily yields gram quantities of nanoparticles, has only been reported to yield sufficiently high specific absorption rates after laborious size selective fractionation. This work focuses on improvements to the aqueous co-precipitation of iron oxide nanoparticles to increase the specific absorption rate (SAR), by optimizing synthesis conditions and the subsequent peptization step. Heating efficiencies up to 1048 W/g{sub Fe} (36.5 kA/m, 341 kHz; ILP=2.3 nH m{sup 2} kg{sup −1}) were obtained, which represent one of the highest values reported for iron oxide particles synthesized by co-precipitation without size-selective fractionation. Furthermore, particles reached SAR values of up to 719 W/g{sub Fe} (36.5 kA/m, 341 kHz; ILP=1.6 nH m{sup 2} kg{sup −1}) when in a solid matrix, demonstrating they were capable of significant rates of energy dissipation even when restricted from physical rotation. Reduction in energy dissipation rate due to immobilization has been identified as an obstacle to clinical translation of MFH. Hence, particles obtained with the conditions reported here have great potential for application in nanoscale thermal

  19. 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

  20. 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.

  1. On the possibility of obtaining high-energy polarized electrons on Yerevan synchrotron

    International Nuclear Information System (INIS)

    Melikyan, R.A.

    1975-01-01

    A possibility of producing high-energy polarized electrons on the Yerevan synchrotron is discussed. A review of a number of low-energy polarized electron sources and of some of experiments with high-energy polarized electrons is given

  2. The use of wet-laid techniques to obtain flax nonwovens with different thermoplastic binding fibers for technical insulation applications

    OpenAIRE

    Fages, E.; Cano, M. A.; Gironés, S.; Boronat Vitoria, Teodomiro; Fenollar Gimeno, Octavio Ángel; Balart Gimeno, Rafael Antonio

    2013-01-01

    In this work, the wet-laid technique has been used to obtain flax nonwovens thermally bonded with different contents of polyvinyl alcohol (PVA) and bicomponent polyamide 6/copolyamide (PA6/CoPA) fibers in the 10-30 wt.% range. Scanning electron microscopy has been used to evaluate the formation of interlock points through melted polymer and flax fibers. Volume porosity has been estimated through determination of thickness and surface mass. Tensile strength and elongation at break have been de...

  3. 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.

  4. 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....

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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...

  11. Experimentally obtainable energy from mixing river water, seawater or brines with reverse electrodialysis

    NARCIS (Netherlands)

    Daniilidis, Alexander; Vermaas, David; Herber, Rien; Nijmeijer, Dorothea C.

    2014-01-01

    Energy is released when feed waters with different salinity mix. This energy can be captured in reverse electrodialysis (RED). This paper examines experimentally the effect of varying feed water concentrations on a RED system in terms of permselectivity of the membrane, energy efficiency, power

  12. Experimentally obtainable energy from mixing river water, seawater or brines with reverse electrodialysis

    NARCIS (Netherlands)

    Daniilidis, Alexandros; Vermaas, David A.; Herber, Rien; Nijmeijer, Kitty

    Energy is released when feed waters with different salinity mix. This energy can be captured in reverse electrodialysis (RED). This paper examines experimentally the effect of varying feed water concentrations on a RED system in terms of permselectivity of the membrane, energy efficiency, power

  13. 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.

  14. 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

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

    Science.gov (United States)

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

    2011-11-24

    The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given. © 2011 American Chemical Society

  16. 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 ...

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. Symmetric energy-momentum tensor in Maxwell, Yang-Mills, and Proca theories obtained using only Noether's theorem

    International Nuclear Information System (INIS)

    Montesinos, M.; Flores, E.

    2006-01-01

    The symmetric and gauge-invariant energy-momentum tensors for source-free Maxwell and Yang-Mills theories are obtained by means of translations in spacetime via a systematic implementation of Noether's theorem. For the source-free neutral Proca field, the same procedure yields also the symmetric energy-momentum tensor. In all cases, the key point to get the right expressions for the energy-momentum tensors is the appropriate handling of their equations of motion and the Bianchi identities. It must be stressed that these results are obtained without using Belinfante's symmetrization techniques which are usually employed to this end. (Author)

  4. Panorama 2010: Which biomass resources should be used to obtain a sustainable energy system?

    International Nuclear Information System (INIS)

    Lorne, D.

    2010-01-01

    Biomass is the leading renewable energy in the world today. Moreover, the introduction of biomass into energy systems presents certain advantages as far as reducing greenhouse gas emissions is concerned. However, its mobilization still presents many challenges relative to the competition between uses and the management of local natural resources (e.g. water, soil and biodiversity). Therefore, the technologies involved should be structured so that this resource can be developed to be truly sustainable. (author)

  5. 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.

  6. 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.

  7. 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.

  8. Nuclear mass formula with the shell energies obtained by a new method

    International Nuclear Information System (INIS)

    Koura, H.; Tachibana, T.; Yamada, M.; Uno, M.

    1998-01-01

    Nuclear shapes and masses are estimated by a new method. The main feature of this method lies in estimating shell energies of deformed nuclei from spherical shell energies by mixing them with appropriate weights. The spherical shell energies are calculated from single-particle potentials, and, till now, two mass formulas have been constructed from two different sets of potential parameters. The standard deviation of the calculated masses from all the experimental masses of the 1995 Mass Evaluation is about 760 keV. Contrary to the mass formula by Tachibana, Uno, Yamada and Yamada in the 1987-1988 Atomic Mass Predictions, the present formulas can give nuclear shapes and predict on super-heavy elements

  9. 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.

  10. Report of test and research results on atomic energy obtained in national institutes in fiscal 1984

    International Nuclear Information System (INIS)

    1985-01-01

    The test and research regarding the utilization of atomic energy carried out in national institutions have produced many valuable results in diverse fields so far, such as nuclear fusion, safety research, food irradiation and medicine, since the budget had been appropriated for the first time in 1956. It has accomplished large role in the promotion of atomic energy utilization in Japan. This report is Volume 25, in which the results of the test and research on atomic energy utilization carried out by national institutions in fiscal year 1984 are summarized. It is hoped that the understanding about the recent trend and the results of the test and research on atomic energy utilization is further promoted by this report. The contents of this report are nuclear fusion; the research on engineering safety and environmental radioactivity safety; food irradiation; the countermeasures against cancer; fertilized soil, the improvement of quality, the protection of plants and the improvement of breeding in agriculture and fishery fields; diagnosis and medical treatment, pharmaceuticals, environmental hygiene and the application to physiology and pathology in medical field; radiation chemistry and radiation measurement in mining and industry fields; nuclear reactor materials and nuclear-powered ships; civil engineering; radioactivation analysis; and the research on the prevention of injuries. (Kako, I.)

  11. Ammonia synthesis over multi-promoted iron catalysts obtained by high-energy ball-milling

    DEFF Research Database (Denmark)

    Jacobsen, C.J.H.; Jiang, Jianzhong; Mørup, Steen

    1999-01-01

    The feasibility of producing ammonia synthesis catalysts from high-energy ball-milling of a simple mixture of the constituent oxides has been investigated. The effect of ball-milling the fused oxidic precursor of the industrial KM1 ammonia synthesis catalyst has also been studied. The results show...

  12. 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.)

  13. Chemical composition and metabolizable energy values of corn germ meal obtained by wet milling for layers

    Directory of Open Access Journals (Sweden)

    CS Albuquerque

    2014-03-01

    Full Text Available An experiment was carried out to determine the chemical composition, metabolizable energy values, and coefficients of nutrient digestibility of corn germ meal for layers. The chemical composition of corn germ meal was determined, and then a metabolism assay was performed to determine its apparent metabolizable energy (AME and apparent metabolizable energy corrected for nitrogen (AMEn values and its dry matter and gross energy apparent metabolizability coefficients (CAMDM and CAMGE, respectively. In the 8-day assay (four days of adaptation and four days of total excreta collection, 60 29-week-old white Lohman LSL layers were used. A completely randomized experimental design, with three treatments with five replicates of four birds each, was applied. Treatments consisted of a reference diet and two test diets, containing 20 or 30% corn germ meal. Results were submitted to analysis of variance and means were compared by the Tukey tests at 5% probability level. The chemical composition of corn germ meal was: 96.39% dry matter, 49.48% ether extract, 1.87% ashes, 7243 kcal gross energy/kg, 11.48% protein, 0.19% methionine, 0.21% cystine, 0.48% lysine, 0.40% threonine, 0.72% arginine, 0.35% isoleucine, 0.83% leucine, 0.57% valine, and 0.37% histidine, on as-fed basis. There were no statistical differences in AME, AMEn, CAMDM, and CAMGE values with the inclusion of 20 and 30% corn germ meal in the diets. On dry matter basis, AME, AMEn, CAMDM, and CAMGE values of corn germ meal were: 4,578 and 4,548 kcal/kg, 4,723 and 4,372 kcal/kg, 64.95 and 61.86%, respectively.

  14. Effect of halo-substituted aromatic salts on counterion binding constants obtained from cationic nanoparticle catalyzed reactions of piperidine and phenyl salicylate

    Science.gov (United States)

    Fagge, Ibrahim I.; Yusof, Nor Saadah M.; Zain, Sharifuddin Md; Khan, M. Niyaz

    2017-12-01

    Halo-substitutions at 3-position of benzene ring of the salts of aromatic carboxylate, MX, revealed the effect of two different halide ions (Br- and Cl-) on the counterion binding constants obtained from cationic nanoparticle catalyzed piperidinolysis of ionized phenyl salicylate (PhS-). The values of observed rate constant, kobs, determined at a constant total concentration of cetyltrimethylammonium bromide, [CTABr]T, piperidine, ([P]T), [PhS-]T, NaOH, and various concentration of MX (MX = 3-BrC6H4CO2Na and 3-ClC6H4CO2Na), were determined using UV-visible X spectrophotometric technique at 35 °C and 370 nm. The average value of nanoparticle binding constant, KXBr, for X- = 3-BrC6H4CO2- (RXBr = 57) was found to be about 2-fold larger than that for X- = 3-ClC6H4CO2- (RXBr = 30). These XX values were dependent of substituents 3-Br and 3-Cl, and independent of [CTABr]T. Both are related to the presence of different extent of viscoelastic worm-like nanoparticles formation in the [CTABr]T of 6 and 10 mM.

  15. 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.

  16. 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

  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. Report of test and research results on atomic energy obtained in national institutes in fiscal 1982

    International Nuclear Information System (INIS)

    1983-01-01

    As for the test and research on the utilization of atomic energy by national organizations, the budget was appropriated for the first time in fiscal year 1956. Since then, many valuable results of research have been produced in the diverse fields of nuclear fusion, safety research, food irradiation, medicine and others, in this way, the test and research have played large roles in the promotion of the utilization of atomic energy in Japan. This is the 23rd report, in which the results of the test and research on the utilization of atomic energy carried out in fiscal year 1982 by national organizations are summarized. 5 researches on nuclear fusion, 12 researches on engineering safety, 5 researches on environmental radioactivity safety, 3 researches on food irradiation, 5 researches on the countermeasures to cancer, 8 researches on soil fertilization, 4 researches on quality improvement, 7 researches on crop protection, 5 researches on the improvement of breeding, 8 researches on diagnosis and treatment, 8 researches on pharmaceuticals, 10 researches on the application to pathology, 6 researches on mining and industry, 6 researches on power reactors and nuclear ships, 1 research on underground water, 6 researches on activation analysis and 3 researches on injury prevention are reported. (Kako, I.)

  19. 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.

  20. 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.

  1. High-energy radiation processing, a smart approach to obtain PVP-graft-AA nanogels

    International Nuclear Information System (INIS)

    Grimaldi, N.; Sabatino, M.A.; Przybytniak, G.; Kaluska, I.; Bondì, M.L.; Bulone, D.; Alessi, S.; Spadaro, G.; Dispenza, C.

    2014-01-01

    Poly(N-vinylpyrrolidone)-grafted-acrylic acid biocompatible nanogels (NGs) were prepared using an exiting industrial-type electron accelerator and setups, starting from semi-dilute aqueous solutions of a commercial PVP and the acrylic acid monomer. As a result, NGs with tunable size and structure can be obtained quantitatively. Sterility was also imparted at the integrated dose absorbed. The chemical structure of the NGs produced was confirmed through Fourier Transformer Infrared Spectroscopy (FT-IR). The molecular and physico-chemical properties of NGs, such as the hydrodynamic dimensions and surface charge densities, for various polymer and monomer concentrations in the irradiated solutions, are discussed here. - Highlights: • Aqueous solutions of PVP and AA were irradiated by industrial electron accelerator. • NGs with different physico-chemical and molecular properties can be obtained. • Carboxyl-functionalized NGs produced are promising building blocks for bio-devices

  2. Research on the Distant Hybrids of Wheat Obtained via Low-Energy Ion-Beam Implantation

    Science.gov (United States)

    Chang, Shouwei; Cheng, Yuhong; Qin, Guangyong; Su, Mingjie

    2003-06-01

    The whole DNA of soybean was implanted into four varieties of wheat of Zhongyu 5, Huaiyin 9628, Wenyou 1, Jimai 5 respectively via ion-beam mediation. There were 5 plants obtained whose protein content was higher than 18.5%, the highest one was 21.44%. There were 3 plants obtained whose protein content was lower than 11.5%, the lowest one was 10.96%. We can see that the whole DNA of soybean transformed into wheat via ion beam implantation can induce the increase in wheat protein content dramatically. The result also shows that the transformation efficiency of different gene types of wheat receptor varies greatly that the implanting time has a certain effect on the efficiency of transformation.

  3. Delta self-consistent field method to obtain potential energy surfaces of excited molecules on surfaces

    DEFF Research Database (Denmark)

    Gavnholt, Jeppe; Olsen, Thomas; Engelund, Mads

    2008-01-01

    is a density-functional method closely resembling standard density-functional theory (DFT), the only difference being that in Delta SCF one or more electrons are placed in higher lying Kohn-Sham orbitals instead of placing all electrons in the lowest possible orbitals as one does when calculating the ground......-photoemission spectroscopy measurements. This comparison shows that the modified Delta SCF method gives results in close agreement with experiment, significantly closer than the comparable methods. For N2 adsorbed on ruthenium (0001) we map out a two-dimensional part of the potential energy surfaces in the ground state...

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

    Science.gov (United States)

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

    2016-01-01

    While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye-Hückel potentials that mimic long-range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX-pKID is largely assisted by electrostatic interactions, which provide direct charge-charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA-binding protein FIS, electrostatics causes frustration in the DNA-binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long-range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes. © 2015 The Protein Society.

  5. Obtaining a radiation beam poly energy using the code Penelope 2006

    International Nuclear Information System (INIS)

    Andrade, Lucio das Chagas; Peixoto, Jose Guilherme Pereira

    2013-01-01

    Obtaining a spectrum X-ray is not a very easy task, one of the techniques used is the simulation by Monte Carlo method. The Penelope code is a code based on this method that simulates the transport of particles such as electrons, positrons and photons in different media and materials. The versions of this program in 2003 and 2006 show significant differences for facilitating the use of the code. The program allows the construction of the desired geometry and definitions of simulation parameters. (author)

  6. Evaluating Solar Resource Data Obtained from Multiple Radiometers Deployed at the National Renewable Energy Laboratory: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Habte, A.; Sengupta, M.; Andreas, A.; Wilcox, S.; Stoffel, T.

    2014-09-01

    Solar radiation resource measurements from radiometers are used to predict and evaluate the performance of photovoltaic and concentrating solar power systems, validate satellite-based models for estimating solar resources, and advance research in solar forecasting and climate change. This study analyzes the performance of various commercially available radiometers used for measuring global horizontal irradiances (GHI) and direct normal irradiances (DNI). These include pyranometers, pyrheliometers, rotating shadowband irradiometers, and a pyranometer with a shading ring deployed at the National Renewable Energy Laboratory's Solar Radiation Research Laboratory (SRRL). The radiometers in this study were deployed for one year (from April 1, 2011, through March 31, 2012) and compared to measurements from radiometers with the lowest values of estimated measurement uncertainties for producing reference GHI and DNI.

  7. Power-generating process of obtaining gas-energy carrier and reducer from coal

    International Nuclear Information System (INIS)

    Tleugabulov, S.; Duncheva, E.; Zubkevich, M.

    1999-01-01

    The manufacture of power-generating gas has the important economic value for Kazakhstan having large territory, raw and fuel resources especially power coal and clean coal wastes. The technology of reception of gas-energy carrier and reducer from power coal is developed. The basic product of technological process is heated reducing gas. Reducing potential of the gas is characterized by a volumetric share of components (CO+H 2 )-RC in relation to volume of whole mix of gases received with gasification of coal. The value of parameter RC is regulated by a degree of enrichment of air by oxygen r 0 , and the temperature - by the charge of a parity of endothermic reaction in the chamber of gas regeneration. The dependence of the gas structure and temperature on the degree of enrichment of air by oxygen is shown and the circuit of the gas generator is given. (author)

  8. 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].

  9. 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)

  10. The Development and Calculation of an Energy-saving Plant for Obtaining Water from Atmospheric Air

    Science.gov (United States)

    Uglanov, D. A.; Zheleznyak, K. E.; Chertykovsev, P. A.

    2018-01-01

    The article shows the calculation of characteristics of energy-efficient water generator from atmospheric air. This installation or the atmospheric water generator is the unique mechanism which produces safe drinking water by extraction it from air. The existing atmospheric generators allow to receive safe drinking water by means of process of condensation at air humidity at least equal to 35% and are capable to give to 25 liters of water in per day, and work from electricity. Authors offer to use instead of the condenser in the scheme of installation for increase volume of produced water by generator in per day, the following refrigerating machines: the vapor compression refrigerating machines (VCRM), the thermoelectric refrigerating machines (TRM) and the Stirling-cycle refrigerating machines (SRM). The paper describes calculation methods for each of refrigerating systems. Calculation of technical-and-economic indexes for the atmospheric water generator was carried out and the optimum system with the maximum volume of received water in per day was picked up. The atmospheric water generator which is considered in article will work from autonomous solar power station.

  11. Clostridium beijerinckii mutant with high inhibitor tolerance obtained by low-energy ion implantation.

    Science.gov (United States)

    Guo, Ting; Tang, Yan; Zhang, Qiu-Yan; Du, Teng-Fei; Liang, Da-Feng; Jiang, Min; Ouyang, Ping-Kai

    2012-03-01

    Clostridium beijerinckii mutant strain IB4, which has a high level of inhibitor tolerance, was screened by low-energy ion implantation and used for butanol fermentation from a non-detoxified hemicellulosic hydrolysate of corn fiber treated with dilute sulfuric acid (SAHHC). Evaluation of toxicity showed C. beijerinckii IB4 had a higher level of tolerance than parent strain C. beijerinckii NCIMB 8052 for five out of six phenolic compounds tested (the exception was vanillin). Using glucose as carbon source, C. beijerinckii IB4 produced 9.1 g l(-1) of butanol with an acetone/butanol/ethanol (ABE) yield of 0.41 g g(-1). When non-detoxified SAHHC was used as carbon source, C. beijerinckii NCIMB 8052 grew well but ABE production was inhibited. By contrast, C. beijerinckii IB4 produced 9.5 g l(-1) of ABE with a yield of 0.34 g g(-1), including 2.2 g l(-1) acetone, 6.8 g l(-1) butanol, and 0.5 g l(-1) ethanol. The remarkable fermentation and inhibitor tolerance of C. beijerinckii IB4 appears promising for ABE production from lignocellulosic materials.

  12. Experience relevant to safety obtained from reactor decommissioning operations in the French Atomic Energy Commission

    International Nuclear Information System (INIS)

    Giraudel, B.; Langlois, G.

    1979-01-01

    From among the nuclear facilities constructed in France the authors cite eight large reactors, ranging from critical assemblies to power reactors, that have been finally shut-down since 1965. A brief account is given of the way in which the various operations were carried out after the final control rod drop, a distinction being drawn between the shut-down proper and the containment and dismantling work. A description is also given, from the technical and regulatory standpoint, of the final stage attained, and mention is made of French safety arrangements and of the part played by the safety services during decommissioning operations. Among the lessons derived from French experience, the authors mention the completion of operations without any serious safety problems, and with guarantees for the protection of personnel and the population as a whole, by conventional techniques; the advantage of planning decommissioning operations from the very beginning of construction of the facilities; and the importance of filing descriptive documents. In view of the experience gained, the French Atomic Energy Commission has devised internal procedures for facilitating the application of regulations governing the shut-down and decommissioning phases, which are aimed at preserving surveillance procedures similar to those in force during normal operation. (author)

  13. 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.

  14. 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.

  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. Oxide-nitride-oxide dielectric stacks with Si nanoparticles obtained by low-energy ion beam synthesis

    International Nuclear Information System (INIS)

    Ioannou-Sougleridis, V; Dimitrakis, P; Vamvakas, V Em; Normand, P; Bonafos, C; Schamm, S; Mouti, A; Assayag, G Ben; Paillard, V

    2007-01-01

    Formation of a thin band of silicon nanoparticles within silicon nitride films by low-energy (1 keV) silicon ion implantation and subsequent thermal annealing is demonstrated. Electrical characterization of metal-insulator-semiconductor capacitors reveals that oxide/Si-nanoparticles-nitride/oxide dielectric stacks exhibit enhanced charge transfer characteristics between the substrate and the silicon nitride layer compared to dielectric stacks using unimplanted silicon nitride. Attractive results are obtained in terms of write/erase memory characteristics and data retention, indicating the large potential of the low-energy ion-beam-synthesis technique in SONOS memory technology

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

    CERN Document Server

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

    2000-01-01

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

  18. 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.

  19. 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.

  20. Improved free-energy interpolation scheme for obtaining gas-phase reaction rates from ring-polymer molecular dynamics

    Science.gov (United States)

    Stecher, Thomas; Althorpe, Stuart C.

    2012-05-01

    Quantum reaction rates for bimolecular gas-phase reactions can be computed efficiently and to a realistic degree of approximation by applying ring-polymer molecular dynamics within a free-energy interpolation scheme [R. Collepardo-Guevara, Y.V. Suleimanov, and D.E. Manolopoulos, J. Chem. Phys. 130, 174713 (2009)]. Here, we present modifications to this scheme which simplify the implementation of the method, and have the advantage of yielding directly the free-energy as a function of the interpolation coordinate. We also take the opportunity to verify the benchmark results obtained for the H + H2 and Cl + HCl reactions by Collepardo-Guevara et al., obtaining excellent agreement for H + H2 and reasonable agreement for Cl + HCl.

  1. Energy Level of Three-Mode Harmonic Oscillator for Coordinate Operators Satisfying Cyclic Commutative Relations Obtained by IEO Method

    Science.gov (United States)

    Wu, Hao; Fan, Hong-Yi

    2008-12-01

    Eigenvalue-solution to those Hamiltonians involving non-commutative coordinates is not easily obtained. In this paper we apply the invariant eigen-operator (IEO) method to solving the energy spectrum of the three-mode harmonic oscillator in non-commutative space with the coordinate operators satisfying cyclic commutative relations, [X1,X2] = [X2,X3] = [X3,X1] = iθ, and this method seems effective and concise.

  2. Comparison of electron-ion energy transfer in dense plasmas obtained from numerical simulations and quantum kinetic theory

    Science.gov (United States)

    Vorberger, J.; Gericke, D. O.

    2014-03-01

    We evaluate various analytical models for the electron-ion energy transfer and compare the results to data from molecular dynamics (MD) simulations. The models tested include energy transfer via strong binary collisions, Landau-Spitzer rates with different choices for the cut-off parameters in the Coulomb logarithm, rates based on Fermi's golden rule (FGR) and theories taking coupled collective modes (CM) into account. In search of a model easy to apply, we first analyze different approximations of the FGR energy transfer rate. Then, we investigate several numerical studies using MD simulations and try to uncover CM effects in the data obtained. Most MD data published so far, except one study by Murillo et al. [23], show no distinct CM effects and, thus, can be interpreted within a FGR or binary collision approach. We show that this finding is related to the parameter regime, in particular the initial temperature difference, considered in these investigations.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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)

  9. 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

  10. Comparative energy content and amino acid digestibility of barley obtained from diverse sources fed to growing pigs

    Directory of Open Access Journals (Sweden)

    Hong Liang Wang

    2017-07-01

    Full Text Available Objective Two experiments were conducted to determine the content of digestible energy (DE and metabolizable energy (ME as well as the apparent ileal digestibility (AID and standardized ileal digestibility (SID of crude protein (CP and amino acids (AA in barley grains obtained from Australia, France or Canada. Methods In Exp. 1, 18 growing barrows (Duroc×Landrace×Yorkshire; 31.5±3.2 kg were individually placed in stainless-steel metabolism crates (1.4×0.7×0.6 m and randomly allotted to 1 of 3 test diets. In Exp. 2, eight crossbred pigs (30.9±1.8 kg were allotted to a replicate 3×4 Youden Square designed experiment with three periods and four diets. Two pigs received each diet during each test period. The diets included one nitrogen-free diet and three test diets. Results The relative amounts of gross energy (GE, CP, and all AA in the Canadian barley were higher than those in Australian and French barley while higher concentrations of neutral detergent fiber, acid detergent fiber, total dietary fiber, insoluble dietary fiber and β-glucan as well as lower concentrations of GE and ether extract were observed in the French barley compared with the other two barley sources. The DE and ME as well as the SID of histidine, isoleucine, leucine and phenylalanine in Canadian barley were higher (p<0.05 than those in French barley but did not differ from Australian barley. Conclusion Differences in the chemical composition, energy content and the SID and AID of AA were observed among barley sources obtained from three countries. The feeding value of barley from Canada and Australia was superior to barley obtained from France which is important information in developing feeding systems for growing pigs where imported grains are used.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. Exact and Effective Pair-Wise Potential for Protein-Ligand Interactions Obtained from a Semiempirical Energy Partition

    Directory of Open Access Journals (Sweden)

    André Melo

    2008-09-01

    Full Text Available In this work, the partition method introduced by Carvalho and Melo was used to study the complex between Cucurbita maxima trypsin inhibitor (CMTI-I and glycerol at the AM1 level. An effective potential, combining non-bonding and polarization plus charge transfer (PLCT terms, was introduced to evaluate the magnitude of the interaction between each amino acid and the ligand. In this case study, the nonbonding–PLCT noncompensation characterizes the stabilization energy of the association process in study. The main residues (Gly29, Cys3 and Arg5 with net attractive effects and Arg1 (with a net repulsive effect, responsible by the stability of protein-ligand complex, are associated with large nonbonding energies non-compensated by PLCT effects. The results obtained enable us to conclude that the present decomposition scheme can be used for understanding the cohesive phenomena in proteins.

  17. 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.

  18. 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.

  19. 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

  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. 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.

  2. Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites

    KAUST Repository

    Beke-Somfai, Tamás

    2010-01-26

    Despite exhaustive chemical and crystal structure studies, the mechanistic details of how FoF1-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent highresolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO3 - ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in βTP and, thus, promote ATP. © 2009 American Chemical Society.

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

    Science.gov (United States)

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

    2017-06-01

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

  4. 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.

  5. Study of unfolding methods for X-ray spectra obtained with CDTE detectors in the mammography energy range

    Energy Technology Data Exchange (ETDEWEB)

    Querol, A.; Gallardo, S.; Rodenas, J.; Verdu, G.; Barrachina, T. [Departamento de Ingenieria Quimica y Nuclear, Universidad Politecnica de Valencia, Cami de Vera, s/n 46022 Valencia (Spain)

    2010-07-01

    Quality control parameters for an X-ray tube strongly depend on the accurate knowledge of the primary spectrum, but it is difficult to obtain it experimentally by direct measurements. Indirect spectrometry techniques such as Compton scattering can be used in X-ray spectrum assessment avoiding the pile-up effect in detectors. However, an unfolding method is required for this kind of measurements. In previous works, a methodology to assess primary X-ray spectra in the diagnostic energy range by means of the Compton scattering technique has been analysed. This methodology included a Monte Carlo simulation model, using the MCNP5 code, of the actual experimental set-up providing a Pulse Height Distribution (PHD) for a given primary spectrum. It reproduced the interaction of photons and electrons with the Compton spectrometer and with a High Purity Germanium detector. In this work, a CdTe detector is proposed instead of the HP Germanium. CdTe detector does not require a liquid nitrogen cooling system, but its resolution is poor for the same energy range and its efficiency comes down for energies greater than 55 keV being 70% at 90 keV. In despite of these disadvantages, CdTe detector has been considered due to its low cost and easy handling and portability. The model can provide a PHD and a Response Matrix, for different X-ray spectra, taken from the IPEM 78 catalogue. The primary spectrum can be estimated applying the MTSVD (Modified Truncated Singular Value Decomposition) and the Tikhonov unfolding method. Both unfolding methods cause some loss of information on the reconstructed primary spectra. In this paper, a comparison of the ability to obtain primary spectra using both MTSVD and Tikhonov unfolding methods has been done. As well a sensitivity analysis in order to test the proposed unfolding methods when they are applied to PHDs obtained with the MCNP model has been developed. A variation on parameters such as target materials and voltages over the mammography

  6. Comparative energy content and amino acid digestibility of barley obtained from diverse sources fed to growing pigs.

    Science.gov (United States)

    Wang, Hong Liang; Shi, Meng; Xu, Xiao; Ma, Xiao Kang; Liu, Ling; Piao, Xiang Shu

    2017-07-01

    Two experiments were conducted to determine the content of digestible energy (DE) and metabolizable energy (ME) as well as the apparent ileal digestibility (AID) and standardized ileal digestibility (SID) of crude protein (CP) and amino acids (AA) in barley grains obtained from Australia, France or Canada. In Exp. 1, 18 growing barrows (Duroc×Landrace×Yorkshire; 31.5±3.2 kg) were individually placed in stainless-steel metabolism crates (1.4×0.7×0.6 m) and randomly allotted to 1 of 3 test diets. In Exp. 2, eight crossbred pigs (30.9±1.8 kg) were allotted to a replicate 3×4 Youden Square designed experiment with three periods and four diets. Two pigs received each diet during each test period. The diets included one nitrogen-free diet and three test diets. The relative amounts of gross energy (GE), CP, and all AA in the Canadian barley were higher than those in Australian and French barley while higher concentrations of neutral detergent fiber, acid detergent fiber, total dietary fiber, insoluble dietary fiber and β-glucan as well as lower concentrations of GE and ether extract were observed in the French barley compared with the other two barley sources. The DE and ME as well as the SID of histidine, isoleucine, leucine and phenylalanine in Canadian barley were higher (pAustralia was superior to barley obtained from France which is important information in developing feeding systems for growing pigs where imported grains are used.

  7. 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

  8. 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...

  9. 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

  10. 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

  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. Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Djalma Menezes de; Mussel, Wagner da Nova; Duarte, Lucienir Pains; Silva, Gracia Divina de Fatima; Duarte, Helio Anderson; Gomes, Elionai Cassiana de Lima [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Quimica; Guimaraes, Luciana [Universidade Federal de Sao Joao Del-Rei (UFSJ), MG (Brazil). Dept. de Ciencias Naturais; Vieira Filho, Sidney A., E-mail: bibo@ef.ufop.br [Universidade Federal de Ouro Preto (UFOP), MG (Brazil). Dept. de Farmacia

    2012-07-01

    Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer. (author)

  13. Predicting the biological effects of mobile phone radiation absorbed energy linked to the MRI-obtained structure.

    Science.gov (United States)

    Krstić, Dejan; Zigar, Darko; Petković, Dejan; Sokolović, Dušan; Dinđić, Boris; Cvetković, Nenad; Jovanović, Jovica; Dinđić, Nataša

    2013-01-01

    The nature of an electromagnetic field is not the same outside and inside a biological subject. Numerical bioelectromagnetic simulation methods for penetrating electromagnetic fields facilitate the calculation of field components in biological entities. Calculating energy absorbed from known sources, such as mobile phones when placed near the head, is a prerequisite for studying the biological influence of an electromagnetic field. Such research requires approximate anatomical models which are used to calculate the field components and absorbed energy. In order to explore the biological effects in organs and tissues, it is necessary to establish a relationship between an analogous anatomical model and the real structure. We propose a new approach in exploring biological effects through combining two different techniques: 1) numerical electromagnetic simulation, which is used to calculate the field components in a similar anatomical model and 2) Magnetic Resonance Imaging (MRI), which is used to accurately locate sites with increased absorption. By overlapping images obtained by both methods, we can precisely locate the spots with maximum absorption effects. This way, we can detect the site where the most pronounced biological effects are to be expected. This novel approach successfully overcomes the standard limitations of working with analogous anatomical models.

  14. 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

  15. Conjugate heat transfer analysis of an energy conversion device with an updated numerical model obtained through inverse identification

    International Nuclear Information System (INIS)

    Hey, Jonathan; Malloy, Adam C.; Martinez-Botas, Ricardo; Lamperth, Michael

    2015-01-01

    Highlights: • Conjugate heat transfer analysis of an electric machine. • Inverse identification method for estimating the model parameters. • Experimentally determined thermal properties and electromagnetic losses. • Coupling of inverse identification method with a numerical model. • Improved modeling accuracy through introduction of interface material. - Abstract: Energy conversion devices undergo thermal loading during their operation as a result of inefficiencies in the energy conversion process. This will eventually lead to degradation and possible failure of the device if the heat generated is not properly managed. The ability to accurately predict the thermal behavior of such a device during the initial developmental stage is an important requirement. However, accurate predictions of critical temperature is challenging due to the variation of heat transfer parameters from one device to another. The ability to determine the model parameters is key to accurately representing the heat transfer in such a device. This paper presents the use of an inverse identification technique to estimate the model parameters of an energy conversion device designed for vehicular applications. To simulate the imperfect contact and the presence of insulating materials in the permanent magnet electric machine, thin material are introduced at the component interface of the numerical model. The proposed inverse identification method is used to estimate the equivalent thermal conductance of the thin material. In addition, the electromagnetic losses generated in the permanent magnet is also derived indirectly from the temperature measurement using the same method. With the thermal properties and input parameters of the numerical model obtained from the inverse identification method, the critical temperature of the device can be predicted more accurately. The deviation between the maximum measured and predicted winding temperature is less than 2.4%

  16. Validations of CNDOL approximate Hamiltonian as a fast and reliable method to obtain vertical excitation energies in polyatomic systems

    International Nuclear Information System (INIS)

    Montero-Alejo, Ana L.; Gonzalez-Santana, Susana; Montero-Cabrera, Luis A.; Hernandez-Rodriguez, Erix Wiliam; Fuentes-Montero, Maria Elena; Bunge-Molina, Carlos F.; Gonzalez, Augusto

    2008-01-01

    Theoretical prediction of vertical excitation energies and an estimation of charge distributions of polyatomic systems can be calculated, through the configuration interaction of single (CIS) excited determinants procedure, with the CNDOL (Complete Neglect of Differential Overlap considering the l azimuthal quantum number) Hamiltonians. This method does not use adjusted parameters to fit experimental data and only employ a priori data on atomic orbitals and simple formulas to substitute large computations of electronic integrals. In this sense, different functions for bi-electron integrals have been evaluated in order to improve the approximate Hamiltonian. The reliability of predictions and theoretical consistence has been tested with a benchmark set of organic molecules that covers important classes of chromophores including polyenes and other unsaturated aliphatic compounds, aromatic, hydrocarbons, heterocycles, carbonyl compounds, and nucleobases. The calculations are done at identical geometries (MP2) with the same basis set (6-31G) for these medium-sized molecules and the obtained results were statistically compared with other analogous methods and experimental data. The accuracy of prediction of each CNDOL vertical transitions energy increases while the active space is more complete allowing the best variational optimization of CIS matrices i.e. molecular excited states. Moreover and due to the feasible computation procedure for large polyatomic systems, the studies have been extended, as a preliminary work, in the field of optoelectronic materials for photovoltaic applications. Hence, the excitation energies of different conjugated Phenyl-cored Thiophene Dendrimers optimized by DFT (Density Functional Theory) were calculated and show good agreement with the experiment data. The predicted charge distribution during the excitation contributes to understand the photophysics process on these kind materials. (Full text)

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. Improvements in the management of rheumatic patients from vertebral image obtained through dual-energy X-ray absorptiometry

    Directory of Open Access Journals (Sweden)

    D. Gatti

    2011-09-01

    Full Text Available The diagnosis of asymptomatic vertebral fracture is clinically useful and the identification of new fractures may influences the choice of appropriate therapeutic measures. In order to identify moderate and asymptomatic vertebral deformities in an objective and reproducible manner, vertebral morphometry is performed. This method measures the vertebral body’s anterior, middle and posterior heights at the dorsal and lumbar level. Currently this technique is performed on lateral images of the spine obtained through the traditional X-ray method (radiological morphometry or morphometric X-ray radiography, MRX and, more recently from images obtained through dual-energy X-ray absorptiometry (DXA machines (visual assessment of x-ray absoptiometry scans or morphometric X-ray absorptiometry, MXA, commonly used to measure bone mineral density. The main advantage of MXA relative to MRX is the lower radiation dose to which the patient is exposed during the exam. In addition, MXA scans offers the advantage of acquiring a single image of thoracic and lumbar spine, without any distortion (e.g.: coning. The most obvious advantage of MXA is the opportunity of obtaining during the same session a bone mineral density evaluation, and digital images that are easily processable, manageable, recordable and comparable for the patient’s follow up. A limitation of the MXA technique is the inferior quality of the images, that make often impossible the detection of the vertebral edges, and the impossibility to visualize the upper thoracic vertebral bodies. MXA, despite its intrinsic limitations, when carried out by trained personnel may provide substantial improvements in the management (diagnosis and follow-up of rheumatic patients.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. Receptor Binding Sites for Substance P, but not Substance K or Neuromedin K, are Expressed in High Concentrations by Arterioles, Venules, and Lymph Nodules in Surgical Specimens Obtained from Patients with Ulcerative Colitis and Crohn Disease

    Science.gov (United States)

    Mantyh, Christopher R.; Gates, Troy S.; Zimmerman, Robert P.; Welton, Mark L.; Passaro, Edward P.; Vigna, Steven R.; Maggio, John E.; Kruger, Lawrence; Mantyh, Patrick W.

    1988-05-01

    Several lines of evidence indicate that tachykinin neuropeptides [substance P (SP), substance K (SK), and neuromedin K (NK)] play a role in regulating the inflammatory and immune responses. To test this hypothesis in a human inflammatory disease, quantitative receptor autoradiography was used to examine possible abnormalities in tachykinin binding sites in surgical specimens from patients with inflammatory bowel disease. Surgical specimens of colon were obtained from patients with ulcerative colitis (n = 4) and Crohn disease (n = 4). Normal tissue was obtained from uninvolved areas of extensive resections for carcinoma (n = 6). In all cases, specimens were obtained <5 min after removal to minimize influences associated with degradation artifacts and were processed for quantitative receptor autoradiography by using 125I-labeled Bolton--Hunter conjugates of NK, SK, and SP. In the normal colon a low concentration of SP receptor binding sites is expressed by submucosal arterioles and venules and a moderate concentration is expressed by the external circular muscle, whereas SK receptor binding sites are expressed in low concentrations by the external circular and longitudinal muscle. In contrast, specific NK binding sites were not observed in any area of the human colon. In colon tissue obtained from ulcerative colitis and Crohn disease patients, however, very high concentrations of SP receptor binding sites are expressed by arterioles and venules located in the submucosa, muscularis mucosa, external circular muscle, external longitudinal muscle, and serosa. In addition, very high concentrations of SP receptor binding sites are expressed within the germinal center of lymph nodules, whereas the concentrations of SP and SK binding sites expressed by the external muscle layers are not altered significantly. These results demonstrate that receptor binding sites for SP, but not SK or NK, are ectopically expressed in high concentrations (1000-2000 times normal) by cells

  8. Evaluation of Functional Marrow Irradiation Based on Skeletal Marrow Composition Obtained Using Dual-Energy Computed Tomography

    Energy Technology Data Exchange (ETDEWEB)

    Magome, Taiki [Department of Radiological Sciences, Faculty of Health Sciences, Komazawa University, Tokyo (Japan); Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota (United States); Department of Radiology, The University of Tokyo Hospital, Tokyo (Japan); Froelich, Jerry [Department of Radiology, University of Minnesota, Minneapolis, Minnesota (United States); Takahashi, Yutaka [Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota (United States); Department of Radiation Oncology, Osaka University, Osaka (Japan); Arentsen, Luke [Department of Therapeutic Radiology, University of Minnesota, Minneapolis, Minnesota (United States); Holtan, Shernan; Verneris, Michael R. [Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, Minnesota (United States); Brown, Keenan [Mindways Software Inc, Austin, Texas (United States); Haga, Akihiro; Nakagawa, Keiichi [Department of Radiology, The University of Tokyo Hospital, Tokyo (Japan); Holter Chakrabarty, Jennifer L. [College of Medicine, Oklahoma Health Sciences Center, Oklahoma City, Oklahoma (United States); Giebel, Sebastian [Department of Bone Marrow Transplantation, Comprehensive Cancer Center M. Curie-Sklodowska Memorial Institute, Gliwice (Poland); Wong, Jeffrey [Department of Radiation Oncology, Beckman Research Institute, City of Hope, Duarte, California (United States); Dusenbery, Kathryn [Department of Therapeutic Radiology, University of Minnesota, Minneapolis, Minnesota (United States); Storme, Guy [Department of Radiotherapy, Universitair Ziekenhuis Brussel, Brussels (Belgium); Hui, Susanta K., E-mail: shui@coh.org [Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota (United States); Department of Therapeutic Radiology, University of Minnesota, Minneapolis, Minnesota (United States); Department of Radiation Oncology, Beckman Research Institute, City of Hope, Duarte, California (United States)

    2016-11-01

    Purpose: To develop an imaging method to characterize and map marrow composition in the entire skeletal system, and to simulate differential targeted marrow irradiation based on marrow composition. Methods and Materials: Whole-body dual energy computed tomography (DECT) images of cadavers and leukemia patients were acquired, segmented to separate bone marrow components, namely, bone, red marrow (RM), and yellow marrow (YM). DECT-derived marrow fat fraction was validated using histology of lumbar vertebrae obtained from cadavers. The fractions of RM (RMF = RM/total marrow) and YMF were calculated in each skeletal region to assess the correlation of marrow composition with sites and ages. Treatment planning was simulated to target irradiation differentially at a higher dose (18 Gy) to either RM or YM and a lower dose (12 Gy) to the rest of the skeleton. Results: A significant correlation between fat fractions obtained from DECT and cadaver histology samples was observed (r=0.861, P<.0001, Pearson). The RMF decreased in the head, neck, and chest was significantly inversely correlated with age but did not show any significant age-related changes in the abdomen and pelvis regions. Conformity of radiation to targets (RM, YM) was significantly dependent on skeletal sites. The radiation exposure was significantly reduced (P<.05, t test) to organs at risk (OARs) in RM and YM irradiation compared with standard total marrow irradiation (TMI). Conclusions: Whole-body DECT offers a new imaging technique to visualize and measure skeletal-wide marrow composition. The DECT-based treatment planning offers volumetric and site-specific precise radiation dosimetry of RM and YM, which varies with aging. Our proposed method could be used as a functional compartment of TMI for further targeted radiation to specific bone marrow environment, dose escalation, reduction of doses to OARs, or a combination of these factors.

  9. 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.

  10. 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

  11. 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.

  12. Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2

    Science.gov (United States)

    Rifai, Eko Aditya; van Dijk, Marc; Vermeulen, Nico P. E.; Geerke, Daan P.

    2018-01-01

    Computational protein binding affinity prediction can play an important role in drug research but performing efficient and accurate binding free energy calculations is still challenging. In the context of phase 2 of the Drug Design Data Resource (D3R) Grand Challenge 2 we used our automated eTOX ALLIES approach to apply the (iterative) linear interaction energy (LIE) method and we evaluated its performance in predicting binding affinities for farnesoid X receptor (FXR) agonists. Efficiency was obtained by our pre-calibrated LIE models and molecular dynamics (MD) simulations at the nanosecond scale, while predictive accuracy was obtained for a small subset of compounds. Using our recently introduced reliability estimation metrics, we could classify predictions with higher confidence by featuring an applicability domain (AD) analysis in combination with protein-ligand interaction profiling. The outcomes of and agreement between our AD and interaction-profile analyses to distinguish and rationalize the performance of our predictions highlighted the relevance of sufficiently exploring protein-ligand interactions during training and it demonstrated the possibility to quantitatively and efficiently evaluate if this is achieved by using simulation data only.

  13. Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2.

    Science.gov (United States)

    Rifai, Eko Aditya; van Dijk, Marc; Vermeulen, Nico P E; Geerke, Daan P

    2018-01-01

    Computational protein binding affinity prediction can play an important role in drug research but performing efficient and accurate binding free energy calculations is still challenging. In the context of phase 2 of the Drug Design Data Resource (D3R) Grand Challenge 2 we used our automated eTOX ALLIES approach to apply the (iterative) linear interaction energy (LIE) method and we evaluated its performance in predicting binding affinities for farnesoid X receptor (FXR) agonists. Efficiency was obtained by our pre-calibrated LIE models and molecular dynamics (MD) simulations at the nanosecond scale, while predictive accuracy was obtained for a small subset of compounds. Using our recently introduced reliability estimation metrics, we could classify predictions with higher confidence by featuring an applicability domain (AD) analysis in combination with protein-ligand interaction profiling. The outcomes of and agreement between our AD and interaction-profile analyses to distinguish and rationalize the performance of our predictions highlighted the relevance of sufficiently exploring protein-ligand interactions during training and it demonstrated the possibility to quantitatively and efficiently evaluate if this is achieved by using simulation data only.

  14. Effect of high energy milling time of the aluminum bronze alloy obtained by powder metallurgy with niobium carbide addition

    Energy Technology Data Exchange (ETDEWEB)

    Dias, Alexandre Nogueira Ottoboni; Silva, Aline da; Rodrigues, Carlos Alberto; Melo, Mirian de Lourdes Noronha Motta; Rodrigues, Geovani; Silva, Gilbert, E-mail: aottoboni@yahoo.com.br [Universidade Federal de Itajuba (UNIFEI), Itajuba, MG (Brazil)

    2017-05-15

    The aluminum bronze alloy is part of a class of highly reliable materials due to high mechanical strength and corrosion resistance being used in the aerospace and shipbuilding industry. It's machined to produce parts and after its use cycle, it's discarded, but third process is considered expensive and besides not being correct for environment reasons. Thus, reusing this material through the powder metallurgy (PM) route is considered advantageous. The aluminum bronze chips were submitted to high energy ball milling process with 3% of niobium carbide (NbC) addition. The NbC is a metal-ceramic composite with a ductile-brittle behaviour. It was analyzed the morphology of powders by scanning electron microscopy as well as particle size it was determined. X ray diffraction identified the phases and the influence of milling time in the diffractogram patterns. Results indicates that milling time and NbC addition improves the milling efficiency significantly and being possible to obtain nanoparticles. (author)

  15. 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.

  16. 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...

  17. 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

  18. 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)

  19. 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.

  20. Adaptive immune stimulation is required to obtain high protection with fatty acid binding protein vaccine candidate against Fasciola hepatica in Balb/C mice.

    Science.gov (United States)

    López-Abán, Julio; Esteban, Ana; Vicente, Belén; Rojas-Caraballo, José; del Olmo, Esther; Martínez-Fernández, Antonio R; Hillyer, George V; Muro, Antonio

    2012-06-01

    Fascioliasis is a parasitic disease that mainly affects cattle and sheep, causing significant economic losses with a great impact in developing countries. Human fascioliasis is becoming more important with the high endemicity in some countries of the world. Previous studies have shown the importance of Fasciola hepatica fatty acid binding proteins (FABP) as protective molecules against fascioliasis in various animal models including mice, rabbits, and sheep. Our studies have shown the protective efficacy of recombinant FABP (rFh15) when the protein is formulated in the adjuvant adaptation system (ADAD), using either natural or synthetic immunomodulators. The ADAD system is most effective when it is used 5 days before each dose of specific vaccine antigen. The results showed survival rates of up to 50% with less severe hepatic lesions and high levels of IgG2a or IFNγ in immunized mice, using the ADAD system, compared to survival rates of 13% with no hepatic lesion reduction and high levels of IgG1 and IL-4 in those mice immunized with the simplified mode (ADADs).

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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)

  7. 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)

  8. 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

  9. 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

  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. Spectroscopic studies of the energy transfer processes important to obtain holmium laser action in the Er:Tm:Ho:YLF

    International Nuclear Information System (INIS)

    Tarelho, Luiz Vicente Gomes

    1995-01-01

    There are several processes of energy transfer between Er, Tm and Ho ions in YLF crystal that could be evaluated using the Foerster-Dexter method. Energy transfer processes, important to understand Holmium laser action, were studied, specially involving the energy transfer between the first excited states of Er and Tm donors and Ho acceptor. The back-transfer processes were evaluated too in order to minimize the system losses. Another important process to understand Ho laser action in the host is the energy diffusion mechanism between donor ions due to excitation migration processes which take place before the energy transfer to Ho. The proposed model of energy transfer was developed to include the diffusion mechanism between donors in the absence and presence of the acceptors. The energy transfer probability was evaluated including the back-transfer processes besides the diffusion assistance. A laser medium model based on the fundamental spectroscopic parameters was used in order to determine the ideal donor acceptor concentrations in order to maximize the laser action of Ho at 2,1 μm. (author)

  12. 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.

  13. Symmetric energy-momentum tensor in Maxwell, Yang-Mills, and Proca theories obtained using only Noether's theorem

    Energy Technology Data Exchange (ETDEWEB)

    Montesinos, M. [CINVESTAV-IPN, 07360 Mexico D.F. (Mexico); Flores, E. [Facultad de Fisica e Inteligencia Artificial, Universidad Veracruzana, 91000 Xalapa, Veracruz (Mexico)]. E-mail: merced@fis.cinvestav.mx

    2006-07-01

    The symmetric and gauge-invariant energy-momentum tensors for source-free Maxwell and Yang-Mills theories are obtained by means of translations in spacetime via a systematic implementation of Noether's theorem. For the source-free neutral Proca field, the same procedure yields also the symmetric energy-momentum tensor. In all cases, the key point to get the right expressions for the energy-momentum tensors is the appropriate handling of their equations of motion and the Bianchi identities. It must be stressed that these results are obtained without using Belinfante's symmetrization techniques which are usually employed to this end. (Author)

  14. 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.

  15. 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.

  16. 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.

  17. 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...

  18. 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.

  19. 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.)

  20. 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.)

  1. 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.

  2. A comparison of specific effective energies values obtained for some radioactive element using 3 different decay data banks

    International Nuclear Information System (INIS)

    Nascimento, J.E.C.; Bertelli Neto, L.

    1990-01-01

    The Specific Effective Energies (SEE) are the dose equivalents received by each of the body organs (targets organs) per nuclear transformation of a radionuclide deposited in an organ or tissue (source organ) after an intake of this isotope. The SEE values were calculated on basis of the dosimetric concepts of Publication 30 of the International Comission on Radiological Protection (ICRP). The results were evaluated using two of the three most known decay data banks. This study shows considerables discrepancies in the evaluation of the SEE values for some radionuclides. In theses cases it is recommended the use of the most complete and detailed decay data bank to perform the SEE calculations. (author) [pt

  3. Obtaining Cosmic-Ray Propagation Parameters from Diffuse Very High Energy Gamma-Ray Emission from the Galactic Center Ridge

    Science.gov (United States)

    Büsching, I.; de Jager, O. C.; Snyman, J.

    2007-02-01

    The recent discovery of diffuse, very high energy (VHE) γ-radiation from the Galactic center ridge by the HESS telescope allows for the first time the direct determination of the parameters of Galactic cosmic-ray propagation models. Whereas this discovery showed that the diffuse γ-radiation can be explained by the interaction of VHE cosmic-ray (CR) protons with the interstellar gas located in several giant molecular clouds, we show in this paper that the associated diffusion coefficient for the protons depends on the epoch of activity of the central source of protons: Assuming that the supernova remnant (SNR) Sgr A East was responsible for the particle acceleration, we infer a diffusion coefficient for the Galactic center region of κ=1-5 kpc2 Myr-1 for a mean proton energy of ~3 TeV. More specifically, for impulsive injection in a 5-10 kyr SNR, we infer a value of κ=1-2 kpc2 Myr-1, whereas for source activity timescales equal to the age of the SNR, the diffusion coefficient would increase to κ~5 kpc2 Myr-1. These values are smaller than those inferred from local CR abundances. Finally, the above-mentioned values of κ for impulsive injection are equally valid if the required transient source of protons was due to an earlier epoch of stellar infall into the black hole Sgr A*.

  4. 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.

  5. 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.

  6. 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.

  7. Characteristics of Cu–Al2O3 composites of various starting particle size obtained by high-energy milling

    Directory of Open Access Journals (Sweden)

    VIŠESLAVA RAJKOVIĆ

    2009-05-01

    Full Text Available The powder Cu– Al2O3 composites were produced by high-energy milling. Various combinations of particle size and mixtures and approximately constant amount of Al2O3 were used as the starting materials. These powders were separately milled in air for up to 20 h in a planetary ball mill. The copper matrix was reinforced by internal oxidation and mechanical alloying. During the milling, internal oxidation of pre-alloyed Cu-2 mass %-Al powder generated 3.7 mass % Al2O3 nano-sized particles finely dispersed in the copper matrix. The effect of different size of the starting copper and Al2O3 powder particles on the lattice parameter, lattice distortion and grain size, as well as on the size, morphology and microstructure of the Cu– Al2O3 composite powder particles was studied.

  8. 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.

  9. 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...

  10. Probabilities and energies to obtain the counting efficiency of electron-capture nuclides. KLMN model; Probabilidades y energias de reestructuracion atomica subsiguientes a la captura electronica. Modelo KLMN

    Energy Technology Data Exchange (ETDEWEB)

    Galiano, G.; Grau, A.

    1994-07-01

    An intelligent computer program has been developed to obtain the mathematical formulae to compute the probabilities and reduced energies of the different atomic rearrangement pathways following electron-capture decay. Creation and annihilation operators for Auger and X processes have been introduced. Taking into account the symmetries associated with each process, 262 different pathways were obtained. This model allows us to obtain the influence of the M-electro capture in the counting efficiency when the atomic number of the nuclide is high. (Author)

  11. Obtaining the conversion curve of CT numbers to electron density from the effective energy of the CT using the dummy SEFM

    International Nuclear Information System (INIS)

    Martin-Viera Cueto, J. A.; Garcia Pareja, S.; Benitez Villegas, E. M.; Moreno Saiz, E. M.; Bodineau Gil, C.; Caudepon Moreno, F.

    2011-01-01

    The objective of this work is to obtain the conversion curve of Hounsfield units (A) versus electron densities using a mannequin with different tissue equivalent materials. This provides for the effective energy beam CT and is used to characterize the linear coefficients of absorption of different materials that comprise the dummy.

  12. 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....

  13. Motivation to obtain a food reward of pregnant ewes in negative energy balance: behavioural, metabolic and endocrine considerations.

    Science.gov (United States)

    Verbeek, E; Waas, J R; Oliver, M H; McLeay, L M; Ferguson, D M; Matthews, L R

    2012-07-01

    Low food availability often coincides with pregnancy in grazing animals. This study investigated how chronic reductions in food intake affected feeding motivation, and metabolic and endocrine parameters in pregnant sheep, which might be indicative of compromised welfare. Ewes with an initial Body Condition Score of 2.7±0.3 (BCS; 0 indicates emaciation and 5 obesity) were fed to attain low (LBC 2.0±0.0,), medium (MBC 2.9±0.1) or high BCS (HBC 3.7±0.1) in the first trimester of pregnancy. A feeding motivation test in which sheep were required to walk a set distance for a palatable food reward was conducted in the second trimester. LBC and MBC ewes consumed more rewards (P=0.001) and displayed a higher expenditure (P=0.02) than HBC ewes, LBC ewes also tended to consume more rewards than MBC ewes (P=0.09). Plasma leptin and glucose concentrations were inversely correlated to expenditure (both Pmotivation and negative energy balance of low BCS ewes suggested an increased risk of compromised welfare. Imposing even a small cost on a food reward reduced motivation substantially in high BCS ewes (despite high intake when food was freely available). Assessment of a willingness to work for rewards, combined with measures of key metabolic and endocrine parameters, may provide sensitive barometers of welfare in energetically-taxed animals. Copyright © 2012 Elsevier Inc. All rights reserved.

  14. 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 )

  15. Core-level spectra and binding energies of transition metal nitrides by non-destructive x-ray photoelectron spectroscopy through capping layers

    Energy Technology Data Exchange (ETDEWEB)

    Greczynski, G., E-mail: grzgr@ifm.liu.se [Thin Film Physics Division, Department of Physics (IFM), Linköping University, SE-581 83 Linköping (Sweden); Primetzhofer, D. [Department of Physics and Astronomy, The Ångström Laboratory, Uppsala University, P.O. Box 516, SE-751 20 Uppsala (Sweden); Lu, J.; Hultman, L. [Thin Film Physics Division, Department of Physics (IFM), Linköping University, SE-581 83 Linköping (Sweden)

    2017-02-28

    Highlights: • First non-destructive measurements of XPS core level binding energies for group IVb-VIb transition metal nitrides are presented. • All films are grown under the same conditions and analyzed in the same instrument, providing a useful reference for future XPS studies. • Extracted core level BE values are more reliable than those obtained from sputter-cleaned N-deficient surfaces. • Comparison to Ar+-etched surfaces reveals that even mild etching conditions result in the formation of a nitrogen-deficient surface layer. • The N/metal concentration ratios from capped samples are found to be 25-90% higher than those from the corresponding ion-etched surfaces. - Abstract: We present the first measurements of x-ray photoelectron spectroscopy (XPS) core level binding energies (BE:s) for the widely-applicable group IVb-VIb polycrystalline transition metal nitrides (TMN’s) TiN, VN, CrN, ZrN, NbN, MoN, HfN, TaN, and WN as well as AlN and SiN, which are common components in the TMN-based alloy systems. Nitride thin film samples were grown at 400 °C by reactive dc magnetron sputtering from elemental targets in Ar/N{sub 2} atmosphere. For XPS measurements, layers are either (i) Ar{sup +} ion-etched to remove surface oxides resulting from the air exposure during sample transfer from the growth chamber into the XPS system, or (ii) in situ capped with a few nm thick Cr or W overlayers in the deposition system prior to air-exposure and loading into the XPS instrument. Film elemental composition and phase content is thoroughly characterized with time-of-flight elastic recoil detection analysis (ToF-E ERDA), Rutherford backscattering spectrometry (RBS), and x-ray diffraction. High energy resolution core level XPS spectra acquired with monochromatic Al Kα radiation on the ISO-calibrated instrument reveal that even mild etching conditions result in the formation of a nitrogen-deficient surface layer that substantially affects the extracted binding energy

  16. 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.

  17. 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).

  18. An improved cluster pair correlation method for obtaining the absolute proton hydration energy and enthalpy evaluated with an expanded data set.

    Science.gov (United States)

    Donald, William A; Williams, Evan R

    2010-10-21

    An improved cluster pair correlation method that is based on the method originally introduced by Tuttle et al. ( Tuttle et al. J. Phys. Chem. A 2002 , 106 , 925 - 932 ) was developed and evaluated using a significantly larger data set than used previously. With this larger data set, values for the absolute proton hydration free energy of -259.3 and -265.0 kcal/mol were obtained using the original and improved method, respectively. The former value is ∼4.5 kcal/mol less negative than previously reported values obtained with the same method but with smaller data sets. The dependence of this value on data set size indicates that the uncertainty in the original method may be greater than previously realized. The improved method has the advantages of higher precision, and the effects of cluster size on the proton hydration free energy and enthalpy values can be more readily evaluated. Data for ions with extreme pK(a)s, many of which were included in previous estimates of the proton hydration free energy, were found to be unreliable and were eliminated from the extended data set. There is only a subtle effect of cluster size on the Gibbs free energy values, and within the limits of the approximation inherent in the cluster pair correlation method, the "best" value for the standard absolute proton hydration free energy obtained with this new method and larger data set is -263.4 kcal/mol (average for clusters with 4-6 water molecules). The absolute proton hydration enthalpy values decrease from -273.1 to -275.3 kcal/mol with increasing cluster size (one to six water molecules, respectively). This trend, along with an anomalously high value for the absolute proton hydration entropy, indicates that the enthalpy obtained with this method may not have converged for these relatively small clusters.

  19. 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).

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. Preparation, characterization and environmental/electrochemical energy storage testing of low-cost biochar from natural chitin obtained via pyrolysis at mild conditions

    Science.gov (United States)

    Magnacca, Giuliana; Guerretta, Federico; Vizintin, Alen; Benzi, Paola; Valsania, Maria C.; Nisticò, Roberto

    2018-01-01

    Chitin (a biopolymer obtained from shellfish industry) was used as precursor for the production of biochars obtained via pyrolysis treatments performed at mild conditions (in the 290-540 °C range). Biochars were physicochemical characterized in order to evaluate the pyrolysis-induced effects in terms of both functional groups and material structure. Moreover, such carbonaceous materials were tested as adsorbent substrates for the removal of target molecules from aqueous environment as well as in solid-gas experiments, to measure the adsorption capacities and selectivity toward CO2. Lastly, biochars were also investigated as possible cathode materials in sustainable and low-cost electrochemical energy storage devices, such as lithium-sulphur (Li-S) batteries. Interestingly, experimental results evidenced that such chitin-derived biochars obtained via pyrolysis at mild conditions are sustainable, low-cost and easy scalable alternative materials suitable for both environmental and energetic applications.

  7. 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.

  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. 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.

  10. 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

  11. 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.

  12. Diffusion Monte Carlo determination of the binding energy of the sup 4 He nucleus for model Wigner potentials

    Energy Technology Data Exchange (ETDEWEB)

    Bishop, R.F. (Manchester Univ. (United Kingdom). Inst. of Science and Technology); Buendia, E. (Granada Univ. (Spain). Dept. de Fisica Moderna); Flynn, M.F. (Kent State Univ., OH (United States). Dept. of Physics); Guardiola, R. (Valencia Univ. (Spain). Dept. de Fisica Atomica y Nuclear)

    1992-02-01

    The diffusion Monte Carlo method is used to integrate the four-body Schroedinger equation corresponding to the {sup 4}He nucleus for several model potentials of Wigner type. Good importance sampling trial functions are used, and the sampling is large enough to obtain the ground-state energy with an error of only 0.01 to 0.02 MeV. (author).

  13. Transverse energy and neutral pion spectra obtained from 16O- and 32S-induced reactions at 200 GeV/nucleon

    International Nuclear Information System (INIS)

    Plasil, F.; Albrecht, R.; Awes, T.C.

    1989-01-01

    The main goal of the CERN heavy-ion experiments is the search for an indication that the predicted state of deconfined quarks and gluons, the quark-gluon plasma (QGP), has been produced. The most promising indication that this may, in fact, be the case comes from the NA38 dimuon measurements, which are focused on the question of J//psi/ suppression. This effect was predicted to be one of the signatures of QGP formation before any measurements were made, and it is the subject of the two other talks at this conference that deal with nucleus-nucleus reactions at ultrarelativistic energies. In this presentation we consider the general (global) features of heavy-ion reactions at CERN energies, and we examine the degree to which they differ from mere superpositions of nucleon-nucleon collisions. We discuss the present status of our data analysis and our main conclusions from the first round of CERN experiments with emphasis on transverse energy measurements, on attained energy densities, and on the spectra of produced neutral pions. Because of time limitations we will not discuss our measurements of distributions of charged particles and the analysis of these distributions in terms of fluctuations nor the results that we have obtained with the Plastic Ball on the behavior of target spectator matter. 20 refs., 5 figs

  14. Upper limit for ultra-high-energy gamma rays from SN 1987A obtained by Cerenkov technique at large zenith angles

    Science.gov (United States)

    Bond, I. A.; Budding, E.; Conway, M. J.; Fenton, K. B.; Fujii, H.; Fujii, Z.; Fujimoto, M.; Hasegawa, H.; Hayashida, S.; Honda, M.; Hotta, N.; Humble, J. E.; Kabe, S.; Kasahara, K.; Kifune, T.; Lythe, G. D.; Masaike, A.; Matsubara, Y.; Mitsui, K.; Miura, Y.; Mori, M.; Murakami, K.; Muraki, Y.; Nagano, M.; Nakamura, K.; Nakamura, T.; Norris, P. M.; Ogio, S.; Ohashi, Y.; Okada, A.; Saito, To.; Sakata, M.; Sato, H.; Shibata, S.; Shima, M.; Shimizu, H. M.; Spencer, M.; Storey, J. R.; Tanimori, T.; Teshima, M.; Torii, S.; Uchino, K.; Watase, Y.; Woodhams, M. D.; Yamamoto, Y.; Yock, P. C. M.; Yuda, T.; JANZOS Collaboration

    1989-09-01

    The supernova SN 1987A has been observed with the JANZOS cosmic-ray facility at the Black Birch Range in New Zealand since October 1987. From May to July 1988, observations were carried out using the Cerenkov telescope at a zenith angle of 68 deg. By working at large zenith angles, the effective detection area and energy threshold are both increased. From 39 hr or greater of observation, an upper bound of 5.7 x 10 to the -14th/sq cm sec on the flux of gamma rays with energies of 75 TeV is obtained at the 95-percent confidence level. This flux limit corresponds to the gamma ray luminosity of 10 to the 37th ergs/sec.

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. Quantum mechanical free energy profiles with post-quantization restraints: Binding free energy of the water dimer over a broad range of temperatures

    Science.gov (United States)

    Bishop, Kevin P.; Roy, Pierre-Nicholas

    2018-03-01

    Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.

  2. Quantum mechanical free energy profiles with post-quantization restraints: Binding free energy of the water dimer over a broad range of temperatures.

    Science.gov (United States)

    Bishop, Kevin P; Roy, Pierre-Nicholas

    2018-03-14

    Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.

  3. 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.

  4. Core-level spectra and binding energies of transition metal nitrides by non-destructive x-ray photoelectron spectroscopy through capping layers

    Science.gov (United States)

    Greczynski, G.; Primetzhofer, D.; Lu, J.; Hultman, L.

    2017-02-01

    We present the first measurements of x-ray photoelectron spectroscopy (XPS) core level binding energies (BE:s) for the widely-applicable group IVb-VIb polycrystalline transition metal nitrides (TMN's) TiN, VN, CrN, ZrN, NbN, MoN, HfN, TaN, and WN as well as AlN and SiN, which are common components in the TMN-based alloy systems. Nitride thin film samples were grown at 400 °C by reactive dc magnetron sputtering from elemental targets in Ar/N2 atmosphere. For XPS measurements, layers are either (i) Ar+ ion-etched to remove surface oxides resulting from the air exposure during sample transfer from the growth chamber into the XPS system, or (ii) in situ capped with a few nm thick Cr or W overlayers in the deposition system prior to air-exposure and loading into the XPS instrument. Film elemental composition and phase content is thoroughly characterized with time-of-flight elastic recoil detection analysis (ToF-E ERDA), Rutherford backscattering spectrometry (RBS), and x-ray diffraction. High energy resolution core level XPS spectra acquired with monochromatic Al Kα radiation on the ISO-calibrated instrument reveal that even mild etching conditions result in the formation of a nitrogen-deficient surface layer that substantially affects the extracted binding energy values. These spectra-modifying effects of Ar+ ion bombardment increase with increasing the metal atom mass due to an increasing nitrogen-to-metal sputter yield ratio. The superior quality of the XPS spectra obtained in a non-destructive way from capped TMN films is evident from that numerous metal peaks, including Ti 2p, V 2p, Zr 3d, and Hf 4f, exhibit pronounced satellite features, in agreement with previously published spectra from layers grown and analyzed in situ. In addition, the N/metal concentration ratios are found to be 25-90% higher than those obtained from the corresponding ion-etched surfaces, and in most cases agree very well with the RBS and ToF-E ERDA values. The N 1 s BE:s extracted from

  5. 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.

  6. 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.

  7. 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.

  8. A structural investigation of SmCo5/Fe nanostructured alloys obtained by high-energy ball milling and subsequent annealing

    International Nuclear Information System (INIS)

    Le Breton, J M; Larde, R; Chiron, H; Pop, V; Givord, D; Isnard, O; Chicinas, I

    2010-01-01

    SmCo 5 /Fe nanostructured alloys with 20 wt% Fe, obtained by high-energy ball milling of SmCo 5 and Fe powders, were investigated by 57 Fe Moessbauer spectrometry, x-ray diffraction and tomographic atom probe. The Moessbauer analysis reveals that during the first stages of milling, an interdiffusion of Co and Fe occurs, leading both to the formation of α-Fe(Co) regions in α-Fe and to the introduction of Fe in SmCo 5 regions. Annealing at temperatures up to 650 0 C for 0.5 h promotes interdiffusion further leading to the formation of a unique α-Fe(Co) phase and a Fe-richer Sm(Co,Fe) 5 phase. The Co/Fe interdiffusion is confirmed by tomographic atom probe analysis. The data are discussed and compared with the results of previous magnetic measurements.

  9. 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.

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

    Science.gov (United States)

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

    2015-01-22

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

  11. Properties of Y-TZP/Al{sub 2}O{sub 3} ceramic nanocomposites obtained by high-energy ball milling

    Energy Technology Data Exchange (ETDEWEB)

    Santos, C. [Universidade de Sao Paulo - Escola de Engenharia de Lorena (USP-EEL), Polo Urbo-Industrial, Gleba AI-6, s/n, Lorena-SP, CEP 12600-000 (Brazil); Universidade do Estado do Rio de Janeiro, Faculdade de Tecnologia (UERJ-FAT), Rodovia Presidente Dutra, km 298, Resende-RJ, CEP 27511-971 (Brazil)], E-mail: claudinei@demar.eel.usp.br; Koizumi, M.H.; Daguano, J.K.M.F.; Santos, F.A. [Universidade de Sao Paulo - Escola de Engenharia de Lorena (USP-EEL), Polo Urbo-Industrial, Gleba AI-6, s/n, Lorena-SP, CEP 12600-000 (Brazil); Elias, C.N. [Instituto Militar de Engenharia - Departamento de Ciencia e Engenharia de Materiais (IME - DCEM), Pca. General Tiburcio, 80, Praia Vermelha, Rio de Janeiro-RJ, CEP 22290-270 (Brazil); Universidade do Estado do Rio de Janeiro, Faculdade de Tecnologia (UERJ-FAT), Rodovia Presidente Dutra, km 298, Resende-RJ, CEP 27511-971 (Brazil); Ramos, A.S. [Universidade do Vale do Paraiba - Instituto de Pesquisa e Desenvolvimento (UNIVAP-IP and D), Av. Shishima Hifumi, 2911, Urbanova, S.J.Campos-SP, CEP 12244-000 (Brazil)

    2009-02-25

    In this work, the synthesis of Y{sub 2}O{sub 3} stabilized tetragonal zirconia polycrystals (Y-TZP)-alumina (Al{sub 2}O{sub 3}) powder mixture was performed by high-energy ball milling and the sintering behavior of this composite was investigated. In order to understand the phase transformations occurring during ball milling, samples were collected after different milling times, from 1 to 60 h. The milled powders were compacted by cold uniaxial pressing and sintered at 1400 and 1600 deg. C. Both powders and sintered samples were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive spectrometry analysis (EDS) and mechanical properties. Fully dense samples were obtained after sintering at 1600 deg. C, while the samples sintered at 1400 deg. C presented a full density for powder mixtures milled for 30 and 60 h. Fracture toughness and Vickers hardness values of the Y-TZP/Al{sub 2}O{sub 3} nanocomposite were improved due to dispersed Al{sub 2}O{sub 3} grains and reduced ZrO{sub 2} grain size. Samples sintered at 1400 deg. C, based on powders milled for 60 h, presented high K{sub IC} and hardness values near to 8.0 MPam{sup 1/2} and 15 GPa, respectively.

  12. How to Obtain a 100% Reliable Grid with Clean, Renewable Wind, Water, and Solar Providing 100% of all Raw Energy for All Purposes

    Science.gov (United States)

    Jacobson, M. Z.; Delucchi, M. A.; Cameron, M. A.; Frew, B. A.

    2016-12-01

    The greatest concern facing the large-scale integration of wind, water, and solar (WWS) into a power grid is the high cost of avoiding load loss caused by WWS variability and uncertainty. This talk discusses the recent development of a new grid integration model to address this issue. The model finds low-cost, no-load-loss, non-unique solutions to this problem upon electrification of all U.S. energy sectors (electricity, transportation, heating/cooling, and industry) while accounting for wind and solar time-series data from a 3-D global weather model that simulates extreme events and competition among wind turbines for available kinetic energy. Solutions are obtained by prioritizing storage for heat (in soil and water); cold (in ice and water); and electricity (in phase-change materials, pumped hydro, hydropower, and hydrogen); and using demand response. No natural gas, biofuels, or stationary batteries are needed. The resulting 2050-2055 U.S. electricity social cost for a full system is much less than for fossil fuels. These results hold for many conditions, suggesting that low-cost, stable 100% WWS systems should work many places worldwide. The paper this talk is based on was published in PNAS, 112, 15,060-15,065, 2015, doi:10.1073/pnas.1510028112.

  13. 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.

  14. Determination of the energy efficiency of sensitized solar cells with pigments obtained from natural extracts, and microbiological processes and nanoparticles of germanium

    International Nuclear Information System (INIS)

    Flores Diaz, Natalie

    2014-01-01

    ,124 ± 1,689 mA/cm 2 , V OC 0,483 ± 0,019 V, P max 1,405 ± 0,422 W/m 2 , FF 0,575 ± 0,063 and %η 0,140 ± 0,042%. The extracts of caimito have obtained J SC 5,229 ± 0,882 mA/cm 2 , V OC 0,477 ± 0,007 V, P max 1,716 ± 0,288 W/m 2 , FF 0,688 ± 0,018 and %η 0,172 ± 0,029%. For the pigment of rosa de jamaica has obtained J SC 5,235 ± 1,360 mA/cm 2 , V OC 0,499 ± 0,013 V, P max 1,892 ± 0,525 W/m 2 , FF 0,723 ± 0,050 and %η 0,189 ± 0,052%. An analysis of variance ANOVA was realized to determine the contribution of each source of variation in the the total observed variation in the energy conversion efficiency of the sensitized solar cells with said pigments. The variability in efficiency data of the cells is due to treatment (pigments) and without random error. A very small value is obtained from the mean square error and indicates that the variability within each treatment has been small and the assembly process of the cells has been reproducible. 6 sensitized cells are assembled with dye Z907 and co-sensitized with nanoparticles of germanium have obtained the characteristic parameters J SC 6,64 ± 0,90 mA/cm 2 , V OC 0,67 ± 0,01 V, P max 28,75 ± 4,8 W/m 2 , FF 0,63 ± 0,02 and %η 2,897 ± 0,48%. These values have been lower than the obtained for the dye Z907, almost 50% for all parameters. The use of the nanoparticle remains without improving the behavior of the cell, affecting him significantly, because without a good anchorage of the nanoparticles to TIO 2 with the bifunctional molecule, cysteine, may affect the injection of electrons to the semiconductor. The pigments obtained from actinomycetes and bacteria, A9, A11, 8, 4.3 and 10.2 to sensitize TIO 2 electrodes are used, however, these remain without be adsorbed in appreciable amount to the semiconductor, and without being used for cells. The lack of adequate functional groups for anchoring may be the main reason for this behavior. The economic cost is estimated from the production of each cell

  15. 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

  16. Information-theoretical feature selection using data obtained by scanning electron microscopy coupled with and energy dispersive X-ray spectrometer for the classification of glass traces.

    Science.gov (United States)

    Ramos, Daniel; Zadora, Grzegorz

    2011-10-31

    In this work, a selection of the best features for multivariate forensic glass classification using Scanning Electron Microscopy coupled with an Energy Dispersive X-ray spectrometer (SEM-EDX) has been performed. This has been motivated by the fact that the databases available for forensic glass classification are sparse nowadays, and the acquisition of SEM-EDX data is both costly and time-consuming for forensic laboratories. The database used for this work consists of 278 glass objects for which 7 variables, based on their elemental compositions obtained with SEM-EDX, are available. Two categories are considered for the classification task, namely containers and car/building windows, both of them typical in forensic casework. A multivariate model is proposed for the computation of the likelihood ratios. The feature selection process is carried out by means of an exhaustive search, with an Empirical Cross-Entropy (ECE) objective function. The ECE metric takes into account not only the discriminating power of the model in use, but also its calibration, which indicates whether or not the likelihood ratios are interpretable in a probabilistic way. Thus, the proposed model is applied to all the 63 possible univariate, bivariate and trivariate combinations taken from the 7 variables in the database, and its performance is ranked by its ECE. Results show remarkable accuracy of the best variables selected following the proposed procedure for the task of classifying glass fragments into windows (from cars or buildings) or containers, obtaining high (almost perfect) discriminating power and good calibration. This allows the proposed models to be used in casework. We also present an in-depth analysis which reveals the benefits of the proposed ECE metric as an assessment tool for classification models based on likelihood ratios. Copyright © 2011 Elsevier B.V. All rights reserved.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. In-Situ X-ray Absorption Spectroscopy as an Unique Tool for Obtaining Information on Hydrogen Binding Site and Electronic Structure of Supported Pt Catalysts: Towards an Understanding of the Compensation Relation in Alkane Hydrogenolysis

    NARCIS (Netherlands)

    Koningsberger, D.C.; Oudenhuijzen, M.K.; Bokhoven, J.A. van; Ramaker, D.E.

    2003-01-01

    L2 and L3 X-ray absorption near edge spectra (XANES) on supported Pt particles, with and without chemisorbed hydrogen, are shown to reflect the type of hydrogen-binding site on the Pt surface. FEFF8 ab initio multiple scattering calculations are used to determine XANES spectral fingerprints for the

  3. 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.

  4. 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

  5. A density-functional study of the structures, binding energies and magnetic moments of the clusters Mo{sub N} (N = 2-13), Mo{sub 12}Fe, Mo{sub 12}Co and Mo{sub 12}Ni

    Energy Technology Data Exchange (ETDEWEB)

    Aguilera-Granja, F [Instituto de Fisica, Universidad Autonoma de San Luis PotosI, SLP 78000 (Mexico); Vega, A [Departamento de Fisica Teorica, Atomica, y Optica, Universidad de Valladolid, E-47011 Valladolid (Spain); Gallego, L J [Departamento de Fisica de la Materia Condensada, Facultad de Fisica, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela (Spain)

    2008-04-09

    We report the results of density-functional calculations of the structures, binding energies and magnetic moments of the clusters Mo{sub N} (N = 2-13), Mo{sub 12}Fe, Mo{sub 12}Co and Mo{sub 12}Ni that were performed using the SIESTA method within the generalized gradient approximation for exchange and correlation. For pure Mo{sub N} clusters, we obtain collinear magnetic structures in all cases, even when the self-consistent calculations were started from non-collinear inputs. Our results for these clusters show that both linear, planar and three-dimensional clusters have a strong tendency to form dimers. In general, even-numbered clusters are more stable than their neighbouring odd-numbered clusters because they can accommodate an integer number of tightly bound dimers. As a consequence, the binding energies of pure Mo{sub N} clusters, in their lowest-energy states, exhibit an odd-even effect in all dimensionalities. Odd-even effects are less noticeable in the magnetic moments than in the binding energies. When comparing our results for pure Mo clusters with those obtained recently by other authors, we observe similarities in some cases, but striking differences in others. In particular, the odd-even effect in three-dimensional Mo clusters was not observed before, and our results for some clusters (e.g. for planar Mo{sub 3} and Mo{sub 7} and for three-dimensional Mo{sub 7} and Mo{sub 13}) differ from those reported by other authors. For Mo{sub 12}Fe and Mo{sub 12}Ni, we obtain that the icosahedral configuration with the impurity atom at the cluster surface is more stable than the configuration with the impurity at the central site, while the opposite occurs in the case of Mo{sub 12}Co. In Mo{sub 12}Co and Mo{sub 12}Ni, the impurities exhibit a weak magnetic moment parallely coupled to the total magnetic moment of the Mo atoms, whereas in Mo{sub 12}Fe the impurity shows a high moment with antiparallel coupling.

  6. 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

  7. 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.

  8. Binding energy and catalysis by D-xylose isomerase: kinetic, product, and X-ray crystallographic analysis of enzyme-catalyzed isomerization of (R)-glyceraldehyde.

    Science.gov (United States)

    Toteva, Maria M; Silvaggi, Nicholas R; Allen, Karen N; Richard, John P

    2011-11-22

    D-Xylose isomerase (XI) and triosephosphate isomerase (TIM) catalyze the aldose-ketose isomerization reactions of D-xylose and d-glyceraldehyde 3-phosphate (DGAP), respectively. D-Glyceraldehyde (DGA) is the triose fragment common to the substrates for XI and TIM. The XI-catalyzed isomerization of DGA to give dihydroxyacetone (DHA) in D(2)O was monitored by (1)H nuclear magnetic resonance spectroscopy, and a k(cat)/K(m) of 0.034 M(-1) s(-1) was determined for this isomerization at pD 7.0. This is similar to the k(cat)/K(m) of 0.017 M(-1) s(-1) for the TIM-catalyzed carbon deprotonation reaction of DGA in D(2)O at pD 7.0 [Amyes, T. L., O'Donoghue, A. C., and Richard, J. P. (2001) J. Am. Chem. Soc. 123, 11325-11326]. The much larger activation barrier for XI-catalyzed isomerization of D-xylose (k(cat)/K(m) = 490 M(-1) s(-1)) versus that for the TIM-catalyzed isomerization of DGAP (k(cat)/K(m) = 9.6 × 10(6) M(-1) s(-1)) is due to (i) the barrier to conversion of cyclic d-xylose to the reactive linear sugar (5.4 kcal/mol) being larger than that for conversion of DGAP hydrate to the free aldehyde (1.7 kcal/mol) and (ii) the intrinsic binding energy [Jencks, W. P. (1975) Adv. Enzymol. Relat. Areas Mol. Biol. 43, 219-410] of the terminal ethylene glycol fragment of D-xylose (9.3 kcal/mol) being smaller than that of the phosphodianion group of DGAP (~12 kcal/mol). The XI-catalyzed isomerization of DGA in D(2)O at pD 7.0 gives a 90% yield of [1-(1)H]DHA and a 10% yield of [1-(2)H]DHA, the product of isomerization with incorporation of deuterium from solvent D(2)O. By comparison, the transfer of (3)H from the labeled hexose substrate to solvent is observed only once in every 10(9) turnovers for the XI-catalyzed isomerization of [2-(3)H]glucose in H(2)O [Allen, K. N., Lavie, A., Farber, G. K., Glasfeld, A., Petsko, G. A., and Ringe, D. (1994) Biochemistry 33, 1481-1487]. We propose that truncation of the terminal ethylene glycol fragment of d-xylose to give DGA results in a

  9. Binding Energy and Catalysis by D-Xylose Isomerase: Kinetic, Product and X-Ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde‡, ¶

    Science.gov (United States)

    Toteva, Maria M.; Silvaggi, Nicholas R.; Allen, Karen N.; Richard, John P.

    2011-01-01

    D-Xylose isomerase (XI) and triosephosphate isomerase (TIM) catalyze the aldose-ketose isomerization reactions of D-xylose and D-glyceraldehyde 3-phosphate (DGAP), respectively. D-Glyceraldehyde (DGA) is the triose fragment common to the substrates for XI and TIM. The XI-catalyzed isomerization of DGA to give dihydroxyacetone (DHA) in D2O was monitored by 1H NMR spectroscopy and kcat/Km = 0.034 M−1 s−1 was determined for this isomerization at pD 7.0. This is similar to kcat/Km = 0.017 M−1 s−1 for the TIM-catalyzed carbon deprotonation reaction of DGA in D2O at pD 7.0 [Amyes, T. L.; O’Donoghue, A. C. and Richard J. P. (2001) J. Am. Chem. Soc. 123, 11325–11326]. The much larger activation barrier for XI-catalyzed isomerization of D-xylose (kcat/Km = 490 M−1 s−1) than for the TIM-catalyzed isomerization of DGAP (kcat/Km = 9.6 x 106 M−1 s−1) is due to: (i) The larger barrier to conversion of cyclic D-xylose to the reactive linear sugar (5.4 kcal/mol) than for conversion of DGAP hydrate to the free aldehyde (1.7 kcal/mol). (ii) The smaller intrinsic binding energy [Jencks, W. P. (1975) Adv. Enzymol. Relat. Areas Mol. Biol. 43, 219–410] of the terminal ethylene glycol fragment of D-xylose (9.3 kcal/mol) than of the phosphodianion group of DGAP (ca. 12 kcal/mol). The XI-catalyzed isomerization of DGA in D2O at pD 7.0 gives a 90% yield of [1-1H]-DHA and a 10% yield of [1-2H]-DHA, the product of isomerization with deuterium incorporation from solvent D2O. By comparison, the transfer of 3H from labeled hexose substrate to solvent is observed only once in every 109 turnovers for the XI-catalyzed isomerization of [2-3H]-glucose in H2O [Allen, K. N., Lavie, A., Farber, G. K., Glasfeld, A., Petsko, G. A., and Ringe, D. (1994), Biochemistry 33, 1481–1487]. We propose that truncation of the terminal ethylene glycol fragment of D-xylose to give DGA results in a large decrease in the rate of XI-catalyzed isomerization with hydride transfer compared with that

  10. Information-theoretical feature selection using data obtained by Scanning Electron Microscopy coupled with and Energy Dispersive X-ray spectrometer for the classification of glass traces

    International Nuclear Information System (INIS)

    Ramos, Daniel; Zadora, Grzegorz

    2011-01-01

    Highlights: → A selection of the best features for multivariate forensic glass classification using SEM-EDX was performed. → The feature selection process was carried out by means of an exhaustive search, with an Empirical Cross-Entropy objective function. → Results show remarkable accuracy of the best variables selected following the proposed procedure for the task of classifying glass fragments into windows or containers. - Abstract: In this work, a selection of the best features for multivariate forensic glass classification using Scanning Electron Microscopy coupled with an Energy Dispersive X-ray spectrometer (SEM-EDX) has been performed. This has been motivated by the fact that the databases available for forensic glass classification are sparse nowadays, and the acquisition of SEM-EDX data is both costly and time-consuming for forensic laboratories. The database used for this work consists of 278 glass objects for which 7 variables, based on their elemental compositions obtained with SEM-EDX, are available. Two categories are considered for the classification task, namely containers and car/building windows, both of them typical in forensic casework. A multivariate model is proposed for the computation of the likelihood ratios. The feature selection process is carried out by means of an exhaustive search, with an Empirical Cross-Entropy (ECE) objective function. The ECE metric takes into account not only the discriminating power of the model in use, but also its calibration, which indicates whether or not the likelihood ratios are interpretable in a probabilistic way. Thus, the proposed model is applied to all the 63 possible univariate, bivariate and trivariate combinations taken from the 7 variables in the database, and its performance is ranked by its ECE. Results show remarkable accuracy of the best variables selected following the proposed procedure for the task of classifying glass fragments into windows (from cars or buildings) or containers

  11. 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.

  12. 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.

  13. Conductance of Graphene Nanoribbon Junctions and the Tight Binding Model

    Directory of Open Access Journals (Sweden)

    Wu Y

    2011-01-01

    Full Text Available Abstract Planar carbon-based electronic devices, including metal/semiconductor junctions, transistors and interconnects, can now be formed from patterned sheets of graphene. Most simulations of charge transport within graphene-based electronic devices assume an energy band structure based on a nearest-neighbour tight binding analysis. In this paper, the energy band structure and conductance of graphene nanoribbons and metal/semiconductor junctions are obtained using a third nearest-neighbour tight binding analysis in conjunction with an efficient nonequilibrium Green's function formalism. We find significant differences in both the energy band structure and conductance obtained with the two approximations.

  14. 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.

  15. On the energy distribution profile of interface states obtained by taking into account of series resistance in Al/TiO{sub 2}/p-Si (MIS) structures

    Energy Technology Data Exchange (ETDEWEB)

    Pakma, O., E-mail: osman@pakma.co [Department of Physics, Faculty of Sciences and Arts, Batman University, Batman (Turkey); Serin, N.; Serin, T. [Department of Engineering Physics, Faculty of Engineering, Ankara University, 06100 Tandogan, Ankara (Turkey); Altindal, S. [Physics Department, Faculty of Arts and Sciences, Gazi University, Teknikokullar, 06500 Ankara (Turkey)

    2011-02-15

    The energy distribution profile of the interface states (N{sub ss}) of Al/TiO{sub 2}/p-Si (MIS) structures prepared using the sol-gel method was obtained from the forward bias current-voltage (I-V) characteristics by taking into account both the bias dependence of the effective barrier height ({phi}{sub e}) and series resistance (R{sub s}) at room temperature. The main electrical parameters of the MIS structure such as ideality factor (n), zero-bias barrier height ({phi}{sub b0}) and average series resistance values were found to be 1.69, 0.519 eV and 659 {Omega}, respectively. This high value of n was attributed to the presence of an interfacial insulator layer at the Al/p-Si interface and the density of interface states (N{sub ss}) localized at the Si/TiO{sub 2} interface. The values of N{sub ss} localized at the Si/TiO{sub 2} interface were found with and without the R{sub s} at 0.25-E{sub v} in the range between 8.4x10{sup 13} and 4.9x10{sup 13} eV{sup -1} cm{sup -2}. In addition, the frequency dependence of capacitance-voltage (C-V) and conductance-voltage (G/{omega}-V) characteristics of the structures have been investigated by taking into account the effect of N{sub ss} and R{sub s} at room temperature. It can be found out that the measured C and G/{omega} are strongly dependent on bias voltage and frequency. -- Research highlights: {yields}We successfully fabricated Al/TiO{sub 2}/p-Si device with interlayer by a sol-gel method. The facts: (i) that the technology of the fabrication of a Al/TiO{sub 2}/p-Si MIS structure much simpler and economical than that for the Si p-n junction and (b) the main advantages of TiO{sub 2} films are low densities of the surface states when compared to SiO{sub 2}.

  16. Brain calbindin-D28k and an Mr 29,000 calcium binding protein in cerebellum are different but related proteins: Evidence obtained from sequence analysis by tandem mass spectroscopy

    International Nuclear Information System (INIS)

    Gabrielides, C.; Christakos, S.; McCormack, A.L.; Hunt, D.F.

    1991-01-01

    A calcium binding protein of M r 29,000 which cross-reacts with antibodies raised against chick calbindin-D 28k was previously reported to be present in rat cerebellum. It was suggested that the M r 29,000 protein represents another form of calbindin-D 28k . In the authors laboratory they were able to identify M r 28,000 and 29,000 proteins in rat, human, and chick cerebellum by their ability to bind 45 Ca in a 45 Ca blot assay. Two calcium binding proteins of M r 27,680 and 29,450 were isolated from rat cerebelli by the use of gel permeation chromatography and preparative gel electrophoresis. After reverse-phase high-performance liquid chromatography (HPLC) the proteins were sequenced. Sequence analysis by tandem mass spectrometry indicated only 52% identity between the rat cerebellar M r 28,000 and 29,000 proteins. Thus they are not different forms of the same protein, as previously suggested. Eighty-nine percent identity was observed between the rate cerebellar M r 29,000 protein and chick calretinin. The difference in identity between the rat cerebellar M r 29,000 protein and chick calretinin may be due to species differences, and thus this protein is most likely rat calretinin. These results suggest either posttranscriptional regulation of calretinin in cerebellum or species differences. The study also suggests that previous immunocytochemical mapping for calbindin using antisera which cross-reacted with both proteins detected brain regions that expressed not only calbindin but also calretinin or a calretinin-like protein

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. Quasi-static method and finite element method for obtaining the modifications of the spontaneous emission rate and energy level shift near a plasmonic nanostructure.

    Science.gov (United States)

    Zhao, Yun-Jin; Tian, Meng; Wang, Xiao-Yun; Yang, Hong; Zhao, Heping; Huang, Yong-Gang

    2018-01-22

    We provide numerical demonstrations of the applicability and accuracy of the quasi-static method and the finite-element method in the investigation of the modifications of the spontaneous emission rate and the energy level shift of an emitter placed near a silver-air interface or a silver nano-sphere. The analytical results are presented as a reference. Our calculations show that the finite element method is an accurate and general method. For frequency away from the radiative mode, the quasi-static method can be applied more effectively for calculating the energy level shift than the spontaneous emission rate. But for frequency around, there is a blue shift for both and this shift increases with the increasing of emitter-silver distance. Applying the theory to the nanosphere dimmer, we see similar phenomenon and find extremely large modifications of the spontaneous emission rate and energy level shift. These findings are instructive in the fields of quantum light-matter interactions.

  3. TiO{sub 2} nanoparticles obtained by laser ablation in water: Influence of pulse energy and duration on the crystalline phase

    Energy Technology Data Exchange (ETDEWEB)

    Giorgetti, E., E-mail: emilia.giorgetti@fi.isc.cnr.it [Istituto dei Sistemi Complessi (ISC) CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Italy); Muniz Miranda, M.; Caporali, S. [Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Italy); Canton, P. [Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari, Via Torino, 30170 Venezia-Mestre (Italy); Marsili, P. [Istituto dei Sistemi Complessi (ISC) CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Italy); Dipartimento di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa (Italy); Vergari, C.; Giammanco, F. [Dipartimento di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa (Italy)

    2015-09-15

    Highlights: • Laser ablation of Ti in water at 1064 nm and comparison of ns and ps temporal regimes. • Structural and spectroscopic characterization of the colloids: TiO{sub 2} is the predominant phase. • Determination of an energy window where ps ablation produces more anatase than rutile. • Modelling of the experimental dependence of anatase/rutile yield on pulse length and energy. - Abstract: We fabricated Ti oxide nanoparticles by laser ablation of a Ti target in doubly deionized water with ps or ns pulses at a laser wavelength of 1064 nm. Electron microscopy, Raman, X-ray diffraction and X-ray photoelectron spectroscopy showed that, while with ns pulses the dominant oxide phase is rutile, with ps pulses anatase is the most abundant form in an intermediate energy window centered around 25 mJ per pulse. This experimental behavior can be described by a theoretical model which calculates the pressure and temperature evolution of the ablated material and, from this, the rutile and anatase yield.

  4. Relativistic contributions to the electromagnetic binding and scattering of pions by atoms

    International Nuclear Information System (INIS)

    Ruijgrok, Th.W.

    1996-01-01

    A relativistic two-particle theory is used for the calculation of the lowest order correction to the electromagnetic binding and scattering of a pion by an atom. The binding energy is found to be equal to the result obtained with the Klein-Gordon equation. The relativistic correction to the differential cross section, however, differs from the corresponding Klein-Gordon result. (author)

  5. CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations

    Directory of Open Access Journals (Sweden)

    Lovorka Perić-Hassler

    2013-12-01

    Full Text Available Because of the large flexibility and malleability of Cytochrome P450 enzymes (CYPs, in silico prediction of CYP binding affinities to drugs and other xenobiotic compounds is a true challenge. In the current work, we use an iterative linear interaction energy (LIE approach to compute CYP binding affinities from molecular dynamics (MD simulation. In order to improve sampling of conformational space, we combine results from simulations starting with different relevant protein-ligand geometries. For calculated binding free energies of a set of thiourea compounds binding to the flexible CYP 2D6 isoform, improved correlation with experiment was obtained by combining results of MD runs starting from distinct protein conformations and ligand-binding orientations. This accuracy was obtained from relatively short MD simulations, which makes our approach computationally attractive for automated calculations of ligand-binding affinities to flexible proteins such as CYPs.

  6. Investigation of naphthofuran moiety as potential dual inhibitor against BACE-1 and GSK-3β: molecular dynamics simulations, binding energy, and network analysis to identify first-in-class dual inhibitors against Alzheimer's disease.

    Science.gov (United States)

    Kumar, Akhil; Srivastava, Gaurava; Srivastava, Swati; Verma, Seema; Negi, Arvind S; Sharma, Ashok

    2017-08-01

    BACE-1 and GSK-3β are potential therapeutic drug targets for Alzheimer's disease. Recently, both the targets received attention for designing dual inhibitors for Alzheimer's disease. Until now, only two-scaffold triazinone and curcumin have been reported as BACE-1 and GSK-3β dual inhibitors. Docking, molecular dynamics, clustering, binding energy, and network analysis of triazinone derivatives with BACE-1 and GSK-3β was performed to get molecular insight into the first reported dual inhibitor. Further, we designed and evaluated a naphthofuran series for its ability to inhibit BACE-1 and GSK-3β with the computational approaches. Docking study of naphthofuran series showed a good binding affinity towards both the targets. Molecular dynamics, binding energy, and network analysis were performed to compare their binding with the targets and amino acids responsible for binding. Naphthofuran series derivatives showed good interaction within the active site residues of both of the targets. Hydrogen bond occupancy and binding energy suggested strong binding with the targets. Dual-inhibitor binding was mostly governed by the hydrophobic interactions for both of the targets. Per residue energy decomposition and network analysis identified the key residues involved in the binding and inhibiting BACE-1 and GSK-3β. The results indicated that naphthofuran series derivative 11 may be a promising first-in-class dual inhibitor against BACE-1 and GSK-3β. This naphthofuran series may be further explored to design better dual inhibitors. Graphical abstract Naphthofuran derivative as a dual inhibitor for BACE-1 and GSK-3β.

  7. Effects of pH on the molecular binding between β-lactoglobulin and bixin.

    Science.gov (United States)

    Zhang, Yue; Wright, Edward; Zhong, Qixin

    2013-01-30

    Binding between β-lactoglobulin (β-Lg), the major whey protein, and bixin, the major carotenoid in annatto, was studied at pH 3.0-10.0. The Fourier transform infrared spectroscopy and UV-vis absorption spectroscopy results showed that the binding involved a complex formation. The tryptophan quenching fluorescence and analytical ultracentrifugation data showed that there were two specific binding sites and that the binding affinity increased significantly with an increase in pH. A higher efficiency of energy transfer from tryptophan fluorescence to bixin was observed at higher pH. Thermodynamic parameters and the number of specific binding sites obtained from isothermal titration calorimetry and analytical ultracentrifugation suggested that binding involved mostly hydrophobic interactions for the two specific binding sites. The impacts of pH on binding were correlated to the conformation of β-Lg, the hydrophobic pocket of which becomes more available at higher pH and ionic strength.

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

    Science.gov (United States)

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

    2009-01-01

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

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

    Science.gov (United States)

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

    2010-02-01

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

  10. Comparison of Mooring Loads in Survivability Mode on the Wave Dragon Wave Energy Converter Obtained by a Numerical Model and Experimental Data

    DEFF Research Database (Denmark)

    Parmeggiani, Stefano; Muliawan, Made Jaya; Gao, Zhen

    2012-01-01

    The Wave Dragon Wave Energy Converter is ready to be up-scaled to commercial size. The design and feasibility analysis of a 1.5 MW pre-commercial unit to be deployed at the DanWEC test center in Hanstholm, Denmark, is currently ongoing. With regard to the mooring system, the design has...... in the frequency domain is performed by the software HydroD, which uses WAMIT as core software. The quadratic damping term, accounting for the viscous effect, is determined through an iterative procedure aimed at matching numerical predictions on the mooring tension, derived through time domain coupled analysis......, with experimental results derived from tank tests of a small scale model. Due to the complex geometry of the device, a sensitivity analysis is performed to discuss the influence of the mean position on the quality of the numerical predictions. Good correspondence is achieved between the experimental and numerical...

  11. Enhanced luminescence of rare-earth Tb (III obtained by mixing of Gd (III in a fumarate complex and intra-molecular energy transfer

    Directory of Open Access Journals (Sweden)

    Shah M.D.

    2015-12-01

    Full Text Available Trivalent lanthanide ions display fascinating optical properties. Therefore, the rare-earth complexes of terbium fumarate heptahydrate and GdTb fumarate heptahydrate were grown by using a single gel diffusion technique. The crystals were characterized by different physicochemical techniques of characterization. UV-Vis and photoluminescence spectrophotometric experiments were carried out to study the optical properties of the grown crystals. Under various excitations (339 nm, 350 nm or 368 nm the terbium fumarate complex emitted characteristic (4f-4f green emission of Tb3+ (5D4-7FJ, J = 6, 5, 4 and 3, respectively. Luminescence spectra showed that Gd3+ ions in the mixed complex have not affected the luminescence emission peak positions, but remarkably increased the luminescent intensities of the terbium complex. The energy-transfer mechanism between the ligand and the central Tb3+ ions and from the Gd3+ to the Tb3+ was discussed.

  12. 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.

  13. Calculation of Positron Binding Energies and Electron-Positron Annihilation Rates for Atomic Systems with the Reduced Explicitly Correlated Hartree-Fock Method in the Nuclear-Electronic Orbital Framework.

    Science.gov (United States)

    Brorsen, Kurt R; Pak, Michael V; Hammes-Schiffer, Sharon

    2017-01-19

    Although the binding of a positron to a neutral atom has not been directly observed experimentally, high-level theoretical methods have predicted that a positron will bind to a neutral atom. In the present study, the binding energies of a positron to lithium, sodium, beryllium, and magnesium, as well as the electron-positron annihilation rates for these systems, are calculated using the reduced explicitly correlated Hartree-Fock (RXCHF) method within the nuclear-electronic orbital (NEO) framework. Due to the lack of explicit electron-positron correlation, NEO Hartree-Fock and full configuration interaction calculations with reasonable electronic and positronic basis sets do not predict positron binding to any of these atoms. In contrast, the RXCHF calculations predict positron binding energies and electron-positron annihilation rates in qualitative agreement with previous highly accurate but computationally expensive stochastic variational method calculations. These results illustrate that the RXCHF method can successfully describe the binding of a positron to a neutral species with no dipole moment. Moreover, the RXCHF method will be computationally tractable for calculating positron binding to molecular systems. The RXCHF approach offers a balance of accuracy and computational tractability for studying these types of positronic systems.

  14. comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence.

    Science.gov (United States)

    Hallen, Mark A; Donald, Bruce R

    2016-05-01

    Practical protein design problems require designing sequences with a combination of affinity, stability, and specificity requirements. Multistate protein design algorithms model multiple structural or binding "states" of a protein to address these requirements. comets provides a new level of versatile, efficient, and provable multistate design. It provably returns the minimum with respect to sequence of any desired linear combination of the energies of multiple protein states, subject to constraints on other linear combinations. Thus, it can target nearly any combination of affinity (to one or multiple ligands), specificity, and stability (for multiple states if needed). Empirical calculations on 52 protein design problems showed comets is far more efficient than the previous state of the art for provable multistate design (exhaustive search over sequences). comets can handle a very wide range of protein flexibility and can enumerate a gap-free list of the best constraint-satisfying sequences in order of objective function value.

  15. Valores de energia metabolizável de alguns alimentos obtidos com aves de diferentes idades Metabolizable energy values of feedstuffs obtained from poultry at different ages

    Directory of Open Access Journals (Sweden)

    Heloisa Helena de Carvalho Mello

    2009-05-01

    Full Text Available Foram realizados quatro ensaios de metabolismo com a finalidade de determinar a energia metabolizável aparente (EMA e a energia metabolizável aparente corrigida (EMAn de dez alimentos em aves em diversas idades. Os alimentos testados foram: milho, farelo de soja, sorgo, farelo de trigo, farelo de arroz integral, duas farinhas de penas, duas farinhas de vísceras e plasma sangüíneo. Utilizou-se o método de coleta total de excretas, em delineamento experimental inteiramente casualizado, com 11 tratamentos (dez alimentos e uma ração-referência e seis repetições. No primeiro ensaio, foram utilizados 528 pintos de corte machos de 10 a 17 dias de idade, totalizando oito aves por repetição; no segundo ensaio, 396 frangos de corte machos de 26 a 33 dias de idade, com seis aves por repetição; no terceiro ensaio, 264 frangos de corte machos de 40 a 47 dias de idade, com quatro aves por repetição; e, no quarto ensaio, 132 galos, com duas aves por repetição. A idade das aves influenciou os valores de EMA e EMAn do farelo de soja, do sorgo, do farelo de arroz integral, das farinhas de penas e do plasma sangüíneo, enquanto, para o farelo de trigo, teve efeito apenas sobre a EMAn.Four assays were carried out to determine the apparent metabolizable energy (AME and the corrected apparent nitrogen metabolizable energy (AMEn of ten feeds for poultry at different poultry ages. The feeds studied were: corn grain, soybean meal, ground sorghum, wheat bran, integral rice bran, two kinds of feather meal, two kinds of poultry viscera meal and spray-dried plasma. The method of total excreta collection was used to determine the AME and AMEn values. The broiler chicks were distributed on a completely randomized experimental design, with 11 treatments, six replications, with different number of animals by replication according to the assay. In the first assay, 528 male broiler chicks in the period from 10 to 17 days of age were used, with eight animals

  16. Comparison of the activation energy barrier for succinimide formation from α- and β-aspartic acid residues obtained from density functional theory calculations.

    Science.gov (United States)

    Nakayoshi, Tomoki; Kato, Koichi; Fukuyoshi, Shuichi; Takahashi, Ohgi; Kurimoto, Eiji; Oda, Akifumi

    2018-01-03

    The l-α-Asp residues in peptides or proteins are prone to undergo nonenzymatic reactions to form l-β-Asp, d-α-Asp, and d-β-Asp residues via a succinimide five-membered ring intermediate. From these three types of isomerized aspartic acid residues, particularly d-β-Asp has been widely detected in aging tissue. In this study, we computationally investigated the cyclization of α- and β-Asp residues to form succinimide with dihydrogen phosphate ion as a catalyst (H 2 PO 4 - ). We performed the study using B3LYP/6-31+G(d,p) density functional theory calculations. The comparison of the activation barriers of both residues is discussed. All the calculations were performed using model compounds in which an α/β-Asp-Gly sequence is capped with acetyl and methylamino groups on the N- and C-termini, respectively. Moreover, H 2 PO 4 - catalyzes all the steps of the succinimide formation (cyclization-dehydration) acting as a proton-relay mediator. The calculated activation energy barriers for succinimide formation of α- and β-Asp residues are 26.9 and 26.0kcalmol -1 , respectively. Although it was experimentally confirmed that β-Asp has higher stability than α-Asp, there was no clear difference between the activation barriers. Therefore, the higher stability of β-Asp residue than α-Asp residue may be caused by an entropic effect associated with the succinimide formation. Copyright © 2018 Elsevier B.V. All rights reserved.

  17. Two-particle separation energy trends in the superdeformed well.

    Science.gov (United States)

    Wilson, A N; Korichi, A; Siem, S; Astier, A; Bazzacco, D; Bednarczyk, P; Bergström, M H; Chmel, S; Cullen, D M; Davidson, P M; Görgen, A; Hannachi, F; Hübel, H; Kintz, N; Lauritsen, T; Lopez-Martens, A; Lunardi, S; Naguleswaran, S; Nyakó, B M; Rejmund, M; Schönwasser, G; Schück, C; Sharpey-Schafer, J F; Timar, J; Wadsworth, R; Libert, J

    2010-04-23

    A measurement of the energy and spin of superdeformed states in 190Hg, obtained through the observation of transitions directly linking superdeformed and normal states, expands the number of isotopes in which binding energies at superdeformation are known. Comparison with neighboring nuclei shows that two-proton separation energies are higher in the superdeformed state than in the normal state, despite the lower Coulomb barrier and lower total binding energy. This unexpected result provides a critical test for nuclear models.

  18. Two-particle separation energy trends in the superdeformed well.

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, A. N.; Korichi, A.; Siem, S.; Astier, A.; Bazzacco, D.; Lauristen, T.; Physics; Australian National Univ.; CSNSM-IN2P3-CNRS; Univ. of Oslo; IPN Lyon; INFN

    2010-04-23

    A measurement of the energy and spin of superdeformed states in {sup 190}Hg, obtained through the observation of transitions directly linking superdeformed and normal states, expands the number of isotopes in which binding energies at superdeformation are known. Comparison with neighboring nuclei shows that two-proton separation energies are higher in the superdeformed state than in the normal state, despite the lower Coulomb barrier and lower total binding energy. This unexpected result provides a critical test for nuclear models.

  19. 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.

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

    Science.gov (United States)

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

    2017-03-01

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

  1. D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies

    Science.gov (United States)

    Gaieb, Zied; Liu, Shuai; Gathiaka, Symon; Chiu, Michael; Yang, Huanwang; Shao, Chenghua; Feher, Victoria A.; Walters, W. Patrick; Kuhn, Bernd; Rudolph, Markus G.; Burley, Stephen K.; Gilson, Michael K.; Amaro, Rommie E.

    2018-01-01

    The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures and affinities for the nuclear receptor farnesoid X receptor (FXR), contributed by F. Hoffmann-La Roche. The dataset contained 102 IC50 values, spanning six orders of magnitude, and 36 high-resolution co-crystal structures with representatives of four major ligand classes. Strong global participation was evident, with 49 participants submitting 262 prediction submission packages in total. Procedurally, GC2 mimicked Grand Challenge 2015 (GC2015), with a Stage 1 subchallenge testing ligand pose prediction methods and ranking and scoring methods, and a Stage 2 subchallenge testing only ligand ranking and scoring methods after the release of all blinded co-crystal structures. Two smaller curated sets of 18 and 15 ligands were developed to test alchemical free energy methods. This overview summarizes all aspects of GC2, including the dataset details, challenge procedures, and participant results. We also consider implications for progress in the field, while highlighting methodological areas that merit continued development. Similar to GC2015, the outcome of GC2 underscores the pressing need for methods development in pose prediction, particularly for ligand scaffolds not currently represented in the Protein Data Bank (http://www.pdb.org), and in affinity ranking and scoring of bound ligands.

  2. The effect of the addition of the elements Ni, Zn and Co in a composite AlTiO2 obtained by high-energy milling and sintering process

    International Nuclear Information System (INIS)

    Carvalho, C.O. de; Coelho, R.E.; Conrado, L.C.; Nascimento, C.S.; Teixeira, C.A.; Mendonca, E.S.

    2016-01-01

    The present work use aluminum scrap with addition of TiO 2 , Ni, Zn or Co to preparation and characterization of nanocomposites. The aluminum were cut and subjected to high energy milling for 2 hours at 1200rpm. The obtained powder was added to TiO 2 , Ni, Zn or Co in a nominal composition 97Al-2TiO 2 -1X (X = Ni, Zn or Co) (weight %) and again, the mixture was subjected to milling for 1 hour at 1000rpm. Grinding powders were hot pressed in the closed die and then removed; the compressed were sintered at 950°C in a tubular furnace N 2 passing atmosphere. The samples obtained were characterized by Scanning Electron Microscopy (SEM), Energy Dispersive Spectroscopy (EDS) and X-ray Diffraction (XRD). The results of SEM images showed a very refined microstructure and an aluminum matrix without porosity. (author)

  3. 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.

  4. Relating the shape of protein binding sites to binding affinity profiles: is there an association?

    Directory of Open Access Journals (Sweden)

    Bitter István

    2010-10-01

    Full Text Available Abstract Background Various pattern-based methods exist that use in vitro or in silico affinity profiles for classification and functional examination of proteins. Nevertheless, the connection between the protein affinity profiles and the structural characteristics of the binding sites is still unclear. Our aim was to investigate the association between virtual drug screening results (calculated binding free energy values and the geometry of protein binding sites. Molecular Affinity Fingerprints (MAFs were determined for 154 proteins based on their molecular docking energy results for 1,255 FDA-approved drugs. Protein binding site geometries were characterized by 420 PocketPicker descriptors. The basic underlying component structure of MAFs and binding site geometries, respectively, were examined by principal component analysis; association between principal components extracted from these two sets of variables was then investigated by canonical correlation and redundancy analyses. Results PCA analysis of the MAF variables provided 30 factors which explained 71.4% of the total variance of the energy values while 13 factors were obtained from the PocketPicker descriptors which cumulatively explained 94.1% of the total variance. Canonical correlation analysis resulted in 3 statistically significant canonical factor pairs with correlation values of 0.87, 0.84 and 0.77, respectively. Redundancy analysis indicated that PocketPicker descriptor factors explain 6.9% of the variance of the MAF factor set while MAF factors explain 15.9% of the total variance of PocketPicker descriptor factors. Based on the salient structures of the factor pairs, we identified a clear-cut association between the shape and bulkiness of the drug molecules and the protein binding site descriptors. Conclusions This is the first study to investigate complex multivariate associations between affinity profiles and the geometric properties of protein binding sites. We found that

  5. Study of the sintering behavior of fine, ultrafine and nanocrystalline WC-CO mixtures obtained by high energy milling; Estudio del comportamiento durante la sinterizacion de mezclas WC-Co finas, ultrafinas y nanocristalinas obtenidas por molienda de alta energia

    Energy Technology Data Exchange (ETDEWEB)

    Salvador, M. D.; Bonache, V.; Amigo, V.; Busquets, D.

    2008-07-01

    In this work the sintering behaviour of fine, ultrafine and nanocrystalline WC-12Co mixtures obtained by high energy milling, as well commercial nano powders, have been studied, in order to evaluate the effect of the particle size and the powder processing, in the densification, microstructural development and mechanical properties of the final product. The consolidation of the mixtures has been made by uniaxial pressing and sintering in vacuum, and by hot isostatic pressing. The sintered materials have been evaluated by measures of density, hardness and indentation fracture toughness, and micro structurally characterized by optical microscopy and scanning and transmission electronic microscopy (SEM and TEM). The results show the improvements in resistant behaviour of the materials obtained from nanocrystalline powders, in spite of the grain growth experienced during the sintering. The best results were obtained for the milling nanocrystalline material, which presents values of hardness higher than 180 HV. (Author) 46 refs.

  6. Universal dependence of hydrogen oxidation and evolution reaction activity of platinum-group metals on pH and hydrogen binding energy.

    Science.gov (United States)

    Zheng, Jie; Sheng, Wenchao; Zhuang, Zhongbin; Xu, Bingjun; Yan, Yushan

    2016-03-01

    Understanding how pH affects the activity of hydrogen oxidation reaction (HOR) and hydrogen evolution reaction (HER) is key to developing active, stable, and affordable HOR/HER catalysts for hydroxide exchange membrane fuel cells and electrolyzers. A common linear correlation between hydrogen binding energy (HBE) and pH is observed for four supported platinum-group metal catalysts (Pt/C, Ir/C, Pd/C, and Rh/C) over a broad pH range (0 to 13), suggesting that the pH dependence of HBE is metal-independent. A universal correlation between exchange current density and HBE is also observed on the four metals, indicating that they may share the same elementary steps and rate-determining steps and that the HBE is the dominant descriptor for HOR/HER activities. The onset potential of CO stripping on the four metals decreases with pH, indicating a stronger OH adsorption, which provides evidence against the promoting effect of adsorbed OH on HOR/HER.

  7. Obtaining of inulin acetate

    OpenAIRE

    Khusenov, Arslonnazar; Rakhmanberdiev, Gappar; Rakhimov, Dilshod; Khalikov, Muzaffar

    2014-01-01

    In the article first obtained inulin ester inulin acetate, by etherification of inulin with acetic anhydride has been exposed. Obtained product has been studied using elementary analysis and IR spectroscopy.

  8. Solute-vacancy binding in aluminum

    International Nuclear Information System (INIS)

    Wolverton, C.

    2007-01-01

    Previous efforts to understand solute-vacancy binding in aluminum alloys have been hampered by a scarcity of reliable, quantitative experimental measurements. Here, we report a large database of solute-vacancy binding energies determined from first-principles density functional calculations. The calculated binding energies agree well with accurate measurements where available, and provide an accurate predictor of solute-vacancy binding in other systems. We find: (i) some common solutes in commercial Al alloys (e.g., Cu and Mg) possess either very weak (Cu), or even repulsive (Mg), binding energies. Hence, we assert that some previously reported large binding energies for these solutes are erroneous. (ii) Large binding energies are found for Sn, Cd and In, confirming the proposed mechanism for the reduced natural aging in Al-Cu alloys containing microalloying additions of these solutes. (iii) In addition, we predict that similar reduction in natural aging should occur with additions of Si, Ge and Au. (iv) Even larger binding energies are found for other solutes (e.g., Pb, Bi, Sr, Ba), but these solutes possess essentially no solubility in Al. (v) We have explored the physical effects controlling solute-vacancy binding in Al. We find that there is a strong correlation between binding energy and solute size, with larger solute atoms possessing a stronger binding with vacancies. (vi) Most transition-metal 3d solutes do not bind strongly with vacancies, and some are even energetically strongly repelled from vacancies, particularly for the early 3d solutes, Ti and V

  9. Sources of high energy particles obtained with intense lasers for applications in nuclear physics; Sources de particules de hautes energies obtenues avec des lasers intenses pour applications a la physique nucleaire

    Energy Technology Data Exchange (ETDEWEB)

    Gerbaux, M

    2007-12-15

    This experimental study concerns the characterization of the beams of electrons and protons with energies above a few MeV produced in the interaction of an ultra-intense (10{sup 19} W/cm{sup 2}) laser beam with a 10 {mu}m thick solid target. This work was issued in the framework to use these beams in nuclear physics experiments. It was hence necessary to know quantitatively the characteristics of these particle beams. Laser accelerated particle beams have very different characteristics from conventional ones produced in accelerators, especially on account of their transience and intensity as well as their continuous energy distribution. These properties make their characterization complex and led us to develop methods combining measurements with diodes spectrometers, radiochromic films, nuclear activation of chosen materials and Monte-Carlo simulations. These methods have been employed on 2 different facilities but with similar characteristics for the study of the electron beams as a function of the target material. The angular aperture of the electron beam appears to be strongly dependent on the atomic number of the target. An experiment was also carried out to characterize at each shot the proton beam produced with the LULI 100 TW laser facility. This experiment also proved the possibility to induce nuclear reactions in plasma and to measure quantitatively the reaction rate in order to scale an experiment on the perturbation of the nucleus electronic-shells coupling via a strong electromagnetic field due to the laser. (author)

  10. Windmills: selection method and results obtained by the Renewable Energy Center of UNESP - Guaratingueta Campus, Sao Paulo state, Brazil; Cata-vento: metodo de selecao e resultados obtidos pelo Centro de Energias Renovaveis da UNESP - Campus Guaratingueta

    Energy Technology Data Exchange (ETDEWEB)

    Moura, Luis Fernando Silva; Souza, Teofilo Miguel de [Universidade Estadual Paulista (UNESP), Guaratingueta, SP (Brazil). Centro de Energias Renovaveis], e-mail: teofilo@feg.unesp.br, e-mail: lfernandosm@uol.com.br

    2004-07-01

    Windmills are always a good option to promote irrigate in areas with adequate potential wind. Its correct selection can guarantee the enough water supply with minimum cost. Since April 2004 the Renewable Energy Center of UNESP - Campus Guaratingueta' has tested a commercial windmill with 18 blades rotor and 3,4 diameter meters, that in a area with approximately 3 m/s average wind speed, has been obtained a average daily 1500 water liters. This volume is enough to supply a small country state, however, it could be get with a smaller capacity machine, if this worked properly. (author)

  11. Energy

    International Nuclear Information System (INIS)

    Meister, F.; Ott, F.

    2002-01-01

    This chapter gives an overview of the current energy economy in Austria. The Austrian political aims of sustainable development and climate protection imply a reorientation of the Austrian energy policy as a whole. Energy consumption trends (1993-1998), final energy consumption by energy carrier (indexed data 1993-1999), comparative analysis of useful energy demand (1993 and 1999) and final energy consumption of renewable energy sources by sector (1996-1999) in Austria are given. The necessary measures to be taken in order to reduce the energy demand and increased the use of renewable energy are briefly mentioned. Figs. 5. (nevyjel)

  12. 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.)

  13. Investigation of three flavonoids binding to bovine serum albumin using molecular fluorescence technique

    International Nuclear Information System (INIS)

    Bi Shuyun; Yan Lili; Pang Bo; Wang Yu

    2012-01-01

    The three flavonoids including naringenin, hesperetin and apigenin binding to bovine serum albumin (BSA) at pH 7.4 was studied by fluorescence quenching, synchronous fluorescence and UV-vis absorption spectroscopic techniques. The results obtained revealed that naringenin, hesperetin and apigenin strongly quenched the intrinsic fluorescence of BSA. The Stern-Volmer curves suggested that these quenching processes were all static quenching processes. At 291 K, the value and the order of the binding constant were K A n aringenin) =4.08x10 4 A(hesperetin) =5.40x10 4 ∼K A(apigenin) =5.32x10 4 L mol -1 . The main binding force between the flavonoid and BSA was hydrophobic and electrostatic force. According to the Foerster theory of non-radiation energy transfer, the binding distances (r 0 ) were obtained as 3.36, 3.47 and 3.30 nm for naringenin-BSA, hesperetin-BSA and apigenin-BSA, respectively. The effect of some common ions such as Fe 3+ , Cu 2+ , Mg 2+ , Mn 2+ , Zn 2+ and Ca 2+ on the binding was also studied in detail. The competition binding was also performed. The apparent binding constant (K' A ) obtained suggested that one flavonoid had an obvious effect on the binding of another flavonoid to protein when they coexisted in BSA solution. - Highlights: → Quenchings of BSA fluorescence by the flavonoids was all static quenchings. → Synchronous fluorescence was applied to study the structural change of BSA. → Binding constant, binding site and binding force were determined. → Competition binding experiments were performed. → One flavonoid had an obvious effect on the binding of another one to BSA.

  14. Reference binding energies of transition metal carbides by core-level x-ray photoelectron spectroscopy free from Ar+ etching artefacts

    Science.gov (United States)

    Greczynski, G.; Primetzhofer, D.; Hultman, L.

    2018-04-01

    We report x-ray photoelectron spectroscopy (XPS) core level binding energies (BE's) for the widely-applicable groups IVb-VIb transition metal carbides (TMCs) TiC, VC, CrC, ZrC, NbC, MoC, HfC, TaC, and WC. Thin film samples are grown in the same deposition system, by dc magnetron co-sputtering from graphite and respective elemental metal targets in Ar atmosphere. To remove surface contaminations resulting from exposure to air during sample transfer from the growth chamber into the XPS system, layers are either (i) Ar+ ion-etched or (ii) UHV-annealed in situ prior to XPS analyses. High resolution XPS spectra reveal that even gentle etching affects the shape of core level signals, as well as BE values, which are systematically offset by 0.2-0.5 eV towards lower BE. These destructive effects of Ar+ ion etch become more pronounced with increasing the metal atom mass due to an increasing carbon-to-metal sputter yield ratio. Systematic analysis reveals that for each row in the periodic table (3d, 4d, and 5d) C 1s BE increases from left to right indicative of a decreased charge transfer from TM to C atoms, hence bond weakening. Moreover, C 1s BE decreases linearly with increasing carbide/metal melting point ratio. Spectra reported here, acquired from a consistent set of samples in the same instrument, should serve as a reference for true deconvolution of complex XPS cases, including multinary carbides, nitrides, and carbonitrides.

  15. Localization-enhanced biexciton binding in semiconductors

    DEFF Research Database (Denmark)

    Langbein, Wolfgang Werner; Hvam, Jørn Märcher

    1999-01-01

    The influence of excitonic localization on the binding energy of biexcitons is investigated for quasi-three-dimensional and quasi-two-dimensional AlxGa1-xAs structures. An increase of the biexciton binding energy is observed for localization energies comparable to or larger than the free biexcito...

  16. Effect of peripartum dietary energy supplementation on thyroid hormones, insulin-like growth factor-i and its binding proteins in early lactation dairy cows

    Directory of Open Access Journals (Sweden)

    Kirovski Danijela

    2012-01-01

    Full Text Available The objective of this study was to examine the effect of dietary energy supplementation on hormones that are considered to be the main signals of a shift in energy balance around parturition. Sixty dry cows, 15 days before calving, were chosen and divided into two eaqual groups: control and experimental (GLY. Both groups were fed a standard ration balanced in accordance to the stage of the productivereproductive cycle. Additionally, each cow in the GLY group was given glycerol based dietary energy supplementation (250 mL daily during the dry and 300 mL daily during the lactation period, which provided additional 9.30 MJ NEL during the dry and 13.95 MJ NEL during the early lactation period. Milk production was measured on days 30 and 60 of lactation and milk production was significantly higher in GLY compared to control group at day 60 of lactation (p<0.05. Service period and insemination index were used as reproductive outcome parameters. Average service period in the control group was significantly longer than in the GLY group (p<0.05. Average insemination index in the control group was not significantly different than the index obtained for the GLY group. Blood samples were taken before the begining of the experiment (15 days before parturition, and at days 7, 30 and 60 of lactation. Concentrations of thyroid hormones, IGF-I, relative abundance of IGFBP-2, IGFBP-3 and IGFBP-4, concentrations of total protein and albumin in the blood were measured. Results showed that at days 7 and 30 after parturition, T4 concentrations were significantly higher (p<0.001, respectively in GLY than in the control group, while T3 concentrations were significantly higher in GLY group only at day 7 after parturition (p<0.001. IGF-I concentrations and IGFBP-3 abundance were significantly higher in the GLY compared to the control group in all three examined postpartum periods. IGFBP-2 and IGFBP-4 concentrations were higher in GLY compared to the control group in all

  17. Discrete persistent-chain model for protein binding on DNA.

    Science.gov (United States)

    Lam, Pui-Man; Zhen, Yi

    2011-04-01

    We describe and solve a discrete persistent-chain model of protein binding on DNA, involving an extra σ(i) at a site i of the DNA. This variable takes the value 1 or 0, depending on whether or not the site is occupied by a protein. In addition, if the site is occupied by a protein, there is an extra energy cost ɛ. For a small force, we obtain analytic expressions for the force-extension curve and the fraction of bound protein on the DNA. For higher forces, the model can be solved numerically to obtain force-extension curves and the average fraction of bound proteins as a function of applied force. Our model can be used to analyze experimental force-extension curves of protein binding on DNA, and hence deduce the number of bound proteins in the case of nonspecific binding. ©2011 American Physical Society

  18. Unbinding pathway energy of glyphosate from the EPSPs enzyme binding site characterized by Steered Molecular Dynamics and Potential of Mean Force.

    Science.gov (United States)

    Ferreira, Moacir F; Franca, Eduardo F; Leite, Fábio L

    2017-03-01

    The quantification of herbicides in the environment, like glyphosate, is extremely important to prevent contamination. Nanobiosensors stands out in the quantization process, because of the high selectivity, sensitivity and short response time of the method. In order to emulate the detection of glyphosate using a specific nanobiossensor through an Atomic Force Microscope (AFM), this work carried out Steered Molecular Dynamics simulations (SMD) in which the herbicide was unbinded from the active site of the enzyme 5- enolpyruvylshikimate 3 phosphate synthase (EPSPS) along three different directions.After the simulations, Potential of Mean Force calculations were carried, from a cumulant expansion of Jarzynski's equation to obtain the profile of free energy of interaction between the herbicide and the active site of the enzyme in the presence of shikimate-3 substrate phosphate (S3P). The set of values for external work, had a Gaussian distribution. The PMF values ranged according to the directions of the unbindong pahway of each simulation, displaying energy values of 10.7, 14.7 and 19.5KJmol -1 . The results provide a theoretical support in order to assist the construction of a specific nanobiossensor to quantify the glyphosate herbicide. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Characterization of the ligand binding of PGRP-L in half-smooth tongue sole (Cynoglossus semilaevis by molecular dynamics and free energy calculation

    Directory of Open Access Journals (Sweden)

    Zisheng Wang

    2018-01-01

    Conclusions: The 3-D structure of csPGRP-L possessed typical PGRP structure and might selectively bind both types of MTP- and MPP-PGNs, which provided useful insights to understanding the functions of fish PGRPs.

  20. Energy

    International Nuclear Information System (INIS)

    Bobin, J.L.

    1996-01-01

    Object of sciences and technologies, energy plays a major part in economics and relations between nations. Jean-Louis Bobin, physicist, analyses the relations between man and energy and wonders about fears that delivers nowadays technologies bound to nuclear energy and about the fear of a possible shortage of energy resources. (N.C.). 17 refs., 14 figs., 2 tabs

  1. Utilization of aluminum to obtaining a duplex type stainless steel using high energy ball milling; Obtencao de um aco inoxidavel de estrutura duplex do sistema FeMnAl processado por moagem de alta energia

    Energy Technology Data Exchange (ETDEWEB)

    Pavlak, I.E.; Cintho, O.M., E-mail: eng.igorpavlak@yahoo.com.b [Universidade Estadual de Ponta Grossa (UEPG), PR (Brazil); Capocchi, J.D.T. [Universidade de Sao Paulo (USP), SP (Brazil)

    2010-07-01

    The obtaining of stainless steel using aluminum in its composition - FeMnAl system, has been researches subject since the sixties, by good mechanical properties and resistance to oxidation presented, when compared with conventional FeNiCr stainless steel system. In another point, the aluminum and manganese are low cost then traditional elements. This work, metallic powders of iron, manganese and pure aluminum, were processed in a Spex type high-energy ball mill in nitrogen atmosphere. The milling products were compressed into pastille form and sintered under inert atmosphere. The final products were characterized by optical and electronic microscopy and microhardness test. The metallographic analysis shows a typical austenite and ferrite duplex type microstructure. The presence of these phases was confirmed according X ray diffraction analysis. (author)

  2. Binding energies of the 1gsub(9/2) and 1hsub(11/2) neutron and average two-body effective interactions anti Vsub(pn) and anti Vsub(nn)

    International Nuclear Information System (INIS)

    Sakai, M.

    1980-01-01

    The binding energies of the single particle or hole orbitals of the 1gsub(9/2) and 1hsub(11/2) neutron shells are given as a simple linear function of the active valence proton and neutron numbers. This function is derived theoretically by the assumption of constant two-body effective interactions anti Vsub(pn) and anti Vsub(nn) in the relevant proton and neutron shell spaces. These values, appearing in the function as the coefficients of the proton and neutron numbers, are determined from the experimental binding energies by a least-squares fit. The good quality of fit between the experimental and fitted binding energies implies the plausibility of the formula and the assumption. The determined anti Vsub(pn) and anti Vsub(nn) have absolute values and signs consistent with those in the literature. The effective interactions in the case of the 1gsub(9/2) hole is found to decrease with increasing mass number. (orig.)

  3. Energy

    CERN Document Server

    Foland, Andrew Dean

    2007-01-01

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

  4. Multiple protonation equilibria in electrostatics of protein-protein binding.

    Science.gov (United States)

    Piłat, Zofia; Antosiewicz, Jan M

    2008-11-27

    All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual "polarization" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics

  5. Binding of two-electron metastable states in semiconductor quantum dots under a magnetic field

    Science.gov (United States)

    Garagiola, Mariano; Pont, Federico M.; Osenda, Omar

    2018-04-01

    Applying a strong enough magnetic field results in the binding of few-electron resonant states. The mechanism was proposed many years ago but its verification in laboratory conditions is far more recent. In this work we study the binding of two-electron resonant states. The electrons are confined in a cylindrical quantum dot which is embedded in a semiconductor wire. The geometry considered is similar to the one used in actual experimental setups. The low-energy two-electron spectrum is calculated numerically from an effective-mass approximation Hamiltonian modelling the system. Methods for binding threshold calculations in systems with one and two electrons are thoroughly studied; in particular, we use quantum information quantities to assess when the strong lateral confinement approximation can be used to obtain reliable low-energy spectra. For simplicity, only cases without bound states in the absence of an external field are considered. Under these conditions, the binding threshold for the one-electron case is given by the lowest Landau energy level. Moreover, the energy of the one-electron bounded resonance can be used to obtain the two-electron binding threshold. It is shown that for realistic values of the two-electron model parameters it is feasible to bind resonances with field strengths of a few tens of tesla.

  6. Acyl-coenzyme A binding protein (ACBP)

    DEFF Research Database (Denmark)

    Kragelund, B B; Knudsen, J; Poulsen, F M

    1999-01-01

    Acyl-coenzyme A binding proteins are known from a large group of eukaryote species and to bind a long chain length acyl-CoA ester with very high affinity. Detailed biochemical mapping of ligand binding properties has been obtained as well as in-depth structural studies on the bovine apo-protein a...

  7. Probing ionization potential, electron affinity and self-energy effect on the spectral shape and exciton binding energy of quantum liquid water with self-consistent many-body perturbation theory and Bethe-Salpeter equation.

    Science.gov (United States)

    Ziaei, Vafa; Bredow, Thomas

    2018-04-18

    An accurate theoretical prediction of ionization potential (IP) and electron affinity (EA) is key for understanding of complex photochemical processes in aqueous environments. There have been numerous efforts in literature to accurately predict IP and EA of liquid water, however with often conflicting results depending on the level of theory and the underlying water structures. In a recent study based on hybrid-non-self-consistent many-body perturbation theory (MBPT) Gaiduk et al. [Nature Communications {\\bf 9}, 247 (2018)] predicted an IP of 10.2 eV and EA of 0.2 eV, resulting in an electronic band gap (i.e. electronic gap (IP-EA) as measured by photoelectron spectroscopy) of about 10 eV, redefining the widely cited experimental gap of 8.7 eV in literature. In the present work, we show that GW self-consistency and an implicit vertex correction in MBPT considerably affect recently reported EA value by Gaiduk et al. \\cite{Gaiduk_affinity} by about 1 eV. Furthermore, the choice of pseudo-potential is critical for an accurate determination of the absolute band positions. Consequently, the self-consistent GW approach with an implicit vertex correction based on projector augmented wave (PAW) method on top of quantum water structures predicts an IP of 10.2, an EA of 1.1, a fundamental gap of 9.1 eV and an exciton binding (Eb) energy of 0.9 eV for the first absorption band of liquid water via Bethe-Salpeter equation (BSE). Only within such a self-consistent approach a \\textit{simultanously} accurate prediction of IP, EA, Eg, Eb is possible. © 2018 IOP Publishing Ltd.

  8. Molecular dynamics study of zinc binding to cysteines in a peptide mimic of the alcohol dehydrogenase structural zinc site.

    Science.gov (United States)

    Brandt, Erik G; Hellgren, Mikko; Brinck, Tore; Bergman, Tomas; Edholm, Olle

    2009-02-14

    The binding of zinc (Zn) ions to proteins is important for many cellular events. The theoretical and computational description of this binding (as well as that of other transition metals) is a challenging task. In this paper the binding of the Zn ion to four cysteine residues in the structural site of horse liver alcohol dehydrogenase (HLADH) is studied using a synthetic peptide mimic of this site. The study includes experimental measurements of binding constants, classical free energy calculations from molecular dynamics (MD) simulations and quantum mechanical (QM) electron structure calculations. The classical MD results account for interactions at the molecular level and reproduce the absolute binding energy and the hydration free energy of the Zn ion with an accuracy of about 10%. This is insufficient to obtain correct free energy differences. QM correction terms were calculated from density functional theory (DFT) on small clusters of atoms to include electronic polarisation of the closest waters and covalent contributions to the Zn-S coordination bond. This results in reasonably good agreement with the experimentally measured binding constants and Zn ion hydration free energies in agreement with published experimental values. The study also includes the replacement of one cysteine residue to an alanine. Simulations as well as experiments showed only a small effect of this upon the binding free energy. A detailed analysis indicate that the sulfur is replaced by three water molecules, thereby changing the coordination number of Zn from four (as in the original peptide) to six (as in water).

  9. Geopolymer obtained from coal ash

    International Nuclear Information System (INIS)

    Conte, V.; Bissari, E.S.; Uggioni, E.; Bernardin, A.M.

    2011-01-01

    Geopolymers are three-dimensional alumino silicates that can be rapidly formed at low temperature from naturally occurring aluminosilicates with a structure similar to zeolites. In this work coal ash (Tractebel Energy) was used as source of aluminosilicate according a full factorial design in eight formulations with three factors (hydroxide type and concentration and temperature) and two-levels. The ash was dried and hydroxide was added according type and concentration. The geopolymer was poured into cylindrical molds, cured (14 days) and subjected to compression test. The coal ash from power plants belongs to the Si-Al system and thus can easily form geopolymers. The compression tests showed that it is possible to obtain samples with strength comparable to conventional Portland cement. As a result, temperature and molarity are the main factors affecting the compressive strength of the obtained geopolymer. (author)

  10. Energy

    CERN Document Server

    Robertson, William C

    2002-01-01

    Confounded by kinetic energy? Suspect that teaching about simple machines isn t really so simple? Exasperated by electricity? If you fear the study of energy is beyond you, this entertaining book will do more than introduce you to the topic. It will help you actually understand it. At the book s heart are easy-to-grasp explanations of energy basics work, kinetic energy, potential energy, and the transformation of energy and energy as it relates to simple machines, heat energy, temperature, and heat transfer. Irreverent author Bill Robertson suggests activities that bring the basic concepts of energy to life with common household objects. Each chapter ends with a summary and an applications section that uses practical examples such as roller coasters and home heating systems to explain energy transformations and convection cells. The final chapter brings together key concepts in an easy-to-grasp explanation of how electricity is generated. Energy is the second book in the Stop Faking It! series published by NS...

  11. Structural parameterization of the binding enthalpy of small ligands.

    Science.gov (United States)

    Luque, Irene; Freire, Ernesto

    2002-11-01

    A major goal in ligand and drug design is the optimization of the binding affinity of selected lead molecules. However, the binding affinity is defined by the free energy of binding, which, in turn, is determined by the enthalpy and entropy changes. Because the binding enthalpy is the term that predominantly reflects the strength of the interactions of the ligand with its target relative to those with the solvent, it is desirable to develop ways of predicting enthalpy changes from structural considerations. The application of structure/enthalpy correlations derived from protein stability data has yielded inconsistent results when applied to small ligands of pharmaceutical interest (MW the enthalpy associated with any possible conformational change in the protein or ligand upon binding; and, (3) the enthalpy associated with protonation/deprotonation events, if present. As in the case of protein stability, the intrinsic binding enthalpy scales with changes in solvent accessible surface areas. However, an accurate estimation of the intrinsic binding enthalpy requires explicit consideration of long-lived water molecules at the binding interface. The best statistical structure/enthalpy correlation is obtained when buried water molecules within 5-7 A of the ligand are included in the calculations. For all seven protein systems considered (HIV-1 protease, dihydrodipicolinate reductase, Rnase T1, streptavidin, pp60c-Src SH2 domain, Hsp90 molecular chaperone, and bovine beta-trypsin) the binding enthalpy of 25 small molecular weight peptide and nonpeptide ligands can be accounted for with a standard error of +/-0.3 kcal x mol(-1). Copyright 2002 Wiley-Liss, Inc.

  12. Energies

    International Nuclear Information System (INIS)

    2003-01-01

    In the framework of the National Debate on the energies in a context of a sustainable development some associations for the environment organized a debate on the nuclear interest facing the renewable energies. The first part presents the nuclear energy as a possible solution to fight against the greenhouse effect and the associated problem of the wastes management. The second part gives information on the solar energy and the possibilities of heat and electric power production. A presentation of the FEE (French wind power association) on the situation and the development of the wind power in France, is also provided. (A.L.B.)

  13. The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations

    Science.gov (United States)

    2011-01-01

    The adsorption of Ag, Au, and Pd atoms on benzene, coronene, and graphene has been studied using post Hartree–Fock wave function theory (CCSD(T), MP2) and density functional theory (M06-2X, DFT-D3, PBE, vdW-DF) methods. The CCSD(T) benchmark binding energies for benzene–M (M = Pd, Au, Ag) complexes are 19.7, 4.2, and 2.3 kcal/mol, respectively. We found that the nature of binding of the three metals is different: While silver binds predominantly through dispersion interactions, the binding of palladium has a covalent character, and the binding of gold involves a subtle combination of charge transfer and dispersion interactions as well as relativistic effects. We demonstrate that the CCSD(T) benchmark binding energies for benzene–M complexes can be reproduced in plane-wave density functional theory calculations by including a fraction of the exact exchange and a nonempirical van der Waals correction (EE+vdW). Applying the EE+vdW method, we obtained binding energies for the graphene–M (M = Pd, Au, Ag) complexes of 17.4, 5.6, and 4.3 kcal/mol, respectively. The trends in binding energies found for the benzene–M complexes correspond to those in coronene and graphene complexes. DFT methods that use empirical corrections to account for the effects of vdW interactions significantly overestimate binding energies in some of the studied systems. PMID:22076121

  14. Analysis of the generation of electric energy through the use of biogas obtained from sanitary fillings in Mexico; Analisis de la generacion de energia electrica a traves de biogas procedente de rellenos sanitarios en Mexico

    Energy Technology Data Exchange (ETDEWEB)

    Cerda Sauvage, Tania Kalinka [Facultad de Ingenieria, Universidad Nacional Autonoma de Mexico, Mexico, D.F. (Mexico)

    2004-06-15

    Through this work a theoretical analysis conducted for the use of biogas obtained from sanitary landfills for the generation of electrical energy is presented, as well as the evaluation of the main elements that limit or favor the development of this technology in our country. In the introductory part of this work are presented some causes considered have favored the development of technologies as the one proposed here. In the first part it is exposed what the biogas is and what conditions are necessary for its production, which explains the production of biogas in the sanitary landfills, in addition, describes the distribution of the solid residues that give raise to the present situation of the sanitary landfills and the biogas production process in these. The work continues with a description of the electrical energy generation process through the gas originated in sanitary landfills, indicating the necessary conditions in order that the filling complies with its basic functions; following our process until obtaining the final item, electrical energy. For the description of the process and to analyze some factors that take part, it is advisable to include the main aspects of a plant located in Monterrey that occupies this technology. This project shows project shows off in a tangible form the barriers that this technology faces, as well as its main advantages and disadvantages. Are exposed the limiting factors of this technology in technological, economic, political and social aspects, the barriers that can and must overcome as well as the reasons that justify the effort to overcome them. Finally are presented the conclusions it arrives, as well as the commentaries and suggestions in respect to the subject. [Spanish] A traves de este trabajo se expone un analisis teorico efectuado al uso de biogas extraido de rellenos sanitarios para la generacion de energia electrica, asi como evaluar los principales elementos que limitan o favorecen el desarrollo de esta

  15. Structural insights into the binding mode and conformational changes of BSA induced by bixin and crocin.

    Science.gov (United States)

    Mohan, Sankari; Hemachandran, Hridya; Sneha, P; George Priya Doss, C; Godwin Christopher, J; Jayaraman, Gurunathan; Ramamoorthy, Siva

    2017-06-30

    Bixin and crocin are natural apocarotenoids utilized as food colorants and additives in food industries worldwide. For safety assessment, it is necessary to understand the biological interaction of food colorants. In our present study, we report the interaction of two apocarotenoids with bovine serum albumin (BSA) at physiological pH using spectroscopic techniques and in silico tools. The binding constant and the mode of binding sites have been studied. The enthalpic and entropic contribution to the intermolecular binding event was analyzed and it was found that the contribution of hydrogen bonding and hydrophobic interactions was dominant. The adverse temperature dependence in the unusual static quenching is found to be a reasonable consequence of the large activation energy requirement in the binding process, which is required to overcome the fundamental block and is a direct result of the unique microstructure of the binding sites. To confirm the experimental analysis, we investigated the binding patterns using different in silico tools. A combination of molecular docking, molecular dynamics, and toxicity analysis was performed, and the obtained results revealed that both the apocarotenoids had high binding affinity with a binding energy of -5.44 and -5.93 kcal/mol for bixin and crocin, respectively, with no toxic effects and are in accordance with our experimental analysis. The results directly revealed the flexibility of the protein toward bixin and crocin which has a great impact on the interaction. Thus bixin and crocin can guardedly be used as food colorants in food industries.

  16. Binding of cyclic carboxylates to octa-acid deep-cavity cavitand

    Science.gov (United States)

    Gibb, Corinne L. D.; Gibb, Bruce C.

    2014-04-01

    As part of the fourth statistical assessment of modeling of proteins and ligands (sampl.eyesopen.com) prediction challenge, the strength of association of nine guests ( 1- 9) binding to octa-acid host was determined by a combination of 1H NMR and isothermal titration calorimetry. Association constants in sodium tetraborate buffered (pH 9.2) aqueous solution ranged from 5.39 × 102 M-1 in the case of benzoate 1, up to 3.82 × 105 M-1 for trans-4-methylcyclohexanoate 7. Overall, the free energy difference between the free energies of complexation of these weakest and strongest binding guests was ΔΔG° = 3.88 kcal mol-1. Based on a multitude of previous studies, the anticipated order of strength of binding was close to that which was actually obtained. However, the binding of guest 3 (4-ethylbenzoate) was considerably stronger than initially estimated.

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

    NARCIS (Netherlands)

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

    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,

  18. Protein binding of psychotropic agents

    International Nuclear Information System (INIS)

    Hassan, H.A.

    1990-01-01

    Based upon fluorescence measurements, protein binding of some psychotropic agents (chlorpromazine, promethazine, and trifluoperazine) to human IgG and HSA was studied in aqueous cacodylate buffer, PH7. The interaction parameters determined from emission quenching of the proteins. The interaction parameters determined include the equilibrium constant (K), calculated from equations derived by Borazan and coworkers, the number of binding sites (n) available to the monomer molecules on a single protein molecule. The results revealed a high level of affinity, as reflected by high values of K, and the existence of specific binding sites, since a limited number of n values are obtained. 39 tabs.; 37 figs.; 83 refs

  19. Mapping of barley alpha-amylases and outer subsite mutants reveals dynamic high-affinity subsites and barriers in the long substrate binding cleft

    DEFF Research Database (Denmark)

    Kandra, L.; Abou Hachem, Maher; Gyemant, G.

    2006-01-01

    Subsite affinity maps of long substrate binding clefts in barley alpha-amylases, obtained using a series of maltooligosaccharides of degree of polymerization of 3-12, revealed unfavorable binding energies at the internal subsites -3 and -5 and at subsites -8 and +3/+4 defining these subsites...... as binding barriers. Barley a-amylase I mutants Y105A and T212Y at subsite -6 and +4 resulted in release or anchoring of bound substrate, thus modifying the affinities of other high-affinity subsites (-2 and +2) and barriers. The double mutant Y105A-T212Y displayed a hybrid subsite affinity profile......, converting barriers to binding areas. These findings highlight the dynamic binding energy distribution and the versatility of long maltooligosaccharide derivatives in mapping extended binding clefts in a-amylases....

  20. Roles of phosphorylation and helix propensity in the binding of the KIX domain of CREB-binding protein by constitutive (c-Myb) and inducible (CREB) activators.

    Science.gov (United States)

    Zor, Tsaffrir; Mayr, Bernhard M; Dyson, H Jane; Montminy, Marc R; Wright, Peter E

    2002-11-01

    cAMP-response element-binding protein (CREB)-binding protein (CBP) is a general transcriptional co-activator that mediates interactions between transcription factors and the basal transcription machinery. To obtain insights into the mechanism by which the KIX domain of CBP can recognize the transactivation domains of many different transcription factors, we have used NMR and biochemical analyses to study the interactions of KIX with the transactivation domain from the constitutive activator c-Myb and with the kinase-inducible transactivation domain (KID) from CREB. NMR chemical shift mapping shows that both activation domains bind to the same surface of KIX. In the unbound state, both the phosphorylated KID and c-Myb activation domains are only partly structured, and binding to KIX is coupled with folding to form an amphipathic helix. Helix-destabilizing mutations significantly impair binding, whereas mutations that increase the intrinsic secondary structure content of the free phosphorylated KID peptide have only a small influence on binding affinity. Low affinity but specific binding of unphosphorylated KID to KIX was measured by ITC and was also observed in Western blot assays and by a fluorescence resonance energy transfer experiment in living cells. The large increase in the affinity for phosphorylated KID is due to favorable intermolecular interactions involving the phosphate moiety. After induction by phosphorylation, CREB is able to compete effectively with other transcriptional activators for binding to CBP.

  1. Hydrostatic pressure effects on the {gamma}-X conduction band mixing and the binding energy of a donor impurity in GaAs-Ga{sub 1-x}Al{sub x}As quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Duque, C.A. [Instituto de Fisica, Universidad de Antioquia, AA 1226, Medellin (Colombia); Lopez, S.Y. [Facultad de Educacion, Universidad de Antioquia, AA 1226, Medellin (Colombia); Mora-Ramos, M.E. [Facultad de Ciencias, Universidad Autonoma del Estado de Morelos, Av. Universidad 1001, C.P. 62210, Cuernavaca (Mexico)

    2007-06-15

    Mixing between {gamma} and X valleys of the conduction band in GaAs-Ga{sub 1-x}Al{sub x}As quantum wells is investigated taken into account the effect of applied hydrostatic pressure. This effect is introduced via the pressure-dependent values of the corresponding energy gaps and the main band parameters. The mixing is considered along the lines of a phenomenological model. Variation of the confined ground state in the well as a function of the pressure is reported. The dependencies of the variationally calculated binding energy of a donor impurity with the hydrostatic pressure and well width are also presented. It is shown that the inclusion of the {gamma}-X mixing explains the non-linear behavior in the photoluminescence peak of confined exciton states that has been observed for pressures above 20 kbar. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  2. Carboplatin binding to histidine

    Energy Technology Data Exchange (ETDEWEB)

    Tanley, Simon W. M. [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom); Diederichs, Kay [University of Konstanz, D-78457 Konstanz (Germany); Kroon-Batenburg, Loes M. J. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Levy, Colin [University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom); Schreurs, Antoine M. M. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Helliwell, John R., E-mail: john.helliwell@manchester.ac.uk [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom)

    2014-08-29

    An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

  3. Stability and Sugar Recognition Ability of Ricin-Like Carbohydrate Binding Domains

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Jianzhuang [ORNL; Nellas, Ricky B [ORNL; Glover, Mary M [ORNL; Shen, Tongye [ORNL

    2011-01-01

    Lectins are a class of proteins known for their novel binding to saccharides. Understanding this sugar recognition process can be crucial in creating structure-based designs of proteins with various biological roles. We focus on the sugar binding of a particular lectin, ricin, which has two -trefoil carbohydrate-binding domains (CRDs) found in several plant protein toxins. The binding ability of possible sites of ricin-like CRD has been puzzling. The apo and various (multiple) ligand-bound forms of the sugar-binding domains of ricin were studied by molecular dynamics simulations. By evaluating structural stability, hydrogen bond dynamics, flexibility, and binding energy, we obtained a detailed picture of the sugar recognition of the ricin-like CRD. Unlike what was previously believed, we found that the binding abilities of the two known sites are not independent of each other. The binding ability of one site is positively affected by the other site. While the mean positions of different binding scenarios are not altered significantly, the flexibility of the binding pockets visibly decreases upon multiple ligand binding. This change in flexibility seems to be the origin of the binding cooperativity. All the hydrogen bonds that are strong in the monoligand state are also strong in the double-ligand complex, although the stability is much higher in the latter form due to cooperativity. These strong hydrogen bonds in a monoligand state are deemed to be the essential hydrogen bonds. Furthermore, by examining the structural correlation matrix, the two domains are structurally one entity. Galactose hydroxyl groups, OH4 and OH3, are the most critical parts in both site 1 and site 2 recognition.

  4. Is It Possible To Obtain Coupled Cluster Quality Energies at near Density Functional Theory Cost? Domain-Based Local Pair Natural Orbital Coupled Cluster vs Modern Density Functional Theory.

    Science.gov (United States)

    Liakos, Dimitrios G; Neese, Frank

    2015-09-08

    the LoosePNO default settings, DLPNO-CCSD(T) is only about 1.2 times slower than B3LYP. With NormalPNO thresholds, DLPNO-CCSD(T) is about a factor of 2 slower than B3LYP and shows a mean absolute deviation of less than 1 kcal/mol to the reference values for the four different data sets used. Our conclusion is that coupled cluster energies can indeed be obtained at near DFT cost.

  5. Obtain of uranium concentrates from fertil liquids

    International Nuclear Information System (INIS)

    Narvaez Castillo, W.A.

    1992-01-01

    This research tried to encounter the form to remove uranium from the rock in the best way, for that it was used different process like leaching, extraction, concentration and precipitation. To leach the mineral was chosen basic leaching, using a mixture of carbonate-sodium bicarbonate, this method is more adequated for the basic nature of the mineral. In extraction was used specific uranium ionic interchanges, so was chosen a tertiary amine like Alamina 336. The concentration phase is intimately binding with the extraction by ionic interchange, for the capability of resine's extraction to obtain concentrated liquids. When the liquids were obtained with high concentration of uranium in the same time were purified and then were precipitated, for that we employed a precipitant agent like: Sodium hydroxide, Amonium hydroxide, Magnesium hydroxide, Hydrogen peroxide and phosphates. With all concentrates we obtain the YELLOW CAKE

  6. Deeply bound π- states in 207Pb formed in the 208Pb(d,3He) reaction. II. Deduced binding energies and widths and the pion-nucleus interaction

    Science.gov (United States)

    Itahashi, K.; Oyama, K.; Hayano, R. S.; Gilg, H.; Gillitzer, A.; Knülle, M.; Münch, M.; Schott, W.; Kienle, P.; Geissel, H.; Iwasa, N.; Münzenberg, G.; Hirenzaki, S.; Toki, H.; Yamazaki, T.

    2000-08-01

    We find a remarkable agreement of the excitation energy spectrum of the 208Pb(d,3He) reaction measured at Td=600 MeV near the π- production threshold with its theoretical prediction. Their comparison leads us to assign the distinct narrow peak observed at about 5 MeV below the threshold to the formation of bound pionic states π-⊗207Pb of the quasisubstitutional configurations (2p)π-(3p3/2,3p1/2)-1n. A small bump observed on the tail of the peak is assigned to the pionic 1s state. The binding energies (Bnl) and the widths (Γnl) of the pionic orbitals are deduced to be B2p=5.13+/-0.02 (stat)+/-0.12 (syst) MeV and Γ2p=0.43+/-0.06 (stat)+/-0.06 (syst) MeV by decomposing the experimental spectrum into the pionic 1s and 2p components. While B2p and Γ2p are determined with small ambiguity, B1s and Γ1s are strongly correlated with each other, and are affected by the relative 1s/2p cross section ratio assumed, since the 1s component is observed only as an unresolved bump. Thus, we have to allow large uncertainties 6.6 MeVbinding energies and widths are compared with theoretically calculated values based on various optical potential parameter sets, and are jointly used to deduce the effective π- mass in the nuclear medium.

  7. Spectroscopic characterization of effective components anthraquinones in Chinese medicinal herbs binding with serum albumins

    Science.gov (United States)

    Bi, Shuyun; Song, Daqian; Kan, Yuhe; Xu, Dong; Tian, Yuan; Zhou, Xin; Zhang, Hanqi

    2005-11-01

    The interactions of serum albumins such as human serum albumin (HSA) and bovine serum albumin (BSA) with emodin, rhein, aloe-emodin and aloin were assessed employing fluorescence quenching and absorption spectroscopic techniques. The results obtained revealed that there are relatively strong binding affinity for the four anthraquinones with HSA and BSA and the binding constants for the interactions of anthraquinones with HSA or BSA at 20 °C were obtained. Anthraquinone-albumin interactions were studied at different temperatures and in the presence of some metal ions. And the competition binding of anthraquinones with serum albumins was also discussed. The Stern-Volmer curves suggested that the quenching occurring in the reactions was the static quenching process. The binding distances and transfer efficiencies for each binding reactions were calculated according to the Föster theory of non-radiation energy transfer. Using thermodynamic equations, the main action forces of these reactions were also obtained. The reasons of the different binding affinities for different anthraquinone-albumin reactions were probed from the point of view of molecular structures.

  8. A comparison of ab initio quantum-mechanical and experimental D-0 binding energies of eleven H-bonded and eleven dispersion-bound complexes

    Czech Academy of Sciences Publication Activity Database

    Haldar, Susanta; Gnanasekaran, Ramachandran; Hobza, Pavel

    2015-01-01

    Roč. 17, č. 40 (2015), s. 26645-26652 ISSN 1463-9076 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : noncovalent interactions * dissociation energy * CCSD(T) Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.449, year: 2015

  9. 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.

  10. FY 1998 annual summary report on International Clean Energy Network Using Hydrogen Conversion (WE-NET) system technology. Subtask 2. Examination and promotion of measures to obtain international understanding and cooperation; 1998 nendo seika hokokusho. Suiso riyo kokusai clean energy system gijutsu (WE-NET) subtask 2 (kokusai kyoryoku shuishin no tame no chosa kento)

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-03-01

    Described herein are the results of examination and promotion of measures to obtain international understanding and cooperation, and examination and development of measures to promote international exchange of technical information, conducted in the FY 1998 continuously from the previous year, with the object to realize the International Clean Energy Network Using Hydrogen Conversion (WE-NET) project. In the FY 1998, the English version of the 1997 annual summary report was distributed to a total of about 150 overseas organizations. The WE-NET project activities were presented to the 12th World Hydrogen Energy Conference, International Joint Power Generation Conference held in 1998 by American Society of Mechanical Engineers, and 2nd International Symposium on Advanced Energy Conversion Systems and Related Technologies. For the examination and development of measures to promote international exchange of technical information, the contracting party of Japan for the Hydrogen Implementation Agreement with IEA has been shifted from the government of Japan to NEDO. NEDO has been representing Japan for various workshops on the tasks. The hydrogen projects conducted by Germany and USA were also surveyed. The WE-NET project homepage was opened in June, 1998. (NEDO)

  11. Evaluation of energy spectral information in nuclear imaging and investigation of protein binding of radiogallium. Progress report, October 1, 1980-September 30, 1981

    International Nuclear Information System (INIS)

    Hoffer, P.B.

    1981-01-01

    Most of the planned modifications on the gamma camera-computer interface are completed. These modifications will allow to determine the contribution of scatter radiation to inaccuracies in cardiac volume and ejection fraction determinations and allow for correction of these inaccuracies. The modifications will also allow testing of the weighted window imaging concept. Specific accomplishments include construction of an energy interface between ZLC-75 camera and DEC gamma 11/34 computer and development and testing of new programs to allow region of interest energy analysis and determination of photopeak and scatter contributions. A new type of converging collimator was built and is being tested which corrects for tissue attenuation at the average cardiac ventricular depth and may prove useful in cardiac chamber volume estimates. A new generator system using a /sup 195m/Hg parent to produce a /sup 195m/Au daughter which will be useful for cardiac studies is being evaluated. The mechanisms by which Ga-67 localizes in abscess and tumor were further elucidated by demonstrating that Ga-67 can transfer from transferrin to ferritin directly. This transfer is facilitated by certain mediators, especially the organic phosphates and does not appear to be energy dependent. A method of labelling viable bacteria with 111 In oxine was developed, and the exact role of siderophores in Ga-67 uptake in bacteria and also Ga-67 uptake in monocytes are being investigated

  12. Large-dimension configuration-interaction calculations of positron binding to the group-II atoms

    International Nuclear Information System (INIS)

    Bromley, M. W. J.; Mitroy, J.

    2006-01-01

    The configuration-interaction (CI) method is applied to the calculation of the structures of a number of positron binding systems, including e + Be, e + Mg, e + Ca, and e + Sr. These calculations were carried out in orbital spaces containing about 200 electron and 200 positron orbitals up to l=12. Despite the very large dimensions, the binding energy and annihilation rate converge slowly with l, and the final values do contain an appreciable correction obtained by extrapolating the calculation to the l→∞ limit. The binding energies were 0.00317 hartree for e + Be, 0.0170 hartree for e + Mg, 0.0189 hartree for e + Ca, and 0.0131 hartree for e + Sr

  13. Studies of superspin glass state and AC-losses in La{sub 0.7}Sr{sub 0.3}MnO{sub 3} nanoparticles obtained by high-energy ball-milling

    Energy Technology Data Exchange (ETDEWEB)

    Phong, P.T., E-mail: ptphong.nh@khanhhoa.edu.vn [Department of Advanced Materials Chemistry, Dongguk University-Gyeongju, 707 Suckjang-dong, Gyeongbuk, Gyeongju-Si 780-714 (Korea, Republic of); Nha Trang Pedagogic College, 1 Nguyen Chanh Street, Khanh Hoa Province, Nha Trang City (Viet Nam); Manh, D.H. [Institute of Materials Science, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Ha Noi City (Viet Nam); Nguyen, L.H. [Nha Trang Pedagogic College, 1 Nguyen Chanh Street, Khanh Hoa Province, Nha Trang City (Viet Nam); Institute of Materials Science, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Ha Noi City (Viet Nam); Tung, D.K. [Institute of Materials Science, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Ha Noi City (Viet Nam); Phuc, N.X., E-mail: phucnx1949@gmail.com [Nha Trang Pedagogic College, 1 Nguyen Chanh Street, Khanh Hoa Province, Nha Trang City (Viet Nam); Lee, I.-J., E-mail: lij@dongguk.ac.kr [Department of Advanced Materials Chemistry, Dongguk University-Gyeongju, 707 Suckjang-dong, Gyeongbuk, Gyeongju-Si 780-714 (Korea, Republic of)

    2014-11-15

    Single-phase perovskite compound La{sub 0.7}Sr{sub 0.3}MnO{sub 3} was synthesized by a high-energy ball milling method. Nanoparticle nature of this manganite with the average particle diameter of 11 nm was revealed from structure and morphology characterizations. The results of ac magnetic susceptibility measurements show that the system can be described as an ensemble of interacting magnetic nanoparticles, which indicates that the dipole–dipole interactions are strong enough to create superspin glass state in the sample. Furthermore, the specific loss power which is exhausted on the irradiation of an ensemble of particles with a magnetic field has been calculated and measured experimentally. - Highlights: • LSMO nanopowder was prepared by the high-energy ball-milling method. • The superspin glass state of LSMO nanopowder was studied. • The SLP has been calculated and measured experimentally.

  14. Entropically-driven binding of mithramycin in the minor groove of C/G-rich DNA sequences

    Science.gov (United States)

    Barceló, Francisca; Scotta, Claudia; Ortiz-Lombardía, Miguel; Méndez, Carmen; Salas, José A.; Portugal, José

    2007-01-01

    The antitumour antibiotic mithramycin A (MTA) is a DNA minor-groove binding ligand. It binds to C/G-rich tracts as a dimer that forms in the presence of divalent cations such as Mg2+. Differential scanning calorimetry, UV thermal denaturation, isothermal titration calorimetry and competition dialysis were used, together with computations of the hydrophobic free energy of binding, to determine the thermodynamic profile of MTA binding to DNA. The results were compared to those obtained in parallel using the structurally related mithramycin SK (MSK). The binding of MTA to salmon testes DNA determined by UV melting studies (Kobs = 1.2 (±0.3) × 105 M−1) is tighter than that of MSK (2.9 (±1.0) × 104 M−1) at 25°C. Competition dialysis studies showed a tighter MTA binding to both salmon testes DNA (42% C + G) and Micrococcus lysodeikticus DNA (72% C + G). The thermodynamic analysis of binding data at 25°C shows that the binding of MTA and MSK to DNA is entropically driven, dominated by the hydrophobic transfer of the antibiotics from solution to the DNA-binding site. Direct molecular recognition between MTA or MSK and DNA through hydrogen bonding and van der Waals contacts may also contribute significantly to complex formation. PMID:17369273

  15. Binding thermodynamics of a glutamate transporter homologue

    Science.gov (United States)

    Reyes, Nicolas; Oh, SeCheol; Boudker, Olga

    2013-01-01

    Glutamate transporters catalyze concentrative uptake of the neurotransmitter into glial cells and neurons. Their transport cycle involves binding and release of the substrate on the extra- and intracellular sides of the plasma membranes, and translocation of the substrate-binding site across the lipid bilayers. The energy of the ionic gradients, mainly sodium, fuels the cycle. Here, we used a cross-linking approach to trap a glutamate transporter homologue from Pyrococcus horikoshii in key conformational states with substrate-binding site facing either the extracellular or intracellular sides of the membrane to study their binding thermodynamics. We show that the chemical potential of sodium ions in solution is exclusively coupled to substrate binding and release, and not to substrate translocation. Despite the structural symmetry, the binding mechanisms are distinct on the opposite sides of the membrane and more complex than the current models suggest. PMID:23563139

  16. Processing of hydroxyapatite obtained by combustion synthesis

    International Nuclear Information System (INIS)

    Canillas, M.; Rivero, R.; García-Carrodeguas, R.; Barba, F.; Rodríguez, M.A.

    2017-01-01

    One of the reasons of implants failure are the stress forces appearing in the material–tissue interface due to the differences between their mechanical properties. For this reason, similar mechanical properties to the surrounding tissue are desirable. The synthesis of hydroxyapatite by solution combustion method and its processing have been studied in order to obtain fully dense ceramic bodies with improved mechanical strength. Combustion synthesis provides nanostructured powders characterized by a high surface area to facilitate the following sintering. Moreover, synthesis was conducted in aqueous and oxidizing media. Oxidizing media improve homogenization and increase the energy released during combustion. It gives rise to particles whose morphology and size suggest lower surface energies compared with aqueous media. The obtained powders were sintered by using a controlled sintering rate schedule. Lower surfaces energies minimize the shrinkage during sintering and relative densities measurements and diametral compression test confirm improved densification and consequently mechanical properties. [es

  17. Processing of hydroxyapatite obtained by combustion synthesis

    Directory of Open Access Journals (Sweden)

    M. Canillas

    2017-09-01

    Full Text Available One of the reasons of implants failure are the stress forces appearing in the material–tissue interface due to the differences between their mechanical properties. For this reason, similar mechanical properties to the surrounding tissue are desirable. The synthesis of hydroxyapatite by solution combustion method and its processing have been studied in order to obtain fully dense ceramic bodies with improved mechanical strength. Combustion synthesis provides nanostructured powders characterized by a high surface area to facilitate the following sintering. Moreover, synthesis was conducted in aqueous and oxidizing media. Oxidizing media improve homogenization and increase the energy released during combustion. It gives rise to particles whose morphology and size suggest lower surface energies compared with aqueous media. The obtained powders were sintered by using a controlled sintering rate schedule. Lower surfaces energies minimize the shrinkage during sintering and relative densities measurements and diametral compression test confirm improved densification and consequently mechanical properties.

  18. 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.

  19. Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding

    Science.gov (United States)

    Smirnov, Alexey; Zubrienė, Asta; Manakova, Elena; Gražulis, Saulius

    2018-01-01

    The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta-substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders—the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders—the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure. PMID:29503769

  20. Tight-binding model for borophene and borophane

    Science.gov (United States)

    Nakhaee, M.; Ketabi, S. A.; Peeters, F. M.

    2018-03-01

    Starting from the simplified linear combination of atomic orbitals method in combination with first-principles calculations, we construct a tight-binding (TB) model in the two-centre approximation for borophene and hydrogenated borophene (borophane). The Slater and Koster approach is applied to calculate the TB Hamiltonian of these systems. We obtain expressions for the Hamiltonian and overlap matrix elements between different orbitals for the different atoms and present the SK coefficients in a nonorthogonal basis set. An anisotropic Dirac cone is found in the band structure of borophane. We derive a Dirac low-energy Hamiltonian and compare the Fermi velocities with that of graphene.

  1. Synthetic LPS-Binding Polymer Nanoparticles

    Science.gov (United States)

    Jiang, Tian

    Lipopolysaccharide (LPS), one of the principal components of most gram-negative bacteria's outer membrane, is a type of contaminant that can be frequently found in recombinant DNA products. Because of its strong and even lethal biological effects, selective LPS removal from bioproducts solution is of particular importance in the pharmaceutical and health care industries. In this thesis, for the first time, a proof-of-concept study on preparing LPS-binding hydrogel-like NPs through facile one-step free-radical polymerization was presented. With the incorporation of various hydrophobic (TBAm), cationic (APM, GUA) monomers and cross-linkers (BIS, PEG), a small library of NPs was constructed. Their FITC-LPS binding behaviors were investigated and compared with those of commercially available LPS-binding products. Moreover, the LPS binding selectivity of the NPs was also explored by studying the NPs-BSA interactions. The results showed that all NPs obtained generally presented higher FITC-LPS binding capacity in lower ionic strength buffer than higher ionic strength. However, unlike commercial poly-lysine cellulose and polymyxin B agarose beads' nearly linear increase of FITC-LPS binding with particle concentration, NPs exhibited serious aggregation and the binding quickly saturated or even decreased at high particle concentration. Among various types of NPs, higher FITC-LPS binding capacity was observed for those containing more hydrophobic monomers (TBAm). However, surprisingly, more cationic NPs with higher content of APM exhibited decreased FITC-LPS binding in high ionic strength conditions. Additionally, when new cationic monomer and cross-linker, GUA and PEG, were applied to replace APM and BIS, the obtained NPs showed improved FITC-LPS binding capacity at low NP concentration. But compared with APM- and BIS-containing NPs, the FITC-LPS binding capacity of GUA- and PEG-containing NPs saturated earlier. To investigate the NPs' binding to proteins, we tested the NPs

  2. Specific insulin binding in bovine chromaffin cells; demonstration of preferential binding to adrenalin-storing cells

    International Nuclear Information System (INIS)

    Serck-Hanssen, G.; Soevik, O.

    1987-01-01

    Insulin binding was studied in subpopulations of bovine chromaffin cells enriched in adrenalin-producing cells (A-cells) or noradrenalin-producing cells (NA-cells). Binding of 125 I-insulin was carried out at 15 0 C for 3 hrs in the absence or presence of excess unlabeled hormone. Four fractions of cells were obtained by centrifugation on a stepwise bovine serum albumin gradient. The four fractions were all shown to bind insulin in a specific manner and the highest binding was measured in the cell layers of higher densities, containing mainly A-cells. The difference in binding of insulin to the four subpopulations of chromaffin cells seemed to be related to differences in numbers of receptors as opposed to receptor affinities. The authors conclude that bovine chromaffin cells possess high affinity binding sites for insulin and that these binding sites are mainly confined to A-cells. 24 references, 2 figures, 1 table

  3. Total iron binding capacity

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003489.htm Total iron binding capacity To use the sharing features on this page, please enable JavaScript. Total iron binding capacity (TIBC) is a blood test to ...

  4. Obtaining the conversion curve of CT numbers to electron density from the effective energy of the CT using the dummy SEFM; Obtencion de la curva de conversion de numeros TC a densidad electronica a partir de la energia efectiva del TC usando el maniqui de la SEFM

    Energy Technology Data Exchange (ETDEWEB)

    Martin-Viera Cueto, J. A.; Garcia Pareja, S.; Benitez Villegas, E. M.; Moreno Saiz, E. M.; Bodineau Gil, C.; Caudepon Moreno, F.

    2011-07-01

    The objective of this work is to obtain the conversion curve of Hounsfield units (A) versus electron densities using a mannequin with different tissue equivalent materials. This provides for the effective energy beam CT and is used to characterize the linear coefficients of absorption of different materials that comprise the dummy.

  5. Process for preparing conifers, particularly conifers with little wood content to obtain energy sources and raw materials. Verfahren zur Aufbereitung von Koniferen, insbesondere holzarmer Koniferen zur Gewinnung von Energietraegern und Rohstoffen

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, K.O.P.

    1981-11-26

    The object of the invention is a process for preparing root stocks, roots, bark and branches and twigs carrying needles or scales and seed capsules of conifers, where fuel and raw materials for hydrotherapy are obtained. The material used is reduced in size by beating and rubbing in pulverisers to a coarse grained mixture, which is reduced in size in further grinding processes in a mill to a mean grain size of 0.5 to 1 mm. The material dried during grinding by waste heat can be used directly as a powdery or fine-grained fuel, made into briquettes or non-wearing shapes or can be taken to a hydrocarbon conversion process or made into a bath extract.

  6. Results in energy saving obtained with the application of speed variator in fossil power stations; Resultados de ahorro de energia obtenidos con la aplicacion de variadores de velocidad en centrales termoelectricas

    Energy Technology Data Exchange (ETDEWEB)

    Merlos Rueda, Rosa Maria [Programa de Ahorro de Energia del Sector Electrico (PAESE), Mexico, D. F. (Mexico)

    1999-07-01

    The project of installation of speed variator in fossil power stations (CT's) of Comision Federal de Electricidad (CFE), as an energy saving measure, is a pilot project that began with the support of the Subdivision de Generacion, and promoted by the Energy Saving Program of the Electric Sector (PAESE), with the putting in operation of an equipment in the condensate pump of the Punta Prieta II C. T. U3. The energy saving observed was substantial, fluctuating between the 19.4% at high loads (at 90% load) and the 71.1% at low loads (at 40% load) of the generating unit. With these results, it was decided to extend the scope of the project with the installation of 6 more equipment for equal number of fossil power stations, located in 4 of the 5 Regions of Generation. The fossil power stations, selected for this stage of the project were: C. T. Felipe Carrillo Puerto U1, C.T. Lerma U4, C.T. Salamanca U1, C.T. Monterrey U6, C.T. Francisco Villa U3 and the C.T. Punta Prieta II-U1. The equipment was in operation during the first quarter of 1998, and the first results indicate an energy savings average per equipment, between 39% and 52%. The recovery of the investment fluctuates between the 48.4% and the 87.6% in less than two years of operation, with which a maximum period of recovery of 3 years is expected. The estimated potential of energy saving, considering the application of these devices in condensate pumps, feedwater pumps (where no speed variator is installed) forced draft fans, induced draft fans and gas recirculation fans, as well as circulation water pumps, of the existing Generating Power stations, ascends to an annual total of 830,000, which represents an approximate 9.4% of the National consumption of self services. [Spanish] El proyecto de instalacion de variadores de velocidad en Centrales Termoelectricas (CT's) de la Comision Federal de Electricidad (CFE), como medida de ahorro de energia, es un proyecto piloto que se inicio con el apoyo de la

  7. Is there a link between selectivity and binding thermodynamics profiles?

    Science.gov (United States)

    Tarcsay, Ákos; Keserű, György M

    2015-01-01

    Thermodynamics of ligand binding is influenced by the interplay between enthalpy and entropy contributions of the binding event. The impact of these binding free energy components, however, is not limited to the primary target only. Here, we investigate the relationship between binding thermodynamics and selectivity profiles by combining publicly available data from broad off-target assay profiling and the corresponding thermodynamics measurements. Our analysis indicates that compounds binding their primary targets with higher entropy contributions tend to hit more off-targets compared with those ligands that demonstrated enthalpy-driven binding. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. A coupled channel study on a binding mechanism of positronic alkali atoms

    International Nuclear Information System (INIS)

    Kubota, Yoshihiro; Kino, Yasushi

    2008-01-01

    In order to investigate the binding mechanism of weakly bound states of positronic alkali atoms, we calculate the energies and wavefunctions using the Gaussian expansion method (GEM) where a positronium (Ps)-alkali ion channel and a positron-alkali atom channel are explicitly introduced. The energies of the bound states are updated using a model potential that reproduces well the observed energy levels of alkali atoms. The binding mechanism of the positronic alkali atom is analyzed by the wavefunctions obtained. The structure of the positronic alkali atom has been regarded as a Ps cluster orbiting the alkali ion, which is described by the Ps-alkali ion channel. We point out that the fraction having the positron-alkali atom configuration is small but plays an indispensable role for the weakly bound system

  9. Results obtained with LEGe detectors applied for partial-body counting in the low-energy range (3-150 keV); Erfahrungen mit LEGe-Detektoren bei Teilkoerpermessungen im Bereich niedriger Energien (3-150 keV)

    Energy Technology Data Exchange (ETDEWEB)

    Dettmann, K. [Bundesamt fuer Strahlenschutz, Berlin (Germany)

    1997-12-01

    Due to a change in the field of duties, the Phoswich detector hitherto used for organ and partial-body scanning for measuring low-energy {gamma} radiation and X-radiation had to be replaced by a modern detector system. A key application of the new system is detection and in vivo measurement of {sup 210}Pb in the human skeleton. This method of measuring {sup 210}Pb as a long-lived daughter product of radon is applied for retrospective assessment of radiation doses emanatingfrom the radon decay chain, applied to former uranium miners (WISMUT) and members of the population living or having lived in houses with high radon concentrations. The bone activities to be expected from relevant exposures are only slightly above those of the normal {sup 210}Pb content in the bones (10-30 Bq), and the Phoswich detector system was not able to detect incorporated activity down to these low levels. The new system was also tested for its suitability and efficiency in detecting radionuclide depositions in body organs, particularly the actinides that are difficult to identify, in compliance with the relevant regulatory guide. (orig./CB) [Deutsch] In der Inkorporationsmessstelle musste auf Grund neuer Aufgabenstellungen der fuer Organ- und Teilkoerpermessungen zum Nachweis niederenergetischer {gamma}- und Roentgenstrahlung eingesetzte Phoswich-Detektor durch ein modernes Detektorsystem ersetzt werden. Ein wichtiges Einsatzgebiet des neuen Systems ist die Bestimmung von {sup 210}Pb im menschlichen Skelett ueber In-vivo-Messungen. Diese Methode der Bestimmung von {sup 210}Pb als langlebiges Folgeprodukt des Radons dient der retrospektiven Ermittlung der Exposition durch Radon-Zerfallsprodukte bei ehemaligen Uranbergleuten (WISMUT) und Personen aus der Bevoelkerung, die in Wohnhaeusern mit hohen Radonkonzentrationen leben bzw. gelebt haben. Die fuer relevante Expositionen zu erwartenden Skelettaktivitaeten liegen nur wenig ueber dem {sup 210}Pb-Normalgehalt (10-30 Bq). Mit einer

  10. Characterization of feline serum-cobalt binding.

    Science.gov (United States)

    Schnelle, Amy N; Barger, Anne M; MacNeill, Amy L; Mitchell, Mark M; Solter, Philip

    2015-06-01

    Oxidative stress inhibits albumin's ability to complex with cobalt. Feline serum-cobalt binding has not been described. The objective was to develop a cobalt binding test for use with feline serum, and correlate the results with other biochemical and cellular constituents in blood, and with clinical diseases of cats. A colorimetric test of cobalt binding, based on the oxidation-reduction reaction of Co(+2) and dithiothreitol, was developed using feline serum. The test was used to measure cobalt binding in stored serum from 176 cats presented to the University of Illinois Veterinary Teaching Hospital for a variety of disease conditions. Time-matched hematology and biochemical data, and clinical information, were obtained from the medical record of each cat and correlated with the serum-cobalt binding results. Serial dilution of feline serum with phosphate-buffered saline resulted in a highly linear decrease in serum-cobalt binding (r(2)  = .9984). Serum-cobalt binding of the clinical samples also correlated with albumin concentrations in a stepwise linear regression model (r(2)  = .425), and both cobalt binding and albumin were significantly decreased in cases of inflammation. Albumin and cobalt binding also shared significant correlations with several erythron variables, and serum concentration of total calcium and bilirubin. The correlation of cobalt binding measured by a colorimetric test with albumin concentration in the clinical samples and with serum dilution is consistent with feline albumin-cobalt complex formation. Hypoalbuminemia is the likely cause of reduced serum-cobalt binding in inflammation and the correlations observed between cobalt binding and other variables. © 2015 American Society for Veterinary Clinical Pathology.

  11. Obtaining additional energy savings from the Filumex project by means of the reactive power compensation; Obtencion de ahorros adicionales del proyecto Filumex mediante la compensacion de la potencia reactiva

    Energy Technology Data Exchange (ETDEWEB)

    Cervantes Jaramillo, Enrique L.; Loredo Gutierrez, Miguel Angel; Hernandez Hernandez, Eduardo [Comision Federal de Electricidad, Mexico, D. F. (Mexico)

    1996-12-31

    This paper presents the proposal for establishing in a parallel way to Flamex project, the compensation in the intermediate tension network for the increment in reactive power supplied to the domestic user. This is due to the following three phenomena that occur in replacing incandescent light bulbs with fluorescent lamps: a) A fluorescent lamp has a power factor of 0.9; consequently it requires the supply of a reactive power of about 50% of its capacity. b) In replacing an incandescent light bulb for a fluorescent lamp, approximately 80% of its capacity is not supplied, this leads to the disappearance of a good deal of the user`s purely resistive load, that will cause that its natural power factor is decreased from 0.91 to 0.86 lagging. c) In decreasing the annual maximum demand in the distribution circuit in a greater proportion than the decrease of the annual consumption, their load factors and the annual losses will be increased and therefore the share of its annual energy losses will be increased in about 18.9%. The above, gives rise to the fact that the compensation of reactive power by means of the installation of capacitor banks in the main leads of the distribution circuit, turns out to be a highly appealing technical-economical solution, with a Benefit/Cost rate of 4, a return time of the investment of 2 years and a net benefit of $4.78/user (Pesos). [Espanol] Se presenta la propuesta para establecer en una forma paralela al proyecto FILUMEX, la compensacion en la red de media tension del incremento de la potencia reactiva suministrada al usuario domestico. Este es debido a los siguientes tres fenomenos que ocurren al sustituir los focos incandescentes por lamparas fluorescentes: a) Una lampara fluorescente tiene un factor de potencia de 0.9, por lo que requiere el suministro de una potencia reactiva de aproximadamente el 50% de su capacidad. b) Al sustituirse un foco incandescente por una lampara fluorescente, se deja de suministrar aproximadamente el 80

  12. Factor VIIa binding and internalization in hepatocytes

    DEFF Research Database (Denmark)

    Hjortoe, G; Sorensen, B B; Petersen, L C

    2005-01-01

    The liver is believed to be the primary clearance organ for coagulation proteases, including factor VIIa (FVIIa). However, at present, clearance mechanisms for FVIIa in liver are unknown. To obtain information on the FVIIa clearance mechanism, we investigated the binding and internalization...... no effect. HEPG2 cells internalized FVIIa with a rate of 10 fmol 10(-5) cells h(-1). In contrast to HEPG2 cells, FVIIa binding to primary rat hepatocytes was completely independent of TF, and excess unlabeled FVIIa partly reduced the binding of 125I-FVIIa to rat hepatocytes. Further, compared with HEPG2...... cells, three- to fourfold more FVIIa bound to rat primary hepatocytes, and the bound FVIIa was internalized at a faster rate. Similar FVIIa binding and internalization profiles were observed in primary human hepatocytes. Plasma inhibitors had no effect on FVIIa binding and internalization in hepatocytes...

  13. A spectroscopic and molecular docking approach on the binding of tinzaparin sodium with human serum albumin

    Science.gov (United States)

    Abdullah, Saleh M. S.; Fatma, Sana; Rabbani, Gulam; Ashraf, Jalaluddin M.

    2017-01-01

    Protein bound toxins are poorly removed by conventional extracorporeal therapies. Venous thromboembolism (VTE) is a major cause of morbidity and mortality in patients with cancer. The interaction between tinzaparin, an inhibitor of angiotensin converting enzyme and human serum albumin, a principal plasma protein in the liver has been investigated in vitro under a simulated physiological condition by UV-vis spectrophotometry and fluorescence spectrometry. The intrinsic fluorescence intensity of human serum albumin was strongly quenched by tinzaparin (TP). The binding constants and binding stoichiometry can be calculated from the data obtained from fluorescence quenching experiments. The negative value of ΔG° reveals that the binding process is a spontaneous process. Thermodynamic analysis shows that the HSA-TP complex formation occurs via hydrogen bonds, hydrophobic interactions and undergoes slight structural changes as evident by far-UV CD. It indicated that the hydrophobic interactions play a main role in the binding of TP to human serum albumin. In addition, the distance between TP (acceptor) and tryptophan residues of human serum albumin (donor) was estimated to be 2.21 nm according to the Förster's resonance energy transfer theory. For the deeper understanding of the interaction, thermodynamic, and molecular docking studies were performed as well. Our docking results suggest that TP forms stable complex with HSA (Kb ∼ 104) and its primary binding site is located in subdomain IIA (Sudlow Site I). The results obtained herein will be of biological significance in pharmacology and clinical medicine.

  14. K- nuclear states: Binding energies and widths

    Czech Academy of Sciences Publication Activity Database

    Hrtánková, Jaroslava; Mareš, Jiří

    2017-01-01

    Roč. 96, č. 1 (2017), č. článku 015205. ISSN 2469-9985 R&D Projects: GA ČR(CZ) GA15-04301S Institutional support: RVO:61389005 Keywords : K- nuclear * kaonic * states Subject RIV: BE - Theoretical Physics OBOR OECD: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect) Impact factor: 3.820, year: 2016

  15. A tight binding and [Formula: see text] study of monolayer stanene.

    Science.gov (United States)

    Jiang, Liming; Marconcini, Paolo; Hossian, Md Sharafat; Qiu, Wanzhi; Evans, Robin; Macucci, Massimo; Skafidas, Efstratios

    2017-09-21

    Stanene is a single layer of tin atoms which has been discovered as an emerging material for quantum spin Hall related applications. In this paper, we present an accurate tight-binding model for single layer stanene near the Fermi level. We parameterized the onsite and hopping energies for the nearest, second nearest, and third nearest neighbor tight-binding method, both without and with spin orbital coupling. We derived the analytical solution for the [Formula: see text]and [Formula: see text] points and numerically investigated the buckling effect on the material electronic properties. In these points of the reciprocal space, we also discuss a corresponding [Formula: see text] description, obtaining the value of the [Formula: see text] parameters both analytically from the tight-binding ones, and numerically, fitting the ab-initio dispersion relations. Our models provide a foundation for large scale atomistic device transport calculations.

  16. Feature Binding in Zebrafish

    Directory of Open Access Journals (Sweden)

    P Neri

    2012-07-01

    Full Text Available Binding operations are primarily ascribed to cortex or similarly complex avian structures. My experiments show that the zebrafish, a lower vertebrate lacking cortex, supports visual feature binding of form and motion for the purpose of social behavior. These results challenge the notion that feature binding may require highly evolved neural structures and demonstrate that the nervous system of lower vertebrates can afford unexpectedly complex computations.

  17. Methods of obtaining thermodynamic data

    International Nuclear Information System (INIS)

    Brewer, L.

    1987-10-01

    The types of thermodynamic data needed to predict behavior of high temperature systems such as an overheated nuclear reactor in which the fuel has been exposed to water and oxygen are discussed. Procedures for obtaining the needed data are reviewed. 14 refs

  18. SHORT COMMUNICATION INTERMEDIATE OBTAINED FROM ...

    African Journals Online (AJOL)

    Preferred Customer

    selectivity is the ratio of the rate constant of the reaction of carbocation with an externally added nucleophile, (nu, aniline) to that of the rate constant of the water. Our intention was to obtain a carbocation with high selectivity, so that one can pave a path for the synthesis of Schiff's base by the reaction of the carbocation ...

  19. DNS & Bind Cookbook

    CERN Document Server

    Liu, Cricket

    2011-01-01

    The DNS & BIND Cookbook presents solutions to the many problems faced by network administrators responsible for a name server. Following O'Reilly's popular problem-and-solution cookbook format, this title is an indispensable companion to DNS & BIND, 4th Edition, the definitive guide to the critical task of name server administration. The cookbook contains dozens of code recipes showing solutions to everyday problems, ranging from simple questions, like, "How do I get BIND?" to more advanced topics like providing name service for IPv6 addresses. It's full of BIND configuration files that yo

  20. Structural and Thermodynamic Insights into Chitooligosaccharide Binding to Human Cartilage Chitinase 3-like Protein 2 (CHI3L2 or YKL-39)*

    Science.gov (United States)

    Ranok, Araya; Wongsantichon, Jantana; Robinson, Robert C.; Suginta, Wipa

    2015-01-01

    Four crystal structures of human YKL-39 were solved in the absence and presence of chitooligosaccharides. The structure of YKL-39 comprises a major (β/α)8 triose-phosphate isomerase barrel domain and a small α + β insertion domain. Structural analysis demonstrates that YKL-39 interacts with chitooligosaccharides through hydrogen bonds and hydrophobic interactions. The binding of chitin fragments induces local conformational changes that facilitate tight binding. Compared with other GH-18 members, YKL-39 has the least extended chitin-binding cleft, containing five subsites for sugars, namely (−3)(−2)(−1)(+1)(+2), with Trp-360 playing a prominent role in the sugar-protein interactions at the center of the chitin-binding cleft. Evaluation of binding affinities obtained from isothermal titration calorimetry and intrinsic fluorescence spectroscopy suggests that YKL-39 binds to chitooligosaccharides with Kd values in the micromolar concentration range and that the binding energies increase with the chain length. There were no significant differences between the Kd values of chitopentaose and chitohexaose, supporting the structural evidence for the five binding subsite topology. Thermodynamic analysis indicates that binding of chitooligosaccharide to YKL-39 is mainly driven by enthalpy. PMID:25477513

  1. Structural and thermodynamic insights into chitooligosaccharide binding to human cartilage chitinase 3-like protein 2 (CHI3L2 or YKL-39).

    Science.gov (United States)

    Ranok, Araya; Wongsantichon, Jantana; Robinson, Robert C; Suginta, Wipa

    2015-01-30

    Four crystal structures of human YKL-39 were solved in the absence and presence of chitooligosaccharides. The structure of YKL-39 comprises a major (β/α)8 triose-phosphate isomerase barrel domain and a small α + β insertion domain. Structural analysis demonstrates that YKL-39 interacts with chitooligosaccharides through hydrogen bonds and hydrophobic interactions. The binding of chitin fragments induces local conformational changes that facilitate tight binding. Compared with other GH-18 members, YKL-39 has the least extended chitin-binding cleft, containing five subsites for sugars, namely (-3)(-2)(-1)(+1)(+2), with Trp-360 playing a prominent role in the sugar-protein interactions at the center of the chitin-binding cleft. Evaluation of binding affinities obtained from isothermal titration calorimetry and intrinsic fluorescence spectroscopy suggests that YKL-39 binds to chitooligosaccharides with Kd values in the micromolar concentration range and that the binding energies increase with the chain length. There were no significant differences between the Kd values of chitopentaose and chitohexaose, supporting the structural evidence for the five binding subsite topology. Thermodynamic analysis indicates that binding of chitooligosaccharide to YKL-39 is mainly driven by enthalpy. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Truncated States Obtained by Iteration

    International Nuclear Information System (INIS)

    Cardoso, W. B.; Almeida, N. G. de

    2008-01-01

    We introduce the concept of truncated states obtained via iterative processes (TSI) and study its statistical features, making an analogy with dynamical systems theory (DST). As a specific example, we have studied TSI for the doubling and the logistic functions, which are standard functions in studying chaos. TSI for both the doubling and logistic functions exhibit certain similar patterns when their statistical features are compared from the point of view of DST

  3. Energies; Energies

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-07-01

    In the framework of the National Debate on the energies in a context of a sustainable development some associations for the environment organized a debate on the nuclear interest facing the renewable energies. The first part presents the nuclear energy as a possible solution to fight against the greenhouse effect and the associated problem of the wastes management. The second part gives information on the solar energy and the possibilities of heat and electric power production. A presentation of the FEE (French wind power association) on the situation and the development of the wind power in France, is also provided. (A.L.B.)

  4. DNS BIND Server Configuration

    Directory of Open Access Journals (Sweden)

    Radu MARSANU

    2011-01-01

    Full Text Available After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  5. DNS BIND Server Configuratio

    OpenAIRE

    Radu MARSANU

    2011-01-01

    After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  6. DNS BIND Server Configuration

    OpenAIRE

    Radu MARSANU

    2011-01-01

    After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  7. Melanin-binding radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

  8. Melanin-binding radiopharmaceuticals

    International Nuclear Information System (INIS)

    Packer, S.; Fairchild, R.G.; Watts, K.P.; Greenberg, D.; Hannon, S.J.

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed

  9. Prediction of Nucleotide Binding Peptides Using Star Graph Topological Indices.

    Science.gov (United States)

    Liu, Yong; Munteanu, Cristian R; Fernández Blanco, Enrique; Tan, Zhiliang; Santos Del Riego, Antonino; Pazos, Alejandro

    2015-11-01

    The nucleotide binding proteins are involved in many important cellular processes, such as transmission of genetic information or energy transfer and storage. Therefore, the screening of new peptides for this biological function is an important research topic. The current study proposes a mixed methodology to obtain the first classification model that is able to predict new nucleotide binding peptides, using only the amino acid sequence. Thus, the methodology uses a Star graph molecular descriptor of the peptide sequences and the Machine Learning technique for the best classifier. The best model represents a Random Forest classifier based on two features of the embedded and non-embedded graphs. The performance of the model is excellent, considering similar models in the field, with an Area Under the Receiver Operating Characteristic Curve (AUROC) value of 0.938 and true positive rate (TPR) of 0.886 (test subset). The prediction of new nucleotide binding peptides with this model could be useful for drug target studies in drug development. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Obtaining zircaloy powder through hydriding

    International Nuclear Information System (INIS)

    Dupim, Ivaldete da Silva; Moreira, Joao M.L.

    2009-01-01

    Zirconium alloys are good options for the metal matrix in dispersion fuels for power reactors due to their low thermal neutron absorption cross-section, good corrosion resistance, good mechanical strength and high thermal conductivity. A necessary step for obtaining such fuels is producing Zr alloy powder for the metal matrix composite material. This article presents results from the Zircaloy-4 hydrogenation tests with the purpose to embrittle the alloy as a first step for comminuting. Several hydrogenation tests were performed and studied through thermogravimetric analysis. They included H 2 pressures of 25 and 50 kPa and temperatures ranging between from 20 to 670 deg C. X-ray diffraction analysis showed in the hydrogenated samples the predominant presence of ZrH 2 and some ZrO 2 . Some kinetics parameters for the Zircaloy-4 hydrogenation reaction were obtained: the time required to reach the equilibrium state at the dwell temperature was about 100 minutes; the hydrogenation rate during the heating process from 20 to 670 deg C was about 21 mg/h, and at constant temperature of 670 deg C, the hydride rate was about 1.15 mg/h. The hydrogenation rate is largest during the heating process and most of it occurs during this period. After hydrogenated, the samples could easily be comminuted indicating that this is a possible technology to obtain Zircaloy powder. The results show that only few minutes of hydrogenation are necessary to reach the hydride levels required for comminuting the Zircaloy. The final hydride stoichiometry was between 2.7 and 2.8 H for each Zr atom in the sample (author)

  11. Heavy metals binding properties of esterified lemon

    International Nuclear Information System (INIS)

    Arslanoglu, Hasan; Altundogan, Hamdi Soner; Tumen, Fikret

    2009-01-01

    Sorption of Cd 2+ , Cr 3+ , Cu 2+ , Ni 2+ , Pb 2+ and Zn 2+ onto a carboxyl groups-rich material prepared from lemon was investigated in batch systems. The results revealed that the sorption is highly pH dependent. Sorption kinetic data indicated that the equilibrium was achieved in the range of 30-240 min for different metal ions and sorption kinetics followed the pseudo-second-order model for all metals studied. Relative sorption rate of various metal cations was found to be in the general order of Ni 2+ > Cd 2+ > Cu 2+ > Pb 2+ > Zn 2+ > Cr 3+ . The binding characteristics of the sorbent for heavy metal ions were analyzed under various conditions and isotherm data was accurately fitted to the Langmuir equation. The metal binding capacity order calculated from Langmuir isotherm was Pb 2+ > Cu 2+ > Ni 2+ > Cd 2+ > Zn 2+ > Cr 3+ . The mean free energy of metal sorption process calculated from Dubinin-Radushkevich parameter and the Polanyi potential was found to be in the range of 8-11 kJ mol -1 for the metals studied showing that the main mechanism governing the sorption process seems to be ion exchange. The basic thermodynamic parameters of metals ion sorption process were calculated by using the Langmuir constants obtained from equilibration study. The ΔG o and ΔH o values for metals ion sorption on the lemon sorbent showed the process to be spontaneous and exothermic in nature. Relatively low ΔH o values revealed that physical adsorption significantly contributed to the mechanism.

  12. Heavy metals binding properties of esterified lemon.

    Science.gov (United States)

    Arslanoglu, Hasan; Altundogan, Hamdi Soner; Tumen, Fikret

    2009-05-30

    Sorption of Cd(2+), Cr(3+), Cu(2+), Ni(2+), Pb(2+) and Zn(2+) onto a carboxyl groups-rich material prepared from lemon was investigated in batch systems. The results revealed that the sorption is highly pH dependent. Sorption kinetic data indicated that the equilibrium was achieved in the range of 30-240 min for different metal ions and sorption kinetics followed the pseudo-second-order model for all metals studied. Relative sorption rate of various metal cations was found to be in the general order of Ni(2+)>Cd(2+)>Cu(2+)>Pb(2+)>Zn(2+)>Cr(3+). The binding characteristics of the sorbent for heavy metal ions were analyzed under various conditions and isotherm data was accurately fitted to the Langmuir equation. The metal binding capacity order calculated from Langmuir isotherm was Pb(2+)>Cu(2+)>Ni(2+)>Cd(2+)>Zn(2+)>Cr(3+). The mean free energy of metal sorption process calculated from Dubinin-Radushkevich parameter and the Polanyi potential was found to be in the range of 8-11 kJ mol(-1) for the metals studied showing that the main mechanism governing the sorption process seems to be ion exchange. The basic thermodynamic parameters of metals ion sorption process were calculated by using the Langmuir constants obtained from equilibration study. The DeltaG degrees and DeltaH degrees values for metals ion sorption on the lemon sorbent showed the process to be spontaneous and exothermic in nature. Relatively low DeltaH degrees values revealed that physical adsorption significantly contributed to the mechanism.

  13. Heavy metals binding properties of esterified lemon

    Energy Technology Data Exchange (ETDEWEB)

    Arslanoglu, Hasan; Altundogan, Hamdi Soner [Department of Chemical Engineering, Firat University, 23279 Elazig (Turkey); Tumen, Fikret, E-mail: ftumen@firat.edu.tr [Department of Chemical Engineering, Firat University, 23279 Elazig (Turkey)

    2009-05-30

    Sorption of Cd{sup 2+}, Cr{sup 3+}, Cu{sup 2+}, Ni{sup 2+}, Pb{sup 2+} and Zn{sup 2+} onto a carboxyl groups-rich material prepared from lemon was investigated in batch systems. The results revealed that the sorption is highly pH dependent. Sorption kinetic data indicated that the equilibrium was achieved in the range of 30-240 min for different metal ions and sorption kinetics followed the pseudo-second-order model for all metals studied. Relative sorption rate of various metal cations was found to be in the general order of Ni{sup 2+} > Cd{sup 2+} > Cu{sup 2+} > Pb{sup 2+} > Zn{sup 2+} > Cr{sup 3+}. The binding characteristics of the sorbent for heavy metal ions were analyzed under various conditions and isotherm data was accurately fitted to the Langmuir equation. The metal binding capacity order calculated from Langmuir isotherm was Pb{sup 2+} > Cu{sup 2+} > Ni{sup 2+} > Cd{sup 2+} > Zn{sup 2+} > Cr{sup 3+}. The mean free energy of metal sorption process calculated from Dubinin-Radushkevich parameter and the Polanyi potential was found to be in the range of 8-11 kJ mol{sup -1} for the metals studied showing that the main mechanism governing the sorption process seems to be ion exchange. The basic thermodynamic parameters of metals ion sorption process were calculated by using the Langmuir constants obtained from equilibration study. The {Delta}G{sup o} and {Delta}H{sup o} values for metals ion sorption on the lemon sorbent showed the process to be spontaneous and exothermic in nature. Relatively low {Delta}H{sup o} values revealed that physical adsorption significantly contributed to the mechanism.

  14. Overview of galactic results obtained by MAGIC

    Energy Technology Data Exchange (ETDEWEB)

    Zanin, Roberta

    2013-06-15

    MAGIC is a system of two atmospheric Cherenkov telescopes which explores the very-high-energy sky, from some tens of GeV up to tens of TeV. Located in the Canary island of La Palma, MAGIC has the lowest energy threshold among the instruments of its kind, well suited to study the still poorly explored energy band below 100 GeV. Although the space-borne gamma-ray telescope Fermi/LAT is sensitive up to 300 GeV, gamma-ray rates drop fast with increasing energy, so γ-ray collection areas larger than 10{sup 4}m{sup 2}, as those provided by grounds-based instruments, are crucial above a few GeV. The combination of MAGIC and Fermi/LAT observations have provided the first astrophysical spectra sampled in the inverse Compton peak region, resulting in a complete coverage from MeV up to TeV energies, as well as the discovery of a pulsed emission in the very-high-energy band. This paper focuses on the latest results on Galactic sources obtained by MAGIC which are highlighted by the detection of the pulsed gamma-ray emission from the Crab pulsar up to 400 GeV. In addition, we will present the morphological study on the W51 complex which allowed to pinpoint the location of the majority of the emission around the interaction point between the supernova remnant W51C and the star forming region W51B, but also to find a possible contribution from the associated pulsar wind nebula. Other important scientific achievements involve the Crab Nebula with an unprecedented spectrum covering three decades in energy starting from 50 GeV and a morphological study of the unidentified source HESS J1857+026 which supports the pulsar wind nebula scenario. Finally we will report on the searches of very-high-energy signals from gamma-ray binaries, mainly LS I 303+ and HESS J0632+057.

  15. Binding of caffeine, theophylline, and theobromine with human serum albumin: A spectroscopic study

    Science.gov (United States)

    Zhang, Hong-Mei; Chen, Ting-Ting; Zhou, Qiu-Hua; Wang, Yan-Qing

    2009-12-01

    The interaction between three purine alkaloids (caffeine, theophylline, and theobromine) and human serum albumin (HSA) was investigated using UV/vis absorption, circular dichroism (CD), fluorescence, synchronous fluorescence, and three-dimensional fluorescence spectra techniques. The results revealed that three alkaloids caused the fluorescence quenching of HSA by the formation of alkaloid-HSA complex. The binding site number n and apparent binding constant KA, corresponding thermodynamic parameters the free energy change (Δ G), enthalpy change (Δ H), and entropy change (Δ S) at different temperatures were calculated. The hydrophobic interaction plays a major role in stabilizing the complex. The distance r between donor (HSA) and acceptor (alkaloids) was obtained according to fluorescence resonance energy transfer. The effect of alkaloids on the conformation of HSA was analyzed using circular dichroism (CD), UV/vis absorption, synchronous fluorescence and three-dimensional fluorescence spectra techniques.

  16. Modulation of calcium oxalate monohydrate crystallization by citrate through selective binding to atomic steps

    Energy Technology Data Exchange (ETDEWEB)

    Qiu, S R; Wierzbicki, A; Salter, E A; Zepeda, S; Orme, C A; Hoyer, J R; Nancollas, G H; Cody, A M; De Yoreo, J J

    2004-10-19

    The majority of human kidney stones are composed primarily of calcium oxalate monohydrate (COM) crystals. Thus, determining the molecular mechanisms by which urinary constituents modulate calcium oxalate crystallization is crucial for understanding and controlling urolithiassis in humans. A comprehensive molecular-scale view of COM shape modification by citrate, a common urinary constituent, obtained through a combination of in situ atomic force microscopy (AFM) and molecular modeling is now presented. We show that citrate strongly influences the growth morphology and kinetics on the (-101) face but has much lower effect on the (010) face. Moreover, binding energy calculations show that the strength of the citrate-COM interaction is much greater at steps than on terraces and is highly step-specific. The maximum binding energy, -166.5 kJ {center_dot} mol{sup -1}, occurs for the [101] step on the (-101) face. In contrast, the value is only -56.9 kJ {center_dot} mol-1 for the [012] step on the (010) face. The binding energies on the (-101) and (010) terraces are also much smaller, -65.4 and -48.9 kJ {center_dot} mol{sup -1} respectively. All other binding energies lie between these extremes. This high selectivity leads to preferential binding of citrate to the acute [101] atomic steps on the (-101) face. The strong citrate-step interactions on this face leads to pinning of all steps, but the anisotropy in interaction strength results in anisotropic reductions in step kinetics. These anisotropic changes in step kinetics are, in turn, responsible for changes in the shape of macroscopic COM crystals. Thus, the molecular scale growth morphology and the bulk crystal habit in the presence of citrate are similar, and the predictions of molecular simulations are fully consistent with the experimental observations.

  17. Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase.

    Science.gov (United States)

    Zhang, Baofeng; D'Erasmo, Michael P; Murelli, Ryan P; Gallicchio, Emilio

    2016-09-30

    We report the results of a binding free energy-based virtual screening campaign of a library of 77 α-hydroxytropolone derivatives against the challenging RNase H active site of the reverse transcriptase (RT) enzyme of human immunodeficiency virus-1. Multiple protonation states, rotamer states, and binding modalities of each compound were individually evaluated. The work involved more than 300 individual absolute alchemical binding free energy parallel molecular dynamics calculations and over 1 million CPU hours on national computing clusters and a local campus computational grid. The thermodynamic and structural measures obtained in this work rationalize a series of characteristics of this system useful for guiding future synthetic and biochemical efforts. The free energy model identified key ligand-dependent entropic and conformational reorganization processes difficult to capture using standard docking and scoring approaches. Binding free energy-based optimization of the lead compounds emerging from the virtual screen has yielded four compounds with very favorable binding properties, which will be the subject of further experimental investigations. This work is one of the few reported applications of advanced-binding free energy models to large-scale virtual screening and optimization projects. It further demonstrates that, with suitable algorithms and automation, advanced-binding free energy models can have a useful role in early-stage drug-discovery programs.

  18. In vitro study on binding interaction of quinapril with bovine serum albumin (BSA) using multi-spectroscopic and molecular docking methods.

    Science.gov (United States)

    Shi, Jie-Hua; Pan, Dong-Qi; Jiang, Min; Liu, Ting-Ting; Wang, Qi

    2017-08-01

    The binding interaction between quinapril (QNPL) and bovine serum albumin (BSA) in vitro has been investigated using UV absorption spectroscopy, steady-state fluorescence spectroscopic, synchronous fluorescence spectroscopy, 3D fluorescence spectroscopy, Fourier transform infrared spectroscopy, circular dichroism, and molecular docking methods for obtaining the binding information of QNPL with BSA. The experimental results confirm that the quenching mechanism of the intrinsic fluorescence of BSA induced by QNPL is static quenching based on the decrease in the quenching constants of BSA in the presence of QNPL with the increase in temperature and the quenching rates of BSA larger than 10 10  L mol -1  s -1 , indicating forming QNPL-BSA complex through the intermolecular binding interaction. The binding constant for the QNPL-BSA complex is in the order of 10 5  M -1 , indicating there is stronger binding interaction of QNPL with BSA. The analysis of thermodynamic parameters together with molecular docking study reveal that the main binding forces in the binding process of QNPL with BSA are van der Waal's forces and hydrogen bonding interaction. And, the binding interaction of BSA with QNPL is an enthalpy-driven process. Based on Förster resonance energy transfer, the binding distance between QNPL and BSA is calculated to be 2.76 nm. The results of the competitive binding experiments and molecular docking confirm that QNPL binds to sub-domain IIA (site I) of BSA. It is confirmed there is a slight change in the conformation of BSA after binding QNPL, but BSA still retains its secondary structure α-helicity.

  19. Formation Energies of Native Point Defects in Strained layer Superlattices (Postprint)

    Science.gov (United States)

    2017-06-05

    AFRL-RX-WP-JA-2017-0440 FORMATION ENERGIES OF NATIVE POINT DEFECTS IN STRAINED-LAYER SUPERLATTICES (POSTPRINT) Zhi Gang Yu...2017 Interim 11 September 2013 – 31 May 2017 4. TITLE AND SUBTITLE FORMATION ENERGIES OF NATIVE POINT DEFECTS IN STRAINED-LAYER SUPERLATTICES...Hamiltonian, tight-binding Hamiltonian, and Green’s function techniques to obtain energy levels arising from native point defects (NPDs) in InAs-GaSb and

  20. Structural features of coke obtained from mixtures of various compositions

    Energy Technology Data Exchange (ETDEWEB)

    Gromova, O.B.; Syskov, K.I.; Mikhailets, S.N.; Gromov, V.E.; Sukhov, Yu.K.

    1985-11-01

    Fundamental aspects are examined for sorptional theory of coking by exposing structural features of coke obtained from charges of varying quantitative proportions of leaning (fillers) and caking (binding) components. Test samples of binding coke (fat coal) and its mixtures with fillers were studied. The samples were boiled with a mixture of xylene and colophony and then freshly spalled so that bonding coke surfaces could be prepared. Microscopic nonuniformity of substances under investigation was taken into consideration during analysis of the results. All varieties of the substance were studied in order to obtain statistically averaged characteristics. It was found that the addition of fillers to the mixture increases the size of structural globular constituents of coke. 6 references.

  1. Drugs obtained by biotechnology processing

    Directory of Open Access Journals (Sweden)

    Hugo Almeida

    2011-06-01

    Full Text Available In recent years, the number of drugs of biotechnological origin available for many different diseases has increased exponentially, including different types of cancer, diabetes mellitus, infectious diseases (e.g. AIDS Virus / HIV as well as cardiovascular, neurological, respiratory, and autoimmune diseases, among others. The pharmaceutical industry has used different technologies to obtain new and promising active ingredients, as exemplified by the fermentation technique, recombinant DNA technique and the hybridoma technique. The expiry of the patents of the first drugs of biotechnological origin and the consequent emergence of biosimilar products, have posed various questions to health authorities worldwide regarding the definition, framework, and requirements for authorization to market such products.Nos últimos anos, tem aumentado exponencialmente o número de fármacos de origem biotecnológica ao dispor das mais diversas patologias, entre elas destacam-se, os diferentes tipos de cancêr, as doenças infecciosas (ex. vírus AIDS/HIV, as doenças autoimunes, as doenças cardiovasculares, a Diabetes Mellitus, as doenças neurológicas, as doenças respiratórias, entre outras. A indústria farmacêutica tem recorrido a diferentes tecnologias para a obtenção de novos e promissores princípios ativos, como são exemplo a fermentação, a técnica de DNA Recombinante, a técnica de hidridoma, entre outras. A queda das patentes dos primeiros fármacos de origem biotecnológica e o consequente aparecimento dos produtos biossimilares têm colocado diferentes questões às autoridades de saúde mundiais, sobre a definição, enquadramento e exigências para a autorização de entrada no mercado deste tipo de produtos.

  2. Study of Binding Properties Between Two New Ibuprofen and Naproxen Based Acyl Hydrazone Derivatives and Trypsin.

    Science.gov (United States)

    Gökoğlu, Elmas; Yılmaz, Esra; Gökoğlu, Esra; Baran, Ayşe Uzgören

    2016-01-01

    Two acyl hydrazone derivatives, AHI and AHN,made from ibuprofen and naproxen-derived hydrazides, were prepared and studied of binding properties with serine protease trypsin by UV-vis absorption and fluorescence quenching at pH 7.4. The results suggest that both hydrazones can interact strongly with trypsin and there are the formation of trypsin-hydrazone complexes. The Stern-Volmer constants, binding constants,binding sites and the corresponding thermodynamic parameters ΔH°, ΔS° and ΔG° were calculated at different temperatures.The effect of common metal ions on the constants was also discussed. The binding modes can be explained on the basis of hydrogen bonds and van der Waals forces. The binding distance(r) ~3 nm between the donor (trypsin) and acceptors (AHI and AHN) was obtained according to Förster's non-radiative energy transfer theory. Moreover, LOD and LOQ of hydrazones were calculated in the presence of trypsin.

  3. New binding mode to TNF-alpha revealed by ubiquitin-based artificial binding protein.

    Directory of Open Access Journals (Sweden)

    Andreas Hoffmann

    Full Text Available A variety of approaches have been employed to generate binding proteins from non-antibody scaffolds. Utilizing a beta-sheet of the human ubiquitin for paratope creation we obtained binding proteins against tumor necrosis factor (TNF-alpha. The bioactive form of this validated pharmacological target protein is a non-covalently linked homo-trimer. This structural feature leads to the observation of a certain heterogeneity concerning the binding mode of TNF-alpha binding molecules, for instance in terms of monomer/trimer specificity. We analyzed a ubiquitin-based TNF-alpha binder, selected by ribosome display, with a particular focus on its mode of interaction. Using enzyme-linked immunosorbent assays, specific binding to TNF-alpha with nanomolar affinity was observed. In isothermal titration calorimetry we obtained comparable results regarding the affinity and detected an exothermic reaction with one ubiquitin-derived binding molecule binding one TNF-alpha trimer. Using NMR spectroscopy and other analytical methods the 1:3 stoichiometry could be confirmed. Detailed binding analysis showed that the interaction is affected by the detergent Tween-20. Previously, this phenomenon was reported only for one other type of alternative scaffold-derived binding proteins--designed ankyrin repeat proteins--without further investigation. As demonstrated by size exclusion chromatography and NMR spectroscopy, the presence of the detergent increases the association rate significantly. Since the special architecture of TNF-alpha is known to be modulated by detergents, the access to the recognized epitope is indicated to be restricted by conformational transitions within the target protein. Our results suggest that the ubiquitin-derived binding protein targets a new epitope on TNF-alpha, which differs from the epitopes recognized by TNF-alpha neutralizing antibodies.

  4. The Movable Type Method Applied to Protein-Ligand Binding.

    Science.gov (United States)

    Zheng, Zheng; Ucisik, Melek N; Merz, Kenneth M

    2013-12-10

    Accurately computing the free energy for biological processes like protein folding or protein-ligand association remains a challenging problem. Both describing the complex intermolecular forces involved and sampling the requisite configuration space make understanding these processes innately difficult. Herein, we address the sampling problem using a novel methodology we term "movable type". Conceptually it can be understood by analogy with the evolution of printing and, hence, the name movable type. For example, a common approach to the study of protein-ligand complexation involves taking a database of intact drug-like molecules and exhaustively docking them into a binding pocket. This is reminiscent of early woodblock printing where each page had to be laboriously created prior to printing a book. However, printing evolved to an approach where a database of symbols (letters, numerals, etc.) was created and then assembled using a movable type system, which allowed for the creation of all possible combinations of symbols on a given page, thereby, revolutionizing the dissemination of knowledge. Our movable type (MT) method involves the identification of all atom pairs seen in protein-ligand complexes and then creating two databases: one with their associated pairwise distant dependent energies and another associated with the probability of how these pairs can combine in terms of bonds, angles, dihedrals and non-bonded interactions. Combining these two databases coupled with the principles of statistical mechanics allows us to accurately estimate binding free energies as well as the pose of a ligand in a receptor. This method, by its mathematical construction, samples all of configuration space of a selected region (the protein active site here) in one shot without resorting to brute force sampling schemes involving Monte Carlo, genetic algorithms or molecular dynamics simulations making the methodology extremely efficient. Importantly, this method explores the free

  5. Binding interaction of phosphorus heterocycles with bovine serum albumin: A biochemical study

    Directory of Open Access Journals (Sweden)

    Swarup Roy

    2017-02-01

    Full Text Available Interaction between bovine serum albumin (BSA and phosphorus heterocycles (PHs was studied using multi-spectroscopic techniques. The results indicated the high binding affinity of PHs to BSA as it quenches the intrinsic fluorescence of BSA. The experimental data suggested the fluorescence quenching mechanism between PHs and BSA as a dynamic quenching. From the UV–vis studies, the apparent association constant (Kapp was found to be 9.25×102, 1.27×104 and 9.01×102 L/mol for the interaction of BSA with PH-1, PH-2 and PH-3 respectively. According to the Förster's non-radiation energy transfer (FRET theory, the binding distances between BSA and PHs were calculated. The binding distances (r of PH-1, PH-2 and PH-3 were found to be 2.86, 3.03, and 5.12 nm, respectively, indicating energy transfer occurs between BSA and PHs. The binding constants of the PHs obtained from the fluorescence quenching data were found to be decreased with increase of temperature. The negative values of the thermodynamic parameters ΔH, ΔS and ΔG at different temperatures revealed that the binding process is spontaneous; hydrogen bonds and van der Waals interaction were the main force to stabilize the complex. The microenvironment of the protein-binding site was studied by synchronous fluorescence and circular dichroism (CD techniques and data indicated that the conformation of BSA changed in the presence of PHs. Finally, we studied the BSA-PHs docking using Autodock and results suggest that PHs is located in the cleft between the domains of BSA.

  6. Human plasminogen binding protein tetranectin

    DEFF Research Database (Denmark)

    Kastrup, J S; Rasmussen, H; Nielsen, B B

    1997-01-01

    The recombinant human plasminogen binding protein tetranectin (TN) and the C-type lectin CRD of this protein (TN3) have been crystallized. TN3 crystallizes in the tetragonal space group P4(2)2(1)2 with cell dimensions a = b = 64.0, c = 75.7 A and with one molecule per asymmetric unit. The crystals...... to at least 2.5 A. A full data set has been collected to 3.0 A. The asymmetric unit contains one monomer of TN. Molecular replacement solutions for TN3 and TN have been obtained using the structure of the C-type lectin CRD of rat mannose-binding protein as search model. The rhombohedral space group indicates...... diffract X-rays to at least 2.0 A resolution. A complete diffraction data set has been collected to 2.7 A resolution. The crystals of TN, obtained by the vapour-diffusion reverse salting-in method at 280 K, are rhombohedral, space group R3, with the hexagonal axes a = b = 89.1, c = 75.8 A, and diffract...

  7. Tight-binding density functional theory: an approximate Kohn-Sham DFT scheme.

    Science.gov (United States)

    Seifert, G

    2007-07-05

    The DFTB method is an approximate KS-DFT scheme with an LCAO representation of the KS orbitals, which can be derived within a variational treatment of an approximate KS energy functional. But it may also be related to cellular Wigner-Seitz methods and to the Harris functional. It is an approximate method, but it avoids any empirical parametrization by calculating the Hamiltonian and overlap matrices out of DFT-derived local orbitals (atomic orbitals, AO's). The method includes ab initio concepts in relating the Kohn-Sham orbitals of the atomic configuration to a minimal basis of the localized atomic valence orbitals of the atoms. Consistent with this approximation, the Hamiltonian matrix elements can strictly be restricted to a two-center representation. Taking advantage of the compensation of the so-called "double counting terms" and the nuclear repulsion energy in the DFT total energy expression, the energy may be approximated as a sum of the occupied KS single-particle energies and a repulsive energy, which can be obtained from DFT calculations in properly chosen reference systems. This relates the method to common standard "tight-binding" (TB) schemes, as they are well-known in solid-state physics. This approach defines the density-functional tight-binding (DFTB) method in its original (non-self-consistent) version.

  8. Computational search for aflatoxin binding proteins

    Science.gov (United States)

    Wang, Ying; Liu, Jinfeng; Zhang, Lujia; He, Xiao; Zhang, John Z. H.

    2017-10-01

    Aflatoxin is one of the mycotoxins that contaminate various food products. Among various aflatoxin types (B1, B2, G1, G2 and M1), aflatoxin B1 is the most important and the most toxic one. In this study, through computational screening, we found that several proteins may bind specifically with different type of aflatoxins. Combination of theoretical methods including target fishing, molecular docking, molecular dynamics (MD) simulation, MM/PBSA calculation were utilized to search for new aflatoxin B1 binding proteins. A recently developed method for calculating entropic contribution to binding free energy called interaction entropy (IE) was employed to compute the binding free energy between the protein and aflatoxin B1. Through comprehensive comparison, three proteins, namely, trihydroxynaphthalene reductase, GSK-3b, and Pim-1 were eventually selected as potent aflatoxin B1 binding proteins. GSK-3b and Pim-1 are drug targets of cancers or neurological diseases. GSK-3b is the strongest binder for aflatoxin B1.

  9. Fluorone dyes have binding sites on both cytoplasmic and extracellular domains of Na,K-ATPase.

    Science.gov (United States)

    Havlíková, Marika; Huličiak, Miroslav; Bazgier, Václav; Berka, Karel; Kubala, Martin

    2013-02-01

    Combination of fluorescence techniques and molecular docking was used to monitor interaction of Na,K-ATPase and its large cytoplasmic loop connecting fourth and fifth transmembrane helices (C45) with fluorone dyes (i.e. eosin Y, 5(6)-carboxyeosin, rose bengal, fluorescein, and erythrosine B). Our data suggested that there are at least two binding sites for all used fluorone dyes, except of 5(6)-carboxyeosin. The first binding site is located on C45 loop, and it is sensitive to the presence of nucleotide. The other site is located on the extracellular part of the enzyme, and it is sensitive to the presence of Na(+) or K(+) ions. The molecular docking revealed that in the open conformation of C45 loop (which is obtained in the presence of ATP) all used fluorone dyes occupy position directly inside the ATP-binding pocket, while in the closed conformation (i.e. in the absence of any ligand) they are located only near the ATP-binding site depending on their different sizes. On the extracellular part of the protein, the molecular docking predicts two possible binding sites with similar binding energy near Asp897(α) or Gln69(β). The former was identified as a part of interaction site between α- and β-subunits, the latter is in contact with conserved FXYD sequence of the γ-subunit. Our findings provide structural explanation for numerous older studies, which were performed with fluorone dyes before the high-resolution structures were known. Further, fluorone dyes seem to be good probes for monitoring of intersubunit interactions influenced by Na(+) and K(+) binding. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. CARBOHYDRATE-CONTAINING COMPOUNDS WHICH BIND TO CARBOHYDRATE BINDING RECEPTORS

    DEFF Research Database (Denmark)

    1995-01-01

    Carbohydrate-containing compounds which contain saccharides or derivatives thereof and which bind to carbohydrate binding receptors are useful in pharmaceutical products for treatment of inflammatory diseases and other diseases.......Carbohydrate-containing compounds which contain saccharides or derivatives thereof and which bind to carbohydrate binding receptors are useful in pharmaceutical products for treatment of inflammatory diseases and other diseases....

  11. Agrobacterium rhizogenes mutants that fail to bind to plant cells.

    OpenAIRE

    Crews, J L; Colby, S; Matthysse, A G

    1990-01-01

    Transposon insertion mutants of Agrobacterium rhizogenes were screened to obtain mutant bacteria that failed to bind to carrot suspension culture cells. A light microscope binding assay was used. The bacterial isolates that were reduced in binding to carrot cells were all avirulent on Bryophyllum diagremontiana leaves and on carrot root disks. The mutants did not appear to be altered in cellulose production. The composition of the medium affected the ability of the parent and mutant bacteria ...

  12. Tension-induced binding of semiflexible biopolymers

    International Nuclear Information System (INIS)

    Benetatos, Panayotis; Heydt, Alice von der; Zippelius, Annette

    2014-01-01

    We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with a sequence of inter-chain binding sites regularly spaced along the contours. Reversible cross-links attach and detach at the sites with an affinity controlled by a chemical potential. In a mean-field approach, we calculate the free energy of the system and find the emergence of a free-energy barrier which controls the reversible (un)binding. The tension affects the conformational entropy of the chains which competes with the binding energy of the cross-links. This competition gives rise to a sudden increase in the fraction of bound sites as the tension increases. We show that this transition is related to the cross-over between weak and strong localization of a directed polymer in a pinning potential. The cross-over to the strongly bound state can be interpreted as a mechanism for force-stiffening which exceeds the capabilities of single-chain elasticity and thus available only to reversibly cross-linked polymers. (paper)

  13. Opioid binding sites in the guinea pig and rat kidney: Radioligand homogenate binding and autoradiography

    Energy Technology Data Exchange (ETDEWEB)

    Dissanayake, V.U.; Hughes, J.; Hunter, J.C. (Parke-Davis Research Unit, Addenbrookes Hospital Site, Cambridge (England))

    1991-07-01

    The specific binding of the selective {mu}-, {delta}-, and {kappa}-opioid ligands (3H)(D-Ala2,MePhe4,Gly-ol5)enkephalin ((3H) DAGOL), (3H)(D-Pen2,D-Pen5)enkephalin ((3H)DPDPE), and (3H)U69593, respectively, to crude membranes of the guinea pig and rat whole kidney, kidney cortex, and kidney medulla was investigated. In addition, the distribution of specific 3H-opioid binding sites in the guinea pig and rat kidney was visualized by autoradiography. Homogenate binding and autoradiography demonstrated the absence of {mu}- and {kappa}-opioid binding sites in the guinea pig kidney. No opioid binding sites were demonstrable in the rat kidney. In the guinea pig whole kidney, cortex, and medulla, saturation studies demonstrated that (3H)DPDPE bound with high affinity (KD = 2.6-3.5 nM) to an apparently homogeneous population of binding sites (Bmax = 8.4-30 fmol/mg of protein). Competition studies using several opioid compounds confirmed the nature of the {delta}-opioid binding site. Autoradiography experiments demonstrated that specific (3H)DPDPE binding sites were distributed radially in regions of the inner and outer medulla and at the corticomedullary junction of the guinea pig kidney. Computer-assisted image analysis of saturation data yielded KD values (4.5-5.0 nM) that were in good agreement with those obtained from the homogenate binding studies. Further investigation of the {delta}-opioid binding site in medulla homogenates, using agonist ((3H)DPDPE) and antagonist ((3H)diprenorphine) binding in the presence of Na+, Mg2+, and nucleotides, suggested that the {delta}-opioid site is linked to a second messenger system via a GTP-binding protein. Further studies are required to establish the precise localization of the {delta} binding site in the guinea pig kidney and to determine the nature of the second messenger linked to the GTP-binding protein in the medulla.

  14. 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...

  15. A look at ligand binding thermodynamics in drug discovery.

    Science.gov (United States)

    Claveria-Gimeno, Rafael; Vega, Sonia; Abian, Olga; Velazquez-Campoy, Adrian

    2017-04-01

    Drug discovery is a challenging endeavor requiring the interplay of many different research areas. Gathering information on ligand binding thermodynamics may help considerably in reducing the risk within a high uncertainty scenario, allowing early rejection of flawed compounds and pushing forward optimal candidates. In particular, the free energy, the enthalpy, and the entropy of binding provide fundamental information on the intermolecular forces driving such interaction. Areas covered: The authors review the current status and recent developments in the application of ligand binding thermodynamics in drug discovery. The thermodynamic binding profile (Gibbs energy, enthalpy, and entropy of binding) can be used for lead selection and optimization (binding enthalpy, selectivity, and adaptability). Expert opinion: Binding thermodynamics provides fundamental information on the forces driving the formation of the drug-target complex. It has been widely accepted that binding thermodynamics may be used as a decision criterion along the ligand optimization process in drug discovery and development. In particular, the binding enthalpy may be used as a guide when selecting and optimizing compounds over a set of potential candidates. However, this has been recently called into question by arguing certain difficulties and in the light of certain experimental examples.

  16. The binding of in vitro synthesized adenovirus DNA binding protein to single-stranded DNA is stimulated by zinc ions

    NARCIS (Netherlands)

    Vos, H.L.; Lee, F.M. van der; Sussenbach, J.S.

    1988-01-01

    We have synthesized wild type DNA binding protein (DBP) of adenovirus type 5 (Ad5) and several truncated forms of this protein by a combination of in vitro transcription and translation. The proteins obtained were tested for binding to a single-stranded DNA-cellulose column. It could be shown that

  17. binding protein (HABP1)

    Indian Academy of Sciences (India)

    Unknown

    adsorbed on carbon coated copper grid (400 mesh) for. 5 min at room temperature. The grids were subsequently .... and inhibition by GAGs and DMA were determined on polystyrene wells of microtitre plates (Costar, ... for binding inhibition assays was carried out by mixing equal volumes of the conjugate and the inhibitor at ...

  18. Sequential memory: Binding dynamics

    Science.gov (United States)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  19. binding protein (HABP1)

    Indian Academy of Sciences (India)

    Unknown

    of HA in a concentration-dependent manner, suggesting its multiligand affinity amongst carbohydrates. rHABP1 shows differential affinity ... site is seen to correspond to the carbohydrate-binding site in E-selectin, which has similarity in the ... adsorbed on carbon coated copper grid (400 mesh) for. 5 min at room temperature.

  20. Identification of binding peptides of the ADAM15 disintegrin domain ...

    Indian Academy of Sciences (India)

    Madhsudhan

    Karkkainen et al. 2006). In this study, the recombinant ADAM15 disintegrin domain (RADD) was expressed in E. coli, and 4 specific binding peptides of RADD were obtained by positive panning and subtractive selection using a phage display 12-mer.

  1. α-Mangostin Extraction from the Native Mangosteen (Garcinia mangostana L.) and the Binding Mechanisms of α-Mangostin to HSA or TRF.

    Science.gov (United States)

    Guo, Ming; Wang, Xiaomeng; Lu, Xiaowang; Wang, Hongzheng; Brodelius, Peter E

    2016-01-01

    In order to obtain the biological active compound, α-mangostin, from the traditional native mangosteen (Garcinia mangostana L.), an extraction method for industrial application was explored. A high yield of α-mangostin (5.2%) was obtained by extraction from dried mangosteen pericarps with subsequent purification on macroporous resin HPD-400. The chemical structure of α-mangostin was verified mass spectrometry (MS), nuclear magnetic resonance (1H NMR and 13C NMR), infrared spectroscopy (IR) and UV-Vis spectroscopy. The purity of the obtained α-mangostin was 95.6% as determined by HPLC analysis. The binding of native α-mangostin to human serum albumin (HSA) or transferrin (TRF) was explored by combining spectral experiments with molecular modeling. The results showed that α-mangostin binds to HSA or TRF as static complexes but the binding affinities were different in different systems. The binding constants and thermodynamic parameters were measured by fluorescence spectroscopy and absorbance spectra. The association constant of HSA or TRF binding to α-mangostin is 6.4832×105 L/mol and 1.4652×105 L/mol at 298 K and 7.8619×105 L/mol and 1.1582×105 L/mol at 310 K, respectively. The binding distance, the energy transfer efficiency between α-mangostin and HSA or TRF were also obtained by virtue of the Förster theory of non-radiation energy transfer. The effect of α-mangostin on the HSA or TRF conformation was analyzed by synchronous spectrometry and fluorescence polarization studies. Molecular docking results reveal that the main interaction between α-mangostin and HSA is hydrophobic interactions, while the main interaction between α-mangostin and TRF is hydrogen bonding and Van der Waals forces. These results are consistent with spectral results.

  2. Binding of Citreoviridin to Human Serum Albumin: Multispectroscopic and Molecular Docking

    Directory of Open Access Journals (Sweden)

    Haifeng Hou

    2015-01-01

    Full Text Available Citreoviridin (CIT, a mycotoxin produced by Penicillium citreonigrum, is a common contaminant of wide range of agriproducts and detrimental to human and animal health. In this study, the interaction of CIT with human serum albumin (HSA is researched by steady-state fluorescence, ultraviolet-visible (UV-Vis absorption, circular dichroism (CD methods, and molecular modeling. The association constants, binding site numbers, and corresponding thermodynamic parameters are used to investigate the quenching mechanism. The alternations of HSA secondary structure in the presence of CIT are demonstrated with UV-Vis, synchronous fluorescence, and CD spectra. The molecular modeling results reveal that CIT can bind with hydrophobic pocket of HSA with hydrophobic and hydrogen bond force. Moreover, an apparent distance of 3.25 nm between Trp214 and CIT is obtained via fluorescence resonance energy transfer method.

  3. Phenylbutazone and ketoprofen binding to serum albumin. Fluorescence study.

    Science.gov (United States)

    Maciążek-Jurczyk, Małgorzata

    2014-10-01

    A combination of phenylbutazone (PBZ) and ketoprofen (KP) is popular in therapy of rheumatoid arthritis (RA) but could be unsafe due to the uncontrolled growth of toxicity. Quenching fluorescence of serum albumin in the presence of the both drugs has been characterized by dynamic KQ [M(-1)], static V [M(-1)] quenching constants and also association constants Ka [M(-1)]. The quenching of tryptophanyl residues fluorescence by the KP and PBZ indicates the capability of these drugs to accept the energy from Trp-214 and Trp-135. Strong displacement of KP and PBZ bound to albumin cause by the binding of the second drug to SA close to Trp-214 (subdomain IIA) has been obtained. The displacement was also confirmed on the basis of quenching and association constants. The conclusion, that both PBZ and KP form a binding site in the same subdomains (IIA or/and IB), points to the necessity of using a monitoring therapy owning to the possible increase of the uncontrolled toxic effects. Copyright © 2014 Institute of Pharmacology, Polish Academy of Sciences. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

  4. Polynomial fitting of tight-binding method in carbon

    Science.gov (United States)

    Haa, Wai Kang; Yeak, Su Hoe

    2017-04-01

    Carbon is very unique in among the elements and its ability to form strong chemical bonds with a variety number such as two carbons (graphene) and four carbons (diamond). This combination of strong bonds with tight mass and high melting point makes them technologically and scientifically important in nanoscience development. Tight-binding model (TB) is one of the semi-empirical approximations used in quantum mechanical world which is restricted to the Linear Combinations of Localized Atomic Orbitals (LCAO). Currently, there are many approaches in tight-binding calculation. In this paper, we have reproduced a polynomial scaling function by fitting to the TB model. The model is then applied into carbon molecules and obtained the energy bands of the system. The elements of the overlap Hamiltonian matrix in the model will be depending on the parameter of the polynomials. Our purpose is to find out a set of parameters in the polynomial which were commonly fit to an independently calculated band structure. We used minimization approach to calculate the polynomial coefficients which involves differentiation of eigenvalues in the eigensystem. The algorithm of fitting the parameters is carried out in FORTRAN.

  5. Human serum albumin binding of certain antimalarials

    Science.gov (United States)

    Marković, Olivera S.; Cvijetić, Ilija N.; Zlatović, Mario V.; Opsenica, Igor M.; Konstantinović, Jelena M.; Terzić Jovanović, Nataša V.; Šolaja, Bogdan A.; Verbić, Tatjana Ž.

    2018-03-01

    Interactions between eight in-house synthesized aminoquinolines, along with well-known chloroquine, and human serum albumin (HSA) have been studied by fluorescence spectroscopy. The synthesized aminoquinolines, despite being structurally diverse, were found to be very potent antimalarials. Fluorescence measurements indicate that three compounds having additional thiophene or benzothiophene substructure bind more strongly to HSA than other studied compounds. Competitive binding experiments indicate that these three compounds bind significantly stronger to warfarin compared to diazepam binding site. Fluorescence quenching at three temperatures (20, 25, and 37 °C) was analyzed using classical Stern-Volmer equation, and a static quenching mechanism was proposed. The enthalpy and entropy changes upon sulphur-containing compound-HSA interactions were calculated using Van't Hoff equation. Positive values of enthalpy and entropy changes indicate that non-specific, hydrophobic interactions are the main contributors to HSA-compound interaction. Molecular docking and calculated lipophilicity descriptors indicate the same, pointing out that the increased lipophilicity of sulphur-containing compounds might be a reason for their better binding to HSA. Obtained results might contribute to design of novel derivatives with improved pharmacokinetic properties and drug efficacy.

  6. Thermodynamic signatures of fragment binding: Validation of direct versus displacement ITC titrations.

    Science.gov (United States)

    Rühmann, Eggert; Betz, Michael; Fricke, Marie; Heine, Andreas; Schäfer, Martina; Klebe, Gerhard

    2015-04-01

    Detailed characterization of the thermodynamic signature of weak binding fragments to proteins is essential to support the decision making process which fragments to take further for the hit-to-lead optimization. Isothermal titration calorimetry (ITC) is the method of choice to record thermodynamic data, however, weak binding ligands such as fragments require the development of meaningful and reliable measuring protocols as usually sigmoidal titration curves are hardly possible to record due to limited solubility. Fragments can be titrated either directly under low c-value conditions (no sigmoidal curve) or indirectly by use of a strong binding ligand displacing the pre-incubated weak fragment from the protein. The determination of Gibbs free energy is reliable and rather independent of the applied titration protocol. Even though the displacement method achieves higher accuracy, the obtained enthalpy-entropy profile depends on the properties of the used displacement ligand. The relative enthalpy differences across different displacement experiments reveal a constant signature and can serve as a thermodynamic fingerprint for fragments. Low c-value titrations are only reliable if the final concentration of the fragment in the sample cell exceeds 2-10 fold its K(D) value. Limited solubility often prevents this strategy. The present study suggests an applicable protocol to characterize the thermodynamic signature of protein-fragment binding. It shows however, that such measurements are limited by protein and fragment solubility. Deviating profiles obtained by use of different displacement ligands indicate that changes in the solvation pattern and protein dynamics most likely take influence on the resulting overall binding signature. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. 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.

  8. The effects of moisture content, particle size and binding agent content on oil palm shell pellet quality parameters

    Directory of Open Access Journals (Sweden)

    Nelson Arzola

    2012-01-01

    Full Text Available Waste-to-energy represents a challenge for the oil palm industry worldwide. Bio-pellet production is an alternative way of adding value to oil palm biomass. This would mean that a product having major energy density becomes more mechanically stable and achieves better performance during combustion. This paper deals with oil palm shell pelleting; using binding agents having up to 25% mass keeping average particle size less than 1mm and moisture content up to 18.7% (d.b. were evaluated. An experimental factorial design used binding agent mass percentage, milled shell particle size and moisture content as factors. Pellet density response surfaces and durability index were obtained. Pellet performance during thermal-chemical transformation was also evaluated by using thermogravimetry equipment. The results led to technical evaluation of scale-up at industrial production level.

  9. In-silico analysis of amotosalen hydrochloride binding to CD-61 of platelets

    International Nuclear Information System (INIS)

    Chaudhary, H.T.

    2016-01-01

    To determine the docking of Amotosalen hydrochloride (AH) at CD-61 of platelets, and to suggest the cause of bleeding in AH treated platelets transfusion. Study Design: Descriptive study. Place and Duration of Study: Medical College, Taif University, Taif, Saudi Arabia, from October 2014 to May 2015. Methodology: The study was carried out in-silico. PDB (protein data bank) code of Tirofiban bound to CD-61 was 2vdm. CD-61 was docked with Tirofiban using online docking tools, i.e. Patchdock and Firedock. Then, Amotosalen hydrochloride and CD-61 were also docked. Best docking poses to active sites of 2vdm were found. Ligplot of interactions of ligands and CD-61 were obtained. Then comparison of hydrogen bonds, hydrogen bond lengths, and hydrophobic bonds of 2vdm molecule and best poses of docking results were done. Patchdock and Firedock results of best poses were also analysed using SPSS version 16. Results: More amino acids were involved in hydrogen and hydrophobic bonds in Patchdock and Firedock docking of Amotosalen hydrochloride with CD-61 than Patchdock and Firedock docking of CD-61 with Tirofiban. The binding energy was more in latter than former. Conclusion: Amotosalen hydrochloride binds to the active site of CD-61 with weaker binding force. Haemorrhage seen in Amotosalen hydrochloride-treated platelets might be due to binding of Amotosalen hydrochloride to CD-61. (author)

  10. Potential toxicity of sulfanilamide antibiotic: Binding of sulfamethazine to human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jiabin [State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092 (China); Zhou, Xuefei [Key Laboratory of Yangtze River Water Environment for Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092 (China); Zhang, Yalei, E-mail: zhangyalei2003@163.com [State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092 (China); Gao, Haiping [Key Laboratory of Yangtze River Water Environment for Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092 (China)

    2012-08-15

    Antibiotics are widely used in daily life but their abuse has posed a potential threat to human health. The interaction between human serum albumin (HSA) and sulfamethazine (SMZ) was investigated by capillary electrophoresis, fluorescence spectrometry, and circular dichroism. The binding constant and site were determined to be 1.09 Multiplication-Sign 10{sup 4} M{sup -1} and 1.14 at 309.5 K. The thermodynamic determination indicated that the interaction was driven by enthalpy change, where the electrostatic interaction and hydrogen bond were the dominant binding force. The binding distance between SMZ and tryptophan residue of HSA was obtained to be 3.07 nm according to Foerster non-radioactive energy transfer theory. The site marker competition revealed that SMZ bound into subdomain IIA of HSA. The binding of SMZ induced the unfolding of the polypeptides of HSA and transferred the secondary conformation of HSA. The equilibrium dialysis showed that only 0.13 mM SMZ decreased vitamin B{sub 2} by 38% transported on the HSA. This work provides a new quantitative evaluation method for antibiotics to cause the protein damage. -- Highlights: Black-Right-Pointing-Pointer Various techniques characterized the interactions between SMZ and HSA. Black-Right-Pointing-Pointer The electrostatic interaction and hydrogen bond dominated in the interaction. Black-Right-Pointing-Pointer SMZ induced the conformation change of HSA. Black-Right-Pointing-Pointer SMZ affected the transportation function of HSA.

  11. Third nearest neighbor parameterized tight binding model for graphene nano-ribbons

    Directory of Open Access Journals (Sweden)

    Van-Truong Tran

    2017-07-01

    Full Text Available The existing tight binding models can very well reproduce the ab initio band structure of a 2D graphene sheet. For graphene nano-ribbons (GNRs, the current sets of tight binding parameters can successfully describe the semi-conducting behavior of all armchair GNRs. However, they are still failing in reproducing accurately the slope of the bands that is directly associated with the group velocity and the effective mass of electrons. In this work, both density functional theory and tight binding calculations were performed and a new set of tight binding parameters up to the third nearest neighbors including overlap terms is introduced. The results obtained with this model offer excellent agreement with the predictions of the density functional theory in most cases of ribbon structures, even in the high-energy region. Moreover, this set can induce electron-hole asymmetry as manifested in results from density functional theory. Relevant outcomes are also achieved for armchair ribbons of various widths as well as for zigzag structures, thus opening a route for multi-scale atomistic simulation of large systems that cannot be considered using density functional theory.

  12. Third nearest neighbor parameterized tight binding model for graphene nano-ribbons

    Science.gov (United States)

    Tran, Van-Truong; Saint-Martin, Jérôme; Dollfus, Philippe; Volz, Sebastian

    2017-07-01

    The existing tight binding models can very well reproduce the ab initio band structure of a 2D graphene sheet. For graphene nano-ribbons (GNRs), the current sets of tight binding parameters can successfully describe the semi-conducting behavior of all armchair GNRs. However, they are still failing in reproducing accurately the slope of the bands that is directly associated with the group velocity and the effective mass of electrons. In this work, both density functional theory and tight binding calculations were performed and a new set of tight binding parameters up to the third nearest neighbors including overlap terms is introduced. The results obtained with this model offer excellent agreement with the predictions of the density functional theory in most cases of ribbon structures, even in the high-energy region. Moreover, this set can induce electron-hole asymmetry as manifested in results from density functional theory. Relevant outcomes are also achieved for armchair ribbons of various widths as well as for zigzag structures, thus opening a route for multi-scale atomistic simulation of large systems that cannot be considered using density functional theory.

  13. Electrolytic Hydrogen obtaining by a photovoltaic source

    International Nuclear Information System (INIS)

    Pasculete, E.; Condrea, F.; Stanoiu, L.

    2005-01-01

    At present, the developed countries allocate large funds for the financing of some global programs for fundamental and applicative research for development of hydrogen non-conventional production technologies. One of these technologies is the photo-assisted electrolysis. This technology is adopted in the research, which results are presented in this paper. The experimental model includes as basic equipment 100 W photovoltaic source, electrolysis battery press filter type, control unit of the electric energy discharged, accumulator, hydrogen storage unit. Five types of material have been tested for the electrolysis cell diaphragm: asbestos; Netrom- unwoven material from fibers of polypropylene; ion changing composite membrane - polysulfone support with an active layer of sulfonated poly-sulfone (PSS/PSJ) and poly-sulfone support with an active layer of sulfonated poly-eter cetone (SPEEK/PSf); ion-exchange membrane made from sulfonated poly-eter cetone (SPEEK). The graphics and results from the test system are presented. The analysis of the experimental results lead to the establishment of the optimal configuration of battery and of the operational conditions of the assembly. The experimental results give the opportunity to obtain electrolytic hydrogen with a photovoltaic source, in an efficient system, and promote the Romanian research at a level of a demonstrative installation

  14. Biodegradable Polyelectrolyte Obtained by Radiation Polymerization

    International Nuclear Information System (INIS)

    Craciun, G.; Martin, D.; Manaila, E.; Nemtanu, M.; Brasoveanu, M.; Ighigeanu, D.

    2009-01-01

    Poly electrolytes are water-soluble polymers carrying ionic charge along the polymer chain. Depending upon the charge, these polymers are anionic or cationic. The inherent solid - liquid separating efficiency makes these poly electrolytes a unique class of polymers which find extensive application in potable water, industrial raw and process water, municipal sewage treatment, mineral processing and metallurgy, oil drilling and recovery, etc. Also, due to their ability to produce advanced induced coagulation, a considerable amount of bacteria and viruses are precipitated together with the suspended solids. Especially the acrylamide polymers are very efficacious for water treatment but acrylamide is a toxic monomer and therefore their use are governed by international standards that provide the residual acrylamide monomer content (RAMC) in them be less than 0.05%. Under these circumstances our attention was focused on the following research steps that are presented in this paper: 1) Preparation of a special class of poly electrolytes, named Pn, with very low RAMC values, based on electron beam (EB), microwave (MW) and EB + MW induced co-polymerization of aqueous solutions containing appropriate mixtures of acrylamide (AMD) and acrylic acid (AA) monomers (AMD - AA co-polymers). The Pn were obtained by radiation technology with very small RAMC (under 0.01%) as well as in a wide range of molecular weights and charge densities. Very low AMD monomer content of Pn is due to the major advantages of radiation induced polymerization in aqueous solution containing monomers. Due to water presence in the EB irradiated system, irradiated water radicals facilitate the polymerization process and increase rate and level of monomers conversion in co-polymers. Also, once again, by the presence of water, which absorbs MW energy very strongly, the MW polymerization reaction rate is much enhanced resulting in a reaction time about 50-100 times lowers than by conventional heating. Also

  15. Megalin binds and mediates cellular internalization of folate binding protein

    DEFF Research Database (Denmark)

    Birn, Henrik; Zhai, Xiaoyue; Holm, Jan

    2005-01-01

    to express high levels of megalin, is inhibitable by excess unlabeled FBP and by receptor associated protein, a known inhibitor of binding to megalin. Immortalized rat yolk sac cells, representing an established model for studying megalin-mediated uptake, reveal (125)I-labeled FBP uptake which is inhibited...... to bind and mediate cellular uptake of FBP. Surface plasmon resonance analysis shows binding of bovine and human milk FBP to immobilized megalin, but not to low density lipoprotein receptor related protein. Binding of (125)I-labeled folate binding protein (FBP) to sections of kidney proximal tubule, known...

  16. Inverse gas chromatography as a method for determination of surface properties of binding materials

    Science.gov (United States)

    Yu, Jihai; Lu, Xiaolei; Yang, Chunxia; Du, Baoli; Wang, Shuxian; Ye, Zhengmao

    2017-09-01

    Inverse gas chromatography (IGC) is a promising measurement technique for investigating the surface properties of binding materials, which are the major influence element for the adsorption performance of superplasticizer. In this work, using the IGC method, blast furnace slag (BFS), sulphoaluminate cement (SAC) and portland cement (P·O) are employed to systematically evaluate the corresponding dispersive component (γsd), specific surface free energy (γsab), and acid-base properties. The obtained results show that γsd contributes to a major section of the surface free energy in the three binding materials, suggesting they are of a relatively low polarity. Compared to the two kinds of cements, the BFS possesses the highest dispersive and specific surface free energies (the values are 45.01 mJ/m2 and 11.68 mJ/m2, respectively), and also exhibits a wider distribution range of γsd, indicating their surfaces are heterogeneous. For acid-base properties, the results indicate the surfaces of three samples are basic in nature. In addition, the adsorption investigation shows that per unit surface of BFS adsorbs the most superplasticizer molecules, which indicates the higher surface free energies is beneficial to the superplasticizer adsorption.

  17. Electron spectra obtained by photon bombadment

    International Nuclear Information System (INIS)

    Tran Minh Duc

    1981-01-01

    The physical factors modifying the kinetic energy of electrons emitted from a surface by photon irradiation are discussed, mamely: photoemission excitation mechanism and Auger emission, effects of the neutral initial state, of chemical displacements, of ionized final state, of relaxation energy. Spectra structure, spin multiplets energy loss peaks are also explained [fr

  18. Optical Binding of Nanowires

    Czech Academy of Sciences Publication Activity Database

    Simpson, Stephen Hugh; Zemánek, Pavel; Marago, O.M.; Jones, P.H.; Hanna, S.

    2017-01-01

    Roč. 17, č. 6 (2017), s. 3485-3492 ISSN 1530-6984 R&D Projects: GA ČR GB14-36681G Grant - others:AV ČR(CZ) CNR-16-12 Program:Bilaterální spolupráce Institutional support: RVO:68081731 Keywords : optical binding nanowires * Brownian motion * self -organization * non-equilibrium thermodynamics * non-equilibrium steady state * spin-orbit coupling * emergent phenomena Subject RIV: BH - Optics, Masers, Lasers OBOR OECD: Optics (including laser optics and quantum optics) Impact factor: 12.712, year: 2016

  19. Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

    Directory of Open Access Journals (Sweden)

    Huiying Zhao

    Full Text Available As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions. A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC of 0.77 with high precision (94% and high sensitivity (65%. We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA] is available as an on-line server at http://sparks-lab.org.

  20. Affinity enhancement of nanobody binding to EGFR: in silico site-directed mutagenesis and molecular dynamics simulation approaches.

    Science.gov (United States)

    Farasat, Alireza; Rahbarizadeh, Fatemeh; Hosseinzadeh, Ghader; Sajjadi, Sharareh; Kamali, Mehdi; Keihan, Amir Homayoun

    2017-06-01

    Epidermal growth factor receptor (EGFR), a transmembrane glycoprotein, is overexpressed in many cancers such as head-neck, breast, prostate, and skin cancers for this reason it is a good target in cancer therapy and diagnosis. In nanobody-based cancer diagnosis and treatment, nanobodies with high affinity toward receptor (e.g. EGFR) results in effective treatment or diagnosis of cancer. In this regard, the main aim of this study is to develop a method based on molecular dynamic (MD) simulations for designing of 7D12 based nanobody with high affinity compared with wild-type nanobody. By surveying electrostatic and desolvation interactions between different residues of 7D12 and EGFR, the critical residues of 7D12 that play the main role in the binding of 7D12 to EGFR were elucidated and based on these residues, five logical variants were designed. Following the 50 ns MD simulations, pull and umbrella sampling simulation were performed for 7D12 and all its variants in complex with EGFR. Binding free energy of 7D12 (and all its variants) with EGFR was obtained by weighted histogram analysis method. According to binding free energy results, GLY101 to GLU mutation showed the highest binding affinity but this variant is unstable after 50 ns MD simulations. ALA100 to GLU mutation shows suitable binding enhancement with acceptable structural stability. Suitable position and orientation of GLU in residue 100 of 7D12 against related amino acids of EGFR formed some extra hydrogen and electrostatic interactions which resulted in binding enhancement.