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Sample records for impurity binding energy

  1. 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 ...

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

    Indian Academy of Sciences (India)

    Administrator

    Calculations are made for the case of not so big impurity concentrations, when impurity bands are not .... Blom et al (2003), but our data correspond qualitatively to Bastard's .... 0113U000612 and by Ukrainian Ministry of Education and Science ...

  3. 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 ...

  4. 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 ...

  5. 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

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

    Science.gov (United States)

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

    2011-01-01

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

  7. Hydrogenic-Donor Impurity Binding Energy Dependence of the Electric Field in GaAs/AlxGa1−xAs Quantum Rings

    Directory of Open Access Journals (Sweden)

    Guangxin Wang

    2013-01-01

    Full Text Available Using a variational method with two-parameter trial wave function and the effective mass approximation, the binding energy of a donor impurity in GaAs/AlxGa1−xAs cylindrical quantum ring (QR subjected to an external field is calculated. It is shown that the donor impurity binding energy is highly dependent on the QR structure parameters (radial thickness and height, impurity position, and external electric field. The binding energy increases inchmeal as the QR parameters (radial thickness and height decrease until a maximum value for a central impurity and then begins to drop quickly. The applied electric field can significantly modify the spread of electronic wave function in the QR and shift electronic wave function from the donor position and then leads to binding energy changes. In addition, results for the binding energies of a hydrogenic donor impurity as functions of the impurity position and applied electric field are also presented.

  8. 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)

  9. Binding energy and photoionization cross-section of hydrogen-like impurity in a Poschl-Teller quantum well

    International Nuclear Information System (INIS)

    Hakimifard, A.

    2010-01-01

    The effect of the donor impurity position and the form of confining potential on the binding energy and the photoionization cross-section if a semiconductor quantum well with Poschl-Teller potential is investigated. An analytical expression for the photoionization cross-section is obtained for the case when the polarization vector of light wave is directed along the direction of size quantization. It is shown that the photoionization cross-section has a threshold behavior

  10. 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

  11. Hydrostatic pressure and conduction band non-parabolicity effects on the impurity binding energy in a spherical quantum dot

    International Nuclear Information System (INIS)

    Sivakami, A.; Mahendran, M.

    2010-01-01

    The binding energy of a shallow hydrogenic impurity in a spherical quantum dot under hydrostatic pressure with square well potential is calculated using a variational approach within the effective mass approximation. The effect of conduction band non-parabolicity on these energies is also estimated. The binding energy is computed for GaAs spherical quantum dot as a function of dot size, hydrostatic pressure both in the presence and absence of the band non-parabolicity effect. Our results show that (i) the hydrostatic pressure increases the impurity binding energy when dot radius increases for a given pressure, (ii) the hydrostatic pressure with the band non-parabolicity effect effectively increases the binding energy such that the variation is large for smaller dots and (iii) the maximum contribution by the non-parabolicity effect is about 15% for narrow dots. Our results are in good agreement with Perez-Merchancano et al. [J. Phys. Condens. Matter 19 (2007) 026225] who have not considered the conduction band non-parabolicity effect.

  12. Simultaneous effects of hydrostatic pressure and electric field on impurity binding energy and polarizability in coupled InAs/GaAs quantum wires

    International Nuclear Information System (INIS)

    Tangarife, E.; Duque, C.A.

    2011-01-01

    This work is concerned with the theoretical study of the combined effects of applied electric field and hydrostatic pressure on the binding energy and impurity polarizability of a donor impurity in laterally coupled double InAs/GaAs quantum-well wires. Calculations have been made in the effective mass and parabolic band approximations and using a variational method. The results are reported for different configurations of wire and barriers widths, impurity position, and electric field and hydrostatic pressure strengths. Our results show that for symmetrical structures the binding energy is an even function of the impurity position along the growth direction of the structure. Also, we found that for hydrostatic pressure strength up to 38 kbar, the binding energy increases linearly with hydrostatic pressure, while for larger values of hydrostatic pressure the binding energy has a non-linear behavior. Finally, we found that the hydrostatic pressure can increase the coupling between the two parallel quantum-well wires. -- Research highlights: → Binding energy for donor impurity in coupled wires strongly depends on the confinement potential. → Polarizability for donor impurity in coupled wires strongly depends on the confinement potential. → Binding energy strongly depends on the direction of the applied electric field. → Polarizability strongly depends on the direction of the applied electric field. → The coupling between the two parallel wires increases with the hydrostatic pressure.

  13. External electric field effect on the binding energy of a hydrogenic donor impurity in InGaAsP/InP concentric double quantum rings

    Science.gov (United States)

    Hu, Min; Wang, Hailong; Gong, Qian; Wang, Shumin

    2018-04-01

    Within the framework of effective-mass envelope-function theory, the ground state binding energy of a hydrogenic donor impurity is calculated in the InGaAsP/InP concentric double quantum rings (CDQRs) using the plane wave method. The effects of geometry, impurity position, external electric field and alloy composition on binding energy are considered. It is shown that the peak value of the binding energy appears in two rings with large gap as the donor impurity moves along the radial direction. The binding energy reaches the peak value at the center of ring height when the donor impurity moves along the axial direction. The binding energy shows nonlinear variation with the increase of ring height. With the external electric field applied along the z-axis, the binding energy of the donor impurity located at zi ≥ 0 decreases while that located at zi < 0 increases. In addition, the binding energy decreases with increasing Ga composition, but increases with the increasing As composition.

  14. 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.

  15. 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.

  16. Hydrogenic impurity binding energy in vertically coupled Ga1-xAlxAs quantum-dots under hydrostatic pressure and applied electric field

    International Nuclear Information System (INIS)

    Duque, C.M.; Barseghyan, M.G.; Duque, C.A.

    2009-01-01

    This work deals with a theoretical study, using a variational method and the effective mass approximation, of the ground state binding energy of a hydrogenic donor impurity in a vertically coupled multiple quantum dot structure under the effects of hydrostatic pressure and in-growth direction applied electric field. The low dimensional structure consists of three cylindrical shaped GaAs quantum dots coupled by Ga 1-x Al x As barriers. For the hydrostatic pressure has been considered the Γ-X crossover in the Ga 1-x Al x As material. As a general, the results show that: (1) the binding energy as a function of the impurity position has a similar shape to that shown by the electron wave function without the Coulomb interaction, (2) the presence of the electric field changes dramatically the binding energy profile destroying (favoring) the symmetry in the structures, and (3) depending on the impurity position the binding energy can increase or decrease with the hydrostatic pressure mainly due to increases or decreases of the carrier-wave function symmetry by changing the height of the potential barrier.

  17. 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)

  18. External electric field and hydrostatic pressure effects on the binding energy and self-polarization of an off-center hydrogenic impurity confined in a GaAs/AlGaAs square quantum well wire

    International Nuclear Information System (INIS)

    Rezaei, G.; Mousavi, S.; Sadeghi, E.

    2012-01-01

    Based on the effective-mass approximation within a variational scheme, binding energy and self-polarization of hydrogenic impurity confined in a finite confining potential square quantum well wire, under the action of external electric field and hydrostatic pressure, are investigated. The binding energy and self-polarization are computed as functions of the well width, impurity position, electric field, and hydrostatic pressure. Our results show that the external electric field and hydrostatic pressure as well as the well width and impurity position have a great influence on the binding energy and self-polarization.

  19. Impurity binding energy of lowest-excited state in (In,Ga)N–GaN spherical QD under electric field effect

    International Nuclear Information System (INIS)

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

    2013-01-01

    External electric field effect on the lowest-excited state in wurtzite (In,Ga)N–GaN spherical quantum dot is considered. By means of a traditional Ritz variational method within the effective-mass approximation and finite potential barrier, the lowest-excited state energy with and without the presence of the impurity is investigated. The normalized binding energy under electric field effect is also performed. Our numerical results are compared with the previous theoretical findings and show a good agreement with those concerning especially the ground-state for different semiconductors materials and different QDs-shapes

  20. Impurity binding energy of lowest-excited state in (In,Ga)N–GaN spherical QD under electric field effect

    Energy Technology Data Exchange (ETDEWEB)

    Ghazi, Haddou El, E-mail: hadghazi@gmail.com [LPS, Faculty of Sciences, Dhar EL Mehrez, B.P 1796 Atlas, Fez (Morocco); Special Mathematics, CPGE Kénitra (Morocco); Jorio, Anouar; Zorkani, Izeddine [LPS, Faculty of Sciences, Dhar EL Mehrez, B.P 1796 Atlas, Fez (Morocco)

    2013-10-01

    External electric field effect on the lowest-excited state in wurtzite (In,Ga)N–GaN spherical quantum dot is considered. By means of a traditional Ritz variational method within the effective-mass approximation and finite potential barrier, the lowest-excited state energy with and without the presence of the impurity is investigated. The normalized binding energy under electric field effect is also performed. Our numerical results are compared with the previous theoretical findings and show a good agreement with those concerning especially the ground-state for different semiconductors materials and different QDs-shapes.

  1. The effects of the electric and intense laser field on the binding energies of donor impurity states (1s and 2p±) and optical absorption between the related states in an asymmetric parabolic quantum well

    Science.gov (United States)

    Kasapoglu, E.; Sakiroglu, S.; Sökmen, I.; Restrepo, R. L.; Mora-Ramos, M. E.; Duque, C. A.

    2016-10-01

    We have calculated the effects of electric and intense laser fields on the binding energies of the ground and some excited states of conduction electrons coupled to shallow donor impurities as well as the total optical absorption coefficient for transitions between 1s and 2p± electron-impurity states in a asymmetric parabolic GaAs/Ga1-x AlxAs quantum well. The binding energies were obtained using the effective-mass approximation within a variational scheme. Total absorption coefficient (linear and nonlinear absorption coefficient) for the transitions between any two impurity states were calculated from first- and third-order dielectric susceptibilities derived within a perturbation expansion for the density matrix formalism. Our results show that the effects of the electric field, intense laser field, and the impurity location on the binding energy of 1s-impurity state are more pronounced compared with other impurity states. If the well center is changed to be Lc0), the effective well width decreases (increases), and thus we can obtain the red or blue shift in the resonant peak position of the absorption coefficient by changing the intensities of the electric and non-resonant intense laser field as well as dimensions of the well and impurity positions.

  2. Impurity energy level in the Haldane gap

    International Nuclear Information System (INIS)

    Wang Wei; Lu Yu

    1995-11-01

    An impurity bond J' in a periodic 1D antiferromagnetic spin 1 chain with exchange J is considered. Using the numerical density matrix renormalization group method, we find an impurity energy level in the Haldane gap, corresponding to a bound state near the impurity bond. When J' J. The impurity level appears only when the deviation dev = (J'- J)/J' is greater than B c , which is close to 0.3 in our calculation. (author). 15 refs, 4 figs

  3. Binding of Helium to Metallic Impurities in Tungsten; Experiments and Computer Simulations

    NARCIS (Netherlands)

    Kolk, G.J. van der; Veen, A. van; Caspers, L.M.; Hosson, J.Th.M. de

    1985-01-01

    A W(100) single crystal was implanted with low doses Ag, Cu, Mn, Cr, Al or In. Subsequent heating to 1600 K removed all vacancies and left the implants in substitutional positions. Low energy He was injected, and binding of He to the substitutional impurities was observed. Binding energies were

  4. Tight-Binding Description of Impurity States in Semiconductors

    Science.gov (United States)

    Dominguez-Adame, F.

    2012-01-01

    Introductory textbooks in solid state physics usually present the hydrogenic impurity model to calculate the energy of carriers bound to donors or acceptors in semiconductors. This model treats the pure semiconductor as a homogeneous medium and the impurity is represented as a fixed point charge. This approach is only valid for shallow impurities…

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

    Science.gov (United States)

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

    2018-04-01

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

  6. Energy bands and gaps near an impurity

    Czech Academy of Sciences Publication Activity Database

    Mihóková, Eva; Schulman, L. S.

    2016-01-01

    Roč. 380, č. 41 (2016), s. 3430-3433 ISSN 0375-9601 R&D Projects: GA ČR GA13-09876S Institutional support: RVO:68378271 Keywords : crystal structure * impurity * modeling * energy bands Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.772, year: 2016

  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. 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.)

  9. Numerical renormalization group calculation of impurity internal energy and specific heat of quantum impurity models

    Science.gov (United States)

    Merker, L.; Costi, T. A.

    2012-08-01

    We introduce a method to obtain the specific heat of quantum impurity models via a direct calculation of the impurity internal energy requiring only the evaluation of local quantities within a single numerical renormalization group (NRG) calculation for the total system. For the Anderson impurity model we show that the impurity internal energy can be expressed as a sum of purely local static correlation functions and a term that involves also the impurity Green function. The temperature dependence of the latter can be neglected in many cases, thereby allowing the impurity specific heat Cimp to be calculated accurately from local static correlation functions; specifically via Cimp=(∂Eionic)/(∂T)+(1)/(2)(∂Ehyb)/(∂T), where Eionic and Ehyb are the energies of the (embedded) impurity and the hybridization energy, respectively. The term involving the Green function can also be evaluated in cases where its temperature dependence is non-negligible, adding an extra term to Cimp. For the nondegenerate Anderson impurity model, we show by comparison with exact Bethe ansatz calculations that the results recover accurately both the Kondo induced peak in the specific heat at low temperatures as well as the high-temperature peak due to the resonant level. The approach applies to multiorbital and multichannel Anderson impurity models with arbitrary local Coulomb interactions. An application to the Ohmic two-state system and the anisotropic Kondo model is also given, with comparisons to Bethe ansatz calculations. The approach could also be of interest within other impurity solvers, for example, within quantum Monte Carlo techniques.

  10. Hydrostatic-pressure effects on the donor binding energy in GaAs-(Ga, Al)As quantum dots

    International Nuclear Information System (INIS)

    Perez-Merchancano, S T; Paredes-Gutierrez, H; Silva-Valencia, J

    2007-01-01

    The binding energy of shallow hydrogenic impurities in a spherical quantum dot under isotropic hydrostatic pressure is calculated using a variational approach within the effective mass approximation. The binding energy is computed as a function of hydrostatic pressure, dot size and impurity position. The results show that the impurity binding energy increases with the pressure for any position of the impurity. Also, we have found that the binding energy depends on the location of the impurity and the pressure effects are less pronounced for impurities on the edge

  11. Protein binding studies with radiolabeled compounds containing radiochemical impurities. Equilibrium dialysis versus dialysis rate determination

    DEFF Research Database (Denmark)

    Honoré, B

    1987-01-01

    The influence of radiochemical impurities in dialysis experiments with high-affinity ligands is investigated. Albumin binding of labeled decanoate (97% pure) is studied by two dialysis techniques. It is shown that equilibrium dialysis is very sensitive to the presence of impurities resulting...

  12. Impurity diffusion activation energies in Al from first principles

    NARCIS (Netherlands)

    Simonovic, D.; Sluiter, M.H.

    2009-01-01

    Activation energies for vacancy-mediated impurity diffusion in face-centered-cubic aluminum have been computed ab initio for all technologically important alloying elements, as well as for most of the lanthanides. The so-called five-frequency rate model is used to establish the limiting vacancy

  13. Binding energies of cluster ions

    International Nuclear Information System (INIS)

    Parajuli, R.; Matt, S.; Scheier, P.; Echt, O.; Stamatovic, A.; Maerk, T.D.

    2002-01-01

    The binding energy of charged clusters may be measured by analyzing the kinetic energy released in the metastable decay of mass selected parent ions. Using finite heat bath theory to determine the binding energies of argon, neon, krypton, oxygen and nitrogen from their respective average kinetic energy released were carried out. A high-resolution double focussing two-sector mass spectrometer of reversed Nier-Johnson type geometry was used. MIKE ( mass-analysed ion kinetic energy) were measured to investigate decay reactions of mass-selected ions. For the inert gases neon (Ne n + ), argon (Ar n + ) and krypton (Kr n + ), it is found that the binding energies initially decrease with increasing size n and then level off at a value above the enthalpy of vaporization of the condensed phase. Oxygen cluster ions shown a characteristic dependence on cluster size (U-shape) indicating a change in the metastable fragmentation mechanism when going from the dimer to the decamer ion. (nevyjel)

  14. Skyrmions with low binding energies

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-06-15

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

  15. Skyrmions with low binding energies

    International Nuclear Information System (INIS)

    Gillard, Mike; Harland, Derek; Speight, Martin

    2015-01-01

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

  16. Skyrmions with low binding energies

    Directory of Open Access Journals (Sweden)

    Mike Gillard

    2015-06-01

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

  17. Impurities in semiconductors: total energy and infrared absorption calculations

    International Nuclear Information System (INIS)

    Yndurain, F.

    1987-01-01

    A new method to calculate the electronic structure of infinite nonperiodic system is discussed. The calculations are performed using atomic pseudopotentials and a basis of atomic Gaussiam wave functions. The Hartree-Fock self consistent equations are solved in the cluster-Bethe lattice system. Electron correlation is partially included in second order pertubation approximation. The formalism is applied to hydrogenated amorphous silicon. Total energy calculations of finite clusters of silicon atom in the presence of impurities, are also presented. The results show how atomic oxygen breaks the covalent silicon silicon bond forming a local configuration similar to that of SiO 2 . Calculations of the infrared absorption due to the presence of atomic oxygen in cristalline silicon are presented. The Born Hamiltonian to calculate the vibrational modes of the system and a simplied model to describe the infrared absorption mechanism are used. The interstitial and the the substitutional cases are considered and analysed. The position of the main infrared absorption peak, their intensities and their isotope shifts are calculated. The results are satisfactory agreement with the available data. (author) [pt

  18. Combined influence of hydrostatic pressure and temperature on interband emission energy of impurity doped quantum dots in presence of noise

    Energy Technology Data Exchange (ETDEWEB)

    Bera, Aindrila; Ghosh, Manas, E-mail: pcmg77@rediffmail.com

    2016-11-01

    We explore the profiles of interband emission energy (IEE) of impurity doped quantum dots (QDs) under the simultaneous influence of hydrostatic pressure (HP) and temperature (T) and in presence and absence of Gaussian white noise. Noise has been incorporated to the system additively and multiplicatively. In this regard, modulation of IEE by the variation of several other relevant quantities such as electric field, magnetic field, confinement potential, dopant location, dopant potential and aluminium concentration has also been investigated. Gradual alteration of HP and T affects IEE discernibly. Inclusion of noise has been found to enhance or deplete the IEE depending upon its mode of application. Moreover, under given conditions of temperature and pressure, the difference between the impurity-free ground state energy and the binding energy appears to be crucial in determining whether or not the profiles of IEE would resemble that of binding energy. The findings reveal fascinating role played by noise in tailoring the IEE of doped QD system under conspicuous presence of hydrostatic pressure and temperature. - Highlights: • Interband emission energy (IEE) of doped quantum dot is studied. • Hydrostatic pressure (HP) and temperature (T) affect IEE. • The dot is subjected to Gaussian white noise. • Noise amplifies and suppresses IEE depending on particular condition.

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

    Indian Academy of Sciences (India)

    Department of Physics, Donbass State Engineering Academy, Shkadinova 72, 84313 Kramatorsk, Ukraine; Grupo de Materia Condensada-UdeA, Instituto de Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA; Calle 70 No. 52-21, Medellin, Colombia; Institute of Physics of National Academy ...

  20. Hydrogenic impurity in double quantum dots

    International Nuclear Information System (INIS)

    Wang, X.F.

    2007-01-01

    The ground state binding energy and the average interparticle distances for a hydrogenic impurity in double quantum dots with Gaussian confinement potential are studied by the variational method. The probability density of the electron is calculated, too. The dependence of the binding energy on the impurity position is investigated for GaAs quantum dots. The result shows that the binding energy has a minimum as a function of the distance between the two quantum dots when the impurity is located at the center of one quantum dot or at the center of the edge of one quantum dot. When the impurity is located at the center of the two dots, the binding energy decreases monotonically

  1. Effect of impurities on vacancy migration energy in Fe-based alloys

    International Nuclear Information System (INIS)

    Hashimoto, N.; Sakuraya, S.; Tanimoto, J.; Ohnuki, S.

    2014-01-01

    Effects of impurities, such as carbon, nitrogen, helium and hydrogen, on microstructural evolution in pure iron were investigated by means of a multi-beam electron microscope. Growth rate of dislocation loops were measured to calculate vacancy migration energies. In all irradiation temperature conditions, both the size and the number density of dislocation loops were increased as a function of dose. Irradiation with more impurities showed an increase in the temperature dependence of the dislocation loop growth rate compared to irradiation with little impurities. The in situ experiment indicated that the net migration energy of vacancies could be increased due to trapping by impurities, and the effect of C and N on the migration energy of vacancy would be larger than that of W, V, Ta. Furthermore, H and He would increase vacancy migration energy greater than C and N, as well as W, V, Ta. The density functional theory (DFT), applied to the atomic models of BCC iron, indicated an increase in vacancy migration energy by the trapping of impurity atoms, that is a good agreement with this in situ experiment

  2. Combined effects of hydrostatic pressure and electric field on the donor binding energy and polarizability in laterally coupled double InAs/GaAs quantum-well wires

    International Nuclear Information System (INIS)

    Tangarife, E.; Duque, C.A.

    2010-01-01

    This work is concerned with the theoretical study of the combined effects of applied electric field and hydrostatic pressure on the binding energy and impurity polarizability of a donor impurity in laterally coupled double InAs/GaAs quantum-well wires. calculations have been made in the effective mass and parabolic band approximations and using a variational method. The results are reported for different configurations of wire and barriers widths, impurity position, and electric field and hydrostatic pressure strengths. Our results show that for symmetrical structures the binding energy is an even function of the impurity position along the growth direction of the structure. Also, we found that for hydrostatic pressure strength up to 38 kbar, the binding energy increases linearly with hydrostatic pressure, while for larger values of hydrostatic pressure the binding energy has a nonlinear behavior. Finally, we found that the hydrostatic pressure can increase the coupling between the two parallel quantum well wires.

  3. P-shell hyperon binding energies

    International Nuclear Information System (INIS)

    Koetsier, D.; Amos, K.

    1991-01-01

    A shell model for lambda hypernuclei has been used to determine the binding energy of the hyperon in nuclei throughout the p shell. Conventional (Cohen and Kurath) potential energies for nucleon-nucleon interactions were used with hyperon-nucleon interactions taken from Nijmegen one boson exchange potentials. The hyperon binding energies calculated from these potentials compare well with measured values. 7 refs., 2 figs

  4. Environment sensitive embedding energies of impurities, and grain boundary stability in tantalum

    International Nuclear Information System (INIS)

    Krasko, G.L.

    1996-01-01

    Metalloid impurities have a very low solubility in tantalum, and therefore prefer to segregate at the grain boundaries (GBs). In order to analyze the energetics of the impurities on the tantalum GB, the LMTO calculations were performed on a simple 8-atom supercell emulating a typical (capped trigonal prism) GB environment. The so-called environment-sensitive embedding energies were calculated for hydrogen, boron, carbon, nitrogen, oxygen, phosphorus, and sulphur, as a function of the electron charge density due to the host atoms at the impurity site. The calculations showed that, at the electron density typical of a GB, carbon has the lowest energy (followed by Nitrogen and Boron) and thus would compete with the other impurities for the site on the GB, tending to displace them from the GB. The above energies were then used in a modified Finnis-Sinclair embedded atom approach for calculating the cohesive energies and the equilibrium interplanar distances in the vicinity of a (111) Σ3 tilt GB plane, both for the clean GB and that with an impurity. These distances were found to oscillate, returning to the value corresponding to the equilibrium spacing between (111) planes in bulk BCC tantalum by the 10th--12th plane off the GB. Carbon, nitrogen and boron somewhat dampen the deformation wave (making the oscillations less than in the clean GB), while oxygen, phosphorus and sulphur result in an increase of the oscillations. The cohesive energies follow the same trend, the GB with carbon being the most stable. Thus, carbon, nitrogen and boron may be thought of as being cohesion enhancers, while oxygen, phosphorus and sulphur result in decohesion effects

  5. Energy levels and far-infrared optical absorption of impurity doped semiconductor nanorings: Intense laser and electric fields effects

    Energy Technology Data Exchange (ETDEWEB)

    Barseghyan, M.G., E-mail: mbarsegh@ysu.am

    2016-11-10

    Highlights: • The electron-impurity interaction on energy levels in nanoring have been investigated. • The electron-impurity interaction on far-infrared absorption have been investigated. • The energy levels are more stable for higher values of electric field. - Abstract: The effects of electron-impurity interaction on energy levels and far-infrared absorption in semiconductor nanoring under the action of intense laser and lateral electric fields have been investigated. Numerical calculations are performed using exact diagonalization technique. It is found that the electron-impurity interaction and external fields change the energy spectrum dramatically, and also have significant influence on the absorption spectrum. Strong dependence on laser field intensity and electric field of lowest energy levels, also supported by the Coulomb interaction with impurity, is clearly revealed.

  6. Magnetic field effect on the ground-state binding energy in InGaN/GaN parabolic QWW

    International Nuclear Information System (INIS)

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

    2013-01-01

    Within the framework of the effective mass scheme, the ground-state binding energy of hydrogenic shallow-donor impurity in wurtzite (WZ) (In,Ga)N/GaN parabolic transversal-section quantum-well wire (PQWW) subjected to magnetic field is investigated. The finite-difference method within the quasi-one-dimensional effective potential model is used. A cylindrical QWW effective radius is introduced to describe the lateral confinement strength. The results show that: (i) the binding energy is the largest for the impurity located at a point corresponding to the largest electron probability density and (ii) it increases with increasing external magnetic field

  7. Magnetic field effect on the ground-state binding energy in InGaN/GaN parabolic QWW

    Energy Technology Data Exchange (ETDEWEB)

    El Ghazi, Haddou, E-mail: hadghazi@gmail.com [LPS, Faculty of sciences, Dhar EL Mehrez, B.P 1796 Atlas Fez (Morocco); Specials Mathematics, CPGE Kénitra, Chakib Arsalane Street, Kénitra (Morocco); Jorio, Anouar; Zorkani, Izeddine [LPS, Faculty of sciences, Dhar EL Mehrez, B.P 1796 Atlas Fez (Morocco)

    2013-07-15

    Within the framework of the effective mass scheme, the ground-state binding energy of hydrogenic shallow-donor impurity in wurtzite (WZ) (In,Ga)N/GaN parabolic transversal-section quantum-well wire (PQWW) subjected to magnetic field is investigated. The finite-difference method within the quasi-one-dimensional effective potential model is used. A cylindrical QWW effective radius is introduced to describe the lateral confinement strength. The results show that: (i) the binding energy is the largest for the impurity located at a point corresponding to the largest electron probability density and (ii) it increases with increasing external magnetic field.

  8. Effect of geometry on the pressure induced donor binding energy in semiconductor nanostructures

    Science.gov (United States)

    Kalpana, P.; Jayakumar, K.; Nithiananthi, P.

    2015-09-01

    The effect of geometry on an on-center hydrogenic donor impurity in a GaAs/(Ga,Al)As quantum wire (QWW) and quantum dot (QD) under the influence of Γ-X band mixing due to an applied hydrostatic pressure is theoretically studied. Numerical calculations are performed in an effective mass approximation. The ground state impurity energy is obtained by variational procedure. Both the effects of pressure and geometry are to exert an additional confinement on the impurity inside the wire as well as dot. We found that the donor binding energy is modified by the geometrical effects as well as by the confining potential when it is subjected to external pressure. The results are presented and discussed.

  9. Ground state energy and wave function of an off-centre donor in spherical core/shell nanostructures: Dielectric mismatch and impurity position effects

    Energy Technology Data Exchange (ETDEWEB)

    Ibral, Asmaa [Equipe d’Optique et Electronique du Solide, Département de Physique, Faculté des Sciences, Université Chouaïb Doukkali, B.P. 20 El Jadida Principale, El Jadida 24000 (Morocco); Laboratoire d’Instrumentation, Mesure et Contrôle, Département de Physique, Université Chouaïb Doukkali, B.P. 20 El Jadida Principale, El Jadida (Morocco); Zouitine, Asmae [Département de Physique, Ecole Nationale Supérieure d’Enseignement Technique, Université Mohammed V Souissi, B.P. 6207 Rabat-Instituts, Rabat (Morocco); Assaid, El Mahdi, E-mail: eassaid@yahoo.fr [Equipe d’Optique et Electronique du Solide, Département de Physique, Faculté des Sciences, Université Chouaïb Doukkali, B.P. 20 El Jadida Principale, El Jadida 24000 (Morocco); Laboratoire d’Instrumentation, Mesure et Contrôle, Département de Physique, Université Chouaïb Doukkali, B.P. 20 El Jadida Principale, El Jadida (Morocco); Feddi, El Mustapha [Département de Physique, Ecole Nationale Supérieure d’Enseignement Technique, Université Mohammed V Souissi, B.P. 6207 Rabat-Instituts, Rabat (Morocco); and others

    2014-09-15

    Ground state energy and wave function of a hydrogen-like off-centre donor impurity, confined anywhere in a ZnS/CdSe spherical core/shell nanostructure are determined in the framework of the envelope function approximation. Conduction band-edge alignment between core and shell of nanostructure is described by a finite height barrier. Dielectric constant mismatch at the surface where core and shell materials meet is taken into account. Electron effective mass mismatch at the inner surface between core and shell is considered. A trial wave function where coulomb attraction between electron and off-centre ionized donor is used to calculate ground state energy via the Ritz variational principle. The numerical approach developed enables access to the dependence of binding energy, coulomb correlation parameter, spatial extension and radial probability density with respect to core radius, shell radius and impurity position inside ZnS/CdSe core/shell nanostructure.

  10. Ground state energy and wave function of an off-centre donor in spherical core/shell nanostructures: Dielectric mismatch and impurity position effects

    International Nuclear Information System (INIS)

    Ibral, Asmaa; Zouitine, Asmae; Assaid, El Mahdi; Feddi, El Mustapha

    2014-01-01

    Ground state energy and wave function of a hydrogen-like off-centre donor impurity, confined anywhere in a ZnS/CdSe spherical core/shell nanostructure are determined in the framework of the envelope function approximation. Conduction band-edge alignment between core and shell of nanostructure is described by a finite height barrier. Dielectric constant mismatch at the surface where core and shell materials meet is taken into account. Electron effective mass mismatch at the inner surface between core and shell is considered. A trial wave function where coulomb attraction between electron and off-centre ionized donor is used to calculate ground state energy via the Ritz variational principle. The numerical approach developed enables access to the dependence of binding energy, coulomb correlation parameter, spatial extension and radial probability density with respect to core radius, shell radius and impurity position inside ZnS/CdSe core/shell nanostructure

  11. 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.

  12. 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

  13. Impurity induced neutralization of MeV energy protons in JET plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Gondhalekar, A [Commission of the European Communities, Abingdon (United Kingdom). JET Joint Undertaking; Korotkov, A A [AF Ioffe Institute, Saint Petersburg (Russian Federation)

    1994-07-01

    A model elucidating the role of carbon and beryllium, the main impurities in JET plasmas, in neutralizing MeV energy protons, which arise during ICRF heating of deuterium plasmas in the hydrogen minority heating mode D(H), and from D-D fusion reactions, is presented. The model establishes charge transfer from hydrogen-like impurity ions to protons as the main process for neutralization. Calculations for deducing the proton energy distribution function from measured hydrogen flux are described. The validity of the model is tested by using it to described the measured flux in different conditions of plasma heating and fueling. Further, it is used to deduce the background thermal deuterium atom density at the plasma center. 9 refs., 6 figs.

  14. 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....

  15. 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.

  16. 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

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  18. 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

  19. Photoionization cross section and binding energy of single dopant in hollow cylindrical core/shell quantum dot

    Science.gov (United States)

    Feddi, E.; El-Yadri, M.; Dujardin, F.; Restrepo, R. L.; Duque, C. A.

    2017-02-01

    In this study, we have investigated the confined donor impurity in a hollow cylindrical-shell quantum dot. The charges are assumed to be completely confined to the interior of the shell with rigid walls. Within the framework of the effective-mass approximation and by using a simple variational approach, we have computed the donor binding energy as a function of the shell sizes in order to study the behavior of the electron-impurity attraction for a very small thickness. Our results show that the binding energy of a donor impurity placed at the center of cylindrical core/shell dots depends strongly on the shell size. The binding energy increases when the shell-wideness becomes smaller and shows the same behavior as in a simple cylindrical quantum dot. A special case has been studied, which corresponds to the ratio between the inner and outer radii near to one (a/b → 1) for which our model gives a non-significant behavior of the impurity binding energy. This fact implies the existence of a critical value (a/b) for which the binding energy of the donor impurity tends to the limit value of 4 effective Rydbergs as in a 2D quantum well. We also analyse the photoionization cross section considering only the in-plane incident radiation polarization. We determine its behavior as a function of photon energy, shell size, and donor position. The measurement of photoionization in such systems would be of great interest to understand the optical properties of carriers in quantum dots.

  20. Electron density of states in a one-dimensional distorted system with impurities: Coherent potential approximation

    International Nuclear Information System (INIS)

    Bulka, B.R.

    1982-04-01

    A tight-binding one-dimensional distorted system with impurities is considered and the electron density of states is calculated in the coherent potential approximation. It is shown that two types of impurities, an impurity built in a chain and a domain wall (a soliton), play the essential role and a drastic reduction of the energy gap is observed for a few per cent of impurities. The experimental situation in polyacetylene is also discussed. (author)

  1. Isotope effect with energy-dependent density of states and impurities

    International Nuclear Information System (INIS)

    Williams, P.J.; Carbotte, J.P.

    1992-01-01

    We have calculated the total isotope coefficient β in a model where there is energy-dependent structure in the electronic density of states. We model the structure with a simple Lorentzian. In our calculation, doping has the effect of shifting the Fermi level and broadening the structure in the density of states. We have treated the dopants both as normal and as magnetic impurities. The asymmetry observed in the experimental data is found in our results. However, the complete range of values observed is difficult to reproduce. We question also whether the shifts in Fermi level required in such models are reasonable

  2. Theoretical investigation of stark effect on shallow donor binding energy in InGaN spherical QD-QW

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-08-01

    In this paper, a simultaneous study of electric field and impurity's position effects on the ground-state shallow-donor binding energy in GaN|InGaN|GaN spherical quantum dot-quantum well (SQD-QW) as a function of the ratio of the inner and the outer radius is reported. The calculations are investigated using variational approach within the framework of the effective-mass approximation. The numerical results show that: (i) the binding energy is strongly affected by the external electric field and the SQD-QW dimension, (ii) a critical value of spherical system's radius is obtained constituting the limit of three dimension confinement and spherical thin layer confinement and (iii) the Stark shift increases with increasing electric field and it is more pronounced around the position of the impurity corresponding to the binding energy maxima than in the spherical layer extremities.

  3. Theoretical investigation of stark effect on shallow donor binding energy in InGaN spherical QD-QW

    International Nuclear Information System (INIS)

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

    2013-01-01

    In this paper, a simultaneous study of electric field and impurity's position effects on the ground-state shallow-donor binding energy in GaN|InGaN|GaN spherical quantum dot-quantum well (SQD-QW) as a function of the ratio of the inner and the outer radius is reported. The calculations are investigated using variational approach within the framework of the effective-mass approximation. The numerical results show that: (i) the binding energy is strongly affected by the external electric field and the SQD-QW dimension, (ii) a critical value of spherical system's radius is obtained constituting the limit of three dimension confinement and spherical thin layer confinement and (iii) the Stark shift increases with increasing electric field and it is more pronounced around the position of the impurity corresponding to the binding energy maxima than in the spherical layer extremities

  4. 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.

  5. Effect of impurity doping on tunneling conductance in AB-stacked bi-layer graphene: A tight-binding study

    Energy Technology Data Exchange (ETDEWEB)

    Rout, G. C., E-mail: siva1987@iopb.res.in, E-mail: skp@iopb.res.in, E-mail: gcr@iopb.res.in [Physics Enclave, Plot No-664/4825, Lane-4A, Shree Vihar, Bhubaneswar-751031, Odisha (India); Sahu, Sivabrata [School of Applied Sciences (Physics), KIIT University, Bhubaneswar-751024, Odisha (India); Panda, S. K. [K.D. Science College, Pochilima, Hinjilicut,Pin-761101 Ganjam, Orissa (India)

    2016-04-13

    We report here a microscopic tight-binding model calculation for AB-stacked bilayer graphene in presence of biasing potential between the two layers and the impurity effects to study the evolution of the total density of states with special emphasis on opening of band gap near Dirac point. We have calculated the electron Green’s functions for both the A and B sub-lattices by Zubarev technique. The imaginary part of the Green’s function gives the partial and total density of states of electrons. The density of states are computed numerically for 1000 × 1000 grid points of the electron momentum. The evolution of the opening of band gap near van-Hove singularities as well as near Dirac point is investigated by varying the different interlayer hoppings and the biasing potentials. The inter layer hopping splits the density of states at van-Hove singularities and produces a V-shaped gap near Dirac point. Further the biasing potential introduces a U shaped gap near Dirac point with a density minimum at the applied potential(i.e. at V/2).

  6. Effect of impurity doping on tunneling conductance in AB-stacked bi-layer graphene: A tight-binding study

    International Nuclear Information System (INIS)

    Rout, G. C.; Sahu, Sivabrata; Panda, S. K.

    2016-01-01

    We report here a microscopic tight-binding model calculation for AB-stacked bilayer graphene in presence of biasing potential between the two layers and the impurity effects to study the evolution of the total density of states with special emphasis on opening of band gap near Dirac point. We have calculated the electron Green’s functions for both the A and B sub-lattices by Zubarev technique. The imaginary part of the Green’s function gives the partial and total density of states of electrons. The density of states are computed numerically for 1000 × 1000 grid points of the electron momentum. The evolution of the opening of band gap near van-Hove singularities as well as near Dirac point is investigated by varying the different interlayer hoppings and the biasing potentials. The inter layer hopping splits the density of states at van-Hove singularities and produces a V-shaped gap near Dirac point. Further the biasing potential introduces a U shaped gap near Dirac point with a density minimum at the applied potential(i.e. at V/2).

  7. Low-energy excitations in impurity substituted CuGeO3

    International Nuclear Information System (INIS)

    Jones, B. R.; Sushkov, A. B.; Musfeldt, J. L.; Wang, Y. J.; Revcolevschi, A.; Dhalenne, G.

    2001-01-01

    We report far-infrared reflectance measurements of Zn- and Si-doped CuGeO 3 single crystals as a function of applied magnetic field at low temperature. Overall, the low-energy far-infrared spectra are extraordinarily sensitive to the various phase boundaries in the H-T diagram, with the features being especially rich in the low-temperature dimerized state. Zn impurity substitution rapidly collapses the 44 cm -1 zone-boundary spin Peierls gap, although broadened magnetic excitations are observed at the lightest doping level (0.2%) and a remnant is still observable at 0.7% substitution. In a 0.7% Si-doped sample, there is no evidence of the spin gap. Impurity substitution effects on the intensity of the 98 cm -1 zone-folding mode are striking as well. The lightly doped Zn crystals display an enhanced response, and even at intermediate doping levels, the mode intensity is larger than that in the pristine material. The Si-doped sample also displays an increased intensity of the 98 cm -1 mode in the spin Peierls phase relative to the pure material. The observed trends are discussed in terms of the effect of disorder on the spin gap and 98 cm -1 mode, local oscillator strength sum rules, and broken selection rules

  8. Energy levels of GaAs/Al{sub x}Ga{sub 1-x}As/AlAs spherical quantum dot with an impurity

    Energy Technology Data Exchange (ETDEWEB)

    Boz, Figen Karaca, E-mail: figenb@trakya.edu.tr; Nisanci, Beyza; Aktas, Saban; Okan, S. Erol

    2016-11-30

    Highlights: • Energy levels and probability distribution of an electron in GaAs/AlxGa1-xAs/AlAs spherical quantum dot were calculated. • The size effects on the electronic binding energy were determined within a core/shell/shell model. • The differences between the impurity energies of the first and the second levels are detected. - Abstract: We have calculated the energy levels and the radial probability distributions of an electron with an impurity in a spherical quantum dot which is layered as GaAs/Al{sub x}Ga{sub 1-x}As/AlAs. The numerical method used is the fourth-order Runge–Kutta method in the framework of the effective mass approximation. The variation of the energy levels have been calculated as functions of the radius of the GaAs sphere and the thickness of Al{sub x}Ga{sub 1-x}As spherical layer considering effective mass and dielectric constant mismatches. The results have presented the importance of the geometry on the electronic properties of the spherical GaAs/Al{sub x}Ga{sub 1-x}As/AlAs quantum dot.

  9. Hydrostatic pressure effects on impurity states in InAs/GaAs quantum dot

    International Nuclear Information System (INIS)

    Xia Congxin; Liu Yaming; Wei Shuyi

    2008-01-01

    Within the framework of effective-mass approximation, the hydrostatic pressure effects on the donor binding energy of a hydrogenic impurity in InAs/GaAs self-assembled quantum dot(QD) are investigated by means of a variational method. Numerical results show that the donor binding energy increases when the hydrostatic pressure increases for any impurity position and QD size. Moreover, the hydrostatic pressure has a remarkable influence on the donor binding energy for small QD. Realistic cases, including the impurity in the QD and the surrounding barrier, are considered

  10. The effect of carbon impurities on molybdenum surface morphology evolution under high-flux low-energy helium ion irradiation

    International Nuclear Information System (INIS)

    Tripathi, J.K.; Novakowski, T.J.; Gonderman, S.; Bharadwaj, N.; Hassanein, A.

    2016-01-01

    We report on the role of carbon (C) impurities, in molybdenum (Mo) fuzz evolutions on Mo surface during 100 eV He + ion irradiations. In this study we considered 0.01, 0.05, and 0.5% C + ion impurities in He + ion irradiations. For introducing such tiny C + ion impurities, gas mixtures of He and CH 4 have been chosen in following ratios; 99.95: 0.05, 99.75: 0.25, and 97.5: 2.5. Apart from these three cases, two additional cases, 100% He + ion (for Mo fuzz growth due to only He + ions) and 100% H + ion (for confirming the significance of tiny 0.04–2.0% H + ions in terms of Mo fuzz evolutions on Mo surface, if any), have also been considered. Ion energy (100 eV), ion fluence (2.6 × 10 24  ions m −2 ), and target temperature (923 K) were kept constant for each experiment and their selections were based on our previous studies [1,2]. Our study shows homogeneously populated and highly dense Mo fuzz evolutions on entire Mo surface for 100% He + ion irradiation case. Enhancement of C + ion impurities in He + ions causes a sequential reduction in Mo fuzz evolutions, leading to almost complete prevention of Mo fuzz evolutions for 0.5% C + ion impurity concentrations. Additionally, no fuzz formation for 100% H + ion irradiation at all, were seen (apart from some tiny nano-structuring, in very limited regions). This indicates that there is no significant role of H + ions in Mo fuzz evolutions (at least for such tiny amount, 0.04–2.0% H + ions). The study is significant to understand the behavior of potential high-Z plasma facing components (PFCs), in the, presence of tiny amount of C impurities, for nuclear fusion relevant applications. - Highlights: • Mo Fuzz evolutions due to low-energy high-flux 100% He + ion irradiation. • Sequential reduction in Mo fuzz evolutions with increasing C + ion impurities in He + ions. • Almost complete prevention of Mo fuzz evolutions for 0.5% C + ion impurity in He + ions. • No Mo fuzz formation for 100% H + ion

  11. Multi-energy soft-x-ray technique for impurity transport measurements in the fusion plasma edge

    International Nuclear Information System (INIS)

    Clayton, D J; Tritz, K; Stutman, D; Finkenthal, M; Kumar, D; Kaye, S M; LeBlanc, B P; Paul, S; Sabbagh, S A

    2012-01-01

    A new diagnostic technique was developed to produce high-resolution impurity transport measurements of the steep-gradient edge of fusion plasmas. Perturbative impurity transport measurements were performed for the first time in the NSTX plasma edge (r/a ∼ 0.6 to the SOL) with short neon gas puffs, and the resulting line and continuum emission was measured with the new edge multi-energy soft-x-ray (ME-SXR) diagnostic. Neon transport is modeled with the radial impurity transport code STRAHL and the resulting x-ray emission is computed using the ADAS atomic database. The radial transport coefficient profiles D(r) and v(r), and the particle flux from the gas puff Φ(t), are the free parameters in this model and are varied to find the best fit to experimental x-ray emissivity measurements, with bolometry used to constrain the impurity source. Initial experiments were successful and results were consistent with previous measurements of core impurity transport and neoclassical transport calculations. New diagnostic tools will be implemented on NSTX-U to further improve these transport measurements. (paper)

  12. The effect of impurity level on ultrafine-grained microstructures and their stability in low stacking fault energy silver

    International Nuclear Information System (INIS)

    Hegedus, Zoltan; Gubicza, Jeno; Kawasaki, Megumi; Chinh, Nguyen Q.; Fogarassy, Zsolt; Langdon, Terence G.

    2011-01-01

    Highlights: → Effect of impurity content on microstructure in ECAP-processed silver was studied. → There is a lower degree of twinning in the less pure material for high strains. → The samples processed for 4-16 passes showed self-annealing during storage at RT. → Small increase of impurity level resulted in a much better stability at RT. - Abstract: The effect of impurity content on the evolution of microstructure in low stacking fault energy silver processed by severe plastic deformation (SPD) was studied. The SPD-processing was carried out on 4N5 and 4N purity Ag samples by equal-channel angular pressing (ECAP) up to 16 passes. It was found that, although the minimum grain size and the maximum dislocation density were not affected by the different impurity atom content, there is a lower degree of twinning in the less pure material for high number of passes. The small increase of impurity level from 4N5 to 4N in Ag resulted in a significantly better thermal stability at room temperature for the ultrafine-grained microstructures obtained by ECAP.

  13. First calculation of the deuteron binding energy

    International Nuclear Information System (INIS)

    Schaegger, B.

    2012-01-01

    No universal constant characterizing the nuclear force has yet been found as for gravity and electromagnetism. The neutron is globally neutral with a zero net charge. The charges contained in a neutron may be separated by the electric field of a nearby proton and therefore being attracted by electrostatic induction in the same way as a rubbed plastic pen attracts small pieces of paper. There is also a magnetic force that may repel the nucleons like magnets in the proper relative orientation. In the deuteron, the heavy hydrogen nucleus, the induced electrostatic attraction is equilibrated by the magnetic repulsion between the opposite and colinear moments of the nucleons. Equilibrium is calculated by minimizing the electromagnetic interaction potential, giving a binding energy of 1.6 MeV, not much lower than the experimental value, 2.2 MeV. No fitting parameter is used: it is a true ab initio calculation

  14. Measuring Intermolecular Binding Energies by Laser Spectroscopy.

    Science.gov (United States)

    Knochenmuss, Richard; Maity, Surajit; Féraud, Géraldine; Leutwyler, Samuel

    2017-02-22

    The ground-state dissociation energy, D0(S0), of isolated intermolecular complexes in the gas phase is a fundamental measure of the interaction strength between the molecules. We have developed a three-laser, triply resonant pump-dump-probe technique to measure dissociation energies of jet-cooled M•S complexes, where M is an aromatic chromophore and S is a closed-shell 'solvent' molecule. Stimulated emission pumping (SEP) via the S0→S1 electronic transition is used to precisely 'warm' the complex by populating high vibrational levels v" of the S0 state. If the deposited energy E(v") is less than D0(S0), the complex remains intact, and is then mass- and isomer-selectively detected by resonant two-photon ionization (R2PI) with a third (probe) laser. If the pumped level is above D0(S0), the hot complex dissociates and the probe signal disappears. Combining the fluorescence or SEP spectrum of the cold complex with the SEP breakoff of the hot complex brackets D0(S0). The UV chromophores 1-naphthol and carbazole were employed; these bind either dispersively via the aromatic rings, or form a hydrogen bond via the -OH or -NH group. Dissociation energies have been measured for dispersively bound complexes with noble gases (Ne, Kr, Ar, Xe), diatomics (N2, CO), alkanes (methane to n-butane), cycloalkanes (cyclopropane to cycloheptane), and unsaturated compounds (ethene, benzene). Hydrogen-bond dissociation energies have been measured for H2O, D2O, methanol, ethanol, ethers (oxirane, oxetane), NH3 and ND3.

  15. Stark effect-dependent of ground-state donor binding energy in InGaN/GaN parabolic QWW

    International Nuclear Information System (INIS)

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

    2013-01-01

    Using the finite-difference method within the quasi-one-dimensional effective potential model and effective mass approximation, the ground-state binding energy of hydrogenic shallow-donor impurity in wurtzite (WZ) (In,Ga)N/GaN parabolic transversal-section quantum-well wires (PQWWs) subjected to external electric field is investigated. An effective radius of a cylindrical QWW describing the strength of the lateral confinement is introduced. The results show that (i) the position of the largest electron probability density in x–y plane is located at a point and it is pushed along the negative sense by the electric field directed along the positive sense, (ii) the ground-state binding energy is largest for the impurity located at this point and starts to decrease when the impurity is away from this point, (iii) the ground-state binding energy decreases with increase in the external electric field and effective radius, and (iv) the Stark-shift increases with the increase of the external electric field and the effective radius

  16. Fitting theories of nuclear binding energies

    International Nuclear Information System (INIS)

    Bertsch, G.F.; Sabbey, B.; Uusnaekki, M.

    2005-01-01

    In developing theories of nuclear binding energy such as density-functional theory, the effort required to make a fit can be daunting because of the large number of parameters that may be in the theory and the large number of nuclei in the mass table. For theories based on the Skyrme interaction, the effort can be reduced considerably by using the singular value decomposition to reduce the size of the parameter space. We find that the sensitive parameters define a space of dimension four or so, and within this space a linear refit is adequate for a number of Skyrme parameters sets from the literature. We find no marked differences in the quality of the fit among the SLy4, the BSk4, and SkP parameter sets. The root-mean-square residual error in even-even nuclei is about 1.5 MeV, half the value of the liquid drop model. We also discuss an alternative norm for evaluating mass fits, the Chebyshev norm. It focuses attention on the cases with the largest discrepancies between theory and experiment. We show how it works with the liquid drop model and make some applications to models based on Skyrme energy functionals. The Chebyshev norm seems to be more sensitive to new experimental data than the root-mean-square norm. The method also has the advantage that candidate improvements to the theories can be assessed with computations on smaller sets of nuclei

  17. 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 fo...

  18. 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

  19. Energy Trapping, Release, and Transport in Three-Dimensional Energetic Solids and Molecular Crystals: Theory of Defects and Impurities.

    Science.gov (United States)

    1984-12-31

    and 3. T. Waber, Concerning the Trapping of Positrons in Ionic Solids, in Positron Annihilation , P. G. Coleman, S. C. Sharma and L. M. Diana, Eds., 682...1982). *144. A. B. Kunz and 3. T. Waber, A Theoretical Study of the Binding of Positrons to Gaseous Molecules, in Positron Annihilation . P. G. Coleman, S...variety of other cases which include systems in unusual charge states such as Fe + in SrTiOz or Fe in MgO . Impurity systems in their excited states are

  20. Interaction between impurities in Ag dilute alloys

    International Nuclear Information System (INIS)

    Krolas, K.; Wodniecka, B.; Wodniecki, P.; Uniwersytet Jagiellonski, Krakow

    1977-01-01

    Time dependent perturbed angular correlation measurements of gamma radiation in 111 Cd after 111 In decay were performed in AgPd and AgPt alloys. The concentration of Pd or Pt atoms being the nearest neighbours to the probe atoms is much higher than that one deduced from random impurity distribution. This effect results from the attractive interaction between the In probe atoms and Pt or Pd impurity atoms in silver host lattice. The binding energy of InPd and InPt complexes was measured as 135 +- 9 meV and 171 +- 9 meV, respectively. (author)

  1. Implicit ligand theory for relative binding free energies

    Science.gov (United States)

    Nguyen, Trung Hai; Minh, David D. L.

    2018-03-01

    Implicit ligand theory enables noncovalent binding free energies to be calculated based on an exponential average of the binding potential of mean force (BPMF)—the binding free energy between a flexible ligand and rigid receptor—over a precomputed ensemble of receptor configurations. In the original formalism, receptor configurations were drawn from or reweighted to the apo ensemble. Here we show that BPMFs averaged over a holo ensemble yield binding free energies relative to the reference ligand that specifies the ensemble. When using receptor snapshots from an alchemical simulation with a single ligand, the new statistical estimator outperforms the original.

  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. Negative compressibility observed in graphene containing resonant impurities

    International Nuclear Information System (INIS)

    Chen, X. L.; Wang, L.; Li, W.; Wang, Y.; He, Y. H.; Wu, Z. F.; Han, Y.; Zhang, M. W.; Xiong, W.; Wang, N.

    2013-01-01

    We observed negative compressibility in monolayer graphene containing resonant impurities under different magnetic fields. Hydrogenous impurities were introduced into graphene by electron beam (e-beam) irradiation. Resonant states located in the energy region of ±0.04 eV around the charge neutrality point were probed in e-beam-irradiated graphene capacitors. Theoretical results based on tight-binding and Lifshitz models agreed well with experimental observations of graphene containing a low concentration of resonant impurities. The interaction between resonant states and Landau levels was detected by varying the applied magnetic field. The interaction mechanisms and enhancement of the negative compressibility in disordered graphene are discussed.

  4. On binding energy of trions in bulk materials

    Science.gov (United States)

    Filikhin, Igor; Kezerashvili, Roman Ya.; Vlahovic, Branislav

    2018-03-01

    We study the negatively T- and positively T+ charged trions in bulk materials in the effective mass approximation within the framework of a potential model. The binding energies of trions in various semiconductors are calculated by employing Faddeev equation in configuration space. Results of calculations of the binding energies for T- are consistent with previous computational studies and are in reasonable agreement with experimental measurements, while the T+ is unbound for all considered cases. The mechanism of formation of the binding energy of trions is analyzed by comparing contributions of a mass-polarization term related to kinetic energy operators and a term related to the Coulomb repulsion of identical particles.

  5. 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.

  6. The effect of carbon impurities on molybdenum surface morphology evolution under high-flux low-energy helium ion irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Tripathi, J.K., E-mail: jtripat@purdue.edu; Novakowski, T.J.; Gonderman, S.; Bharadwaj, N.; Hassanein, A.

    2016-09-15

    We report on the role of carbon (C) impurities, in molybdenum (Mo) fuzz evolutions on Mo surface during 100 eV He{sup +} ion irradiations. In this study we considered 0.01, 0.05, and 0.5% C{sup +} ion impurities in He{sup +} ion irradiations. For introducing such tiny C{sup +} ion impurities, gas mixtures of He and CH{sub 4} have been chosen in following ratios; 99.95: 0.05, 99.75: 0.25, and 97.5: 2.5. Apart from these three cases, two additional cases, 100% He{sup +} ion (for Mo fuzz growth due to only He{sup +} ions) and 100% H{sup +} ion (for confirming the significance of tiny 0.04–2.0% H{sup +} ions in terms of Mo fuzz evolutions on Mo surface, if any), have also been considered. Ion energy (100 eV), ion fluence (2.6 × 10{sup 24} ions m{sup −2}), and target temperature (923 K) were kept constant for each experiment and their selections were based on our previous studies [1,2]. Our study shows homogeneously populated and highly dense Mo fuzz evolutions on entire Mo surface for 100% He{sup +} ion irradiation case. Enhancement of C{sup +} ion impurities in He{sup +} ions causes a sequential reduction in Mo fuzz evolutions, leading to almost complete prevention of Mo fuzz evolutions for 0.5% C{sup +} ion impurity concentrations. Additionally, no fuzz formation for 100% H{sup +} ion irradiation at all, were seen (apart from some tiny nano-structuring, in very limited regions). This indicates that there is no significant role of H{sup +} ions in Mo fuzz evolutions (at least for such tiny amount, 0.04–2.0% H{sup +} ions). The study is significant to understand the behavior of potential high-Z plasma facing components (PFCs), in the, presence of tiny amount of C impurities, for nuclear fusion relevant applications. - Highlights: • Mo Fuzz evolutions due to low-energy high-flux 100% He{sup +} ion irradiation. • Sequential reduction in Mo fuzz evolutions with increasing C{sup +} ion impurities in He{sup +} ions. • Almost complete prevention of Mo

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-10-15

    Simultaneous study of magnetic field and impurity's position effects on the ground-state shallow-donor binding energy in GaN|InGaN|GaN (core|well|shell) spherical quantum dot–quantum well (SQDQW) as a function of the ratio of the inner and the outer radius is reported. The calculations are investigated within the framework of the effective-mass approximation and an infinite deep potential describing the quantum confinement effect. A Ritz variational approach is used taking into account of the electron-impurity correlation and the magnetic field effect in the trial wave-function. It appears that the binding energy depends strongly on the external magnetic field, the impurity's position and the structure radius. It has been found that: (i) the magnetic field effect is more marked in large layer than in thin layer and (ii) it is more pronounced in the spherical layer center than in its extremities.

  9. 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.

  10. Predicting accurate absolute binding energies in aqueous solution

    DEFF Research Database (Denmark)

    Jensen, Jan Halborg

    2015-01-01

    Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic. In this paper I summarize some of the many factors that could easily contribute 1-3 kcal......-represented by continuum models. While I focus on binding free energies in aqueous solution the approach also applies (with minor adjustments) to any free energy difference such as conformational or reaction free energy differences or activation free energies in any solvent....

  11. Investigation of energy levels of Er-impurity centers in Si by the method of ballistic electron emission spectroscopy

    International Nuclear Information System (INIS)

    Filatov, D. O.; Zimovets, I. A.; Isakov, M. A.; Kuznetsov, V. P.; Kornaukhov, A. V.

    2011-01-01

    The method of ballistic electron emission spectroscopy is used for the first time to study the energy spectrum of Er-impurity complexes in Si. The features are observed in the ballistic electron spectra of mesa diodes based on p + -n + Si structures with a thin (∼30 nm) p + -Si:Er surface layer in the region of ballistic-electron energies eV t lower than the conduction-band-edge energy E c in this layer. They are associated with the tunnel injection of ballistic electrons from the probe of the scanning tunnel microscope to the deep donor levels of the Er-impurity complexes in the p + -Si:Er layer with subsequent thermal excitation into the conduction band and the diffusion to the p + -n + junction and the direct tunneling in it. To verify this assumption, the ballistic-electron transport was simulated in the system of the Pt probe, native-oxide layer SiO 2 -p + -Si:Er-n + , and Si substrate. By approximating the experimental ballistic-electron spectra with the modeling spectra, the ground-state energy of the Er complex in Si was determined: E d ≈ E c − 0.27 eV. The indicated value is consistent with the data published previously and obtained from the measurements of the temperature dependence of the free-carrier concentration in Si:Er layers.

  12. Polarizability and binding energy of a shallow donor in spherical quantum dot-quantum well (QD-QW)

    Science.gov (United States)

    Rahmani, K.; Chrafih, Y.; M’Zred, S.; Janati, S.; Zorkani, I.; Jorio, A.; Mmadi, A.

    2018-03-01

    The polarizability and the binding energy is estimated for a shallow donor confined to move in inhomogeneous quantum dots (CdS/HgS/CdS). In this work, the Hass variational method within the effective mass approximation in used in the case of an infinitely deep well. The polarizability and the binding energy depend on the inner and the outer radius of the QDQW, also it depends strongly on the donor position. It’s found that the stark effect is more important when the impurity is located at the center of the (QDQW) and becomes less important when the donor moves toward the extremities of the spherical layer. When the electric field increases, the binding energy and the polarizability decreases. Its effects is more pronounced when the impurity is placed on the center of the spherical layer and decrease when the donor move toward extremities of this spherical layer. We have demonstrated the existence of a critical value {≤ft( {{{{R_1}} \\over {{R_2}}}} \\right)cri} which can be used to distinguish the tree dimension confinement from the spherical surface confinement and it’s may be important for the nanofabrication techniques.

  13. First-principles thermodynamic calculations of diffusion characteristics of impurities in γ-iron

    International Nuclear Information System (INIS)

    Tsuru, T.; Kaji, Y.

    2013-01-01

    Because solute impurities have an effect on embrittlement through segregation under irradiation, solute stability and the influence of irradiation on the diffusion characteristics of impurities become prominent due to several acceleration effects of high irradiance circumstances in irradiated materials. In this study, the diffusion characteristics of several impurities in non-magnetic fcc iron are investigated using first-principles density functional theory (DFT) calculations. In accordance with classical diffusion and transition state theories, we nonempirically evaluated the contribution to properties of the binding energy between vacancy and each impurity and the migration enthalpy. The migration energy was calculated using the nudged elastic band method with DFT. The vacancy formation energy, including the entropic contributions to free energies in γ-iron, was evaluated by considering vibrational phonon frequencies based on frozen phonons employing the harmonic approximation for the lattice dynamics. Consequently, we confirmed that the binding energy between large-radius impurities and vacancies is larger than that with an equivalent size of the solvent element, and that the migration enthalpies of these impurities are quite small compared with self diffusion. This finding may indicate that the electronic binding states at the saddle point have a large influence on the migration of impurities

  14. Binding energy and single-particle energies in the 16O Region

    International Nuclear Information System (INIS)

    Fiase, J.O.; Sharma, L.K.

    2004-01-01

    In this paper we present the binding energy of 16 O together with 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 Nijmegen 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.Our calculated binding energy, E B = - 127.8 MeV with r c = 0.241 fm compares well with the experimental binding energy, E B = - 127.6 MeV

  15. The effects of optical phonon on the binding energy of bound polaron in a wurtzite ZnO/MgxZn1−xO quantum well

    International Nuclear Information System (INIS)

    Zhao, Feng-Qi; Guo, Zi-Zheng; Zhu, Jun

    2014-01-01

    An improved Lee-Low-Pines intermediate coupling method is used to study the energies and binding energies of bound polarons in a wurtzite ZnO/Mg x Zn 1−x O quantum well. The contributions from different branches of long-wave optical phonons, i.e., confined optical phonons, interface optical phonons, and half-space optical phonons are considered. In addition to electron-phonon interaction, the impurity-phonon interaction, and the anisotropy of material parameters, such as phonon frequency, electron effective mass, and dielectric constant, are also included in our computation. Ground-state energies, binding energies and detailed phonon contributions from various phonons as functions of well width, impurity position and composition are presented. Our result suggests that total phonon contribution to ground state and binding energies in the studied wurtzite ZnO/Mg 0.3 Zn 0.7 O quantum wells varies between 28–23 meV and 62–45 meV, respectively, which are much larger than the corresponding values (about 3.2–1.8 meV and 1.6–0.3 meV) in GaAs/Al 0.3 Ga 0.7 As quantum wells. For a narrower quantum well, the phonon contribution mainly comes from interface and half-space phonons, for a wider quantum well, most of phonon contribution originates from confined phonons. The contribution from all the phonon modes to binding energies increases slowly either when impurity moves far away from the well center in the z direction or with the increase in magnesium composition (x). It is found that different phonons have different influences on the binding energies of bound polarons. Furthermore, the phonon contributions to binding energies as functions of well width, impurity position, and composition are very different from one another. In general, the electron-optical phonon interaction and the impurity center-optical phonon interaction play an important role in electronic states of ZnO-based quantum wells and cannot be neglected.

  16. Binding energy effects in cascade evolution and sputtering

    International Nuclear Information System (INIS)

    Robinson, M.T.

    1995-06-01

    The MARLOWE model was extended to include a binding energy dependent on the local crystalline order, so that atoms are bound less strongly to their lattice sites near surfaces or associated damage. Sputtering and cascade evolution were studied on the examples of self-ion irradiations of Cu and Au monocrystals. In cascades, the mean binding energy is reduced ∼8% in Cu with little dependence on the initial recoil energy; in Au, it is reduced ∼9% at 1 keV and ∼15% at 100 keV. In sputtering, the mean binding energy is reduced ∼8% in Cu and ∼15% in Au with little energy dependence; the yields are increased about half as much. Most sites from which sputtered atoms originate are isolated in both metals. Small clusters of such sites occur in Cu, but there are some large clusters in Au, especially in [111] targets. There are always more large clusters with damage-dependent binding than with a constant binding energy, but only a few clusters are compact enough to be regarded as pits

  17. 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

  18. Exciton binding energy in a pyramidal quantum dot

    Indian Academy of Sciences (India)

    A ANITHA

    2018-03-27

    Mar 27, 2018 ... screening function on exciton binding energy in a pyramid-shaped quantum dot of ... tures may generate unique properties and they show .... where Ee is the ground-state energy of the electron in ... Figure 1. The geometry of the pyramidal quantum dot. base and H is the height of the pyramid which is taken.

  19. Self-consistent tight-binding model of B and N doping in graphene

    DEFF Research Database (Denmark)

    Pedersen, Thomas Garm; Pedersen, Jesper Goor

    2013-01-01

    . The impurity potential depends sensitively on the impurity occupancy, leading to a self-consistency requirement. We solve this problem using the impurity Green's function and determine the self-consistent local density of states at the impurity site and, thereby, identify acceptor and donor energy resonances.......Boron and nitrogen substitutional impurities in graphene are analyzed using a self-consistent tight-binding approach. An analytical result for the impurity Green's function is derived taking broken electron-hole symmetry into account and validated by comparison to numerical diagonalization...

  20. 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.

  1. 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…

  2. Polaron binding energy in polymers: poly[methyl(phenyl)silylene

    Czech Academy of Sciences Publication Activity Database

    Nožár, Juraj; Nešpůrek, Stanislav; Šebera, Jakub

    2012-01-01

    Roč. 18, č. 2 (2012), s. 623-629 ISSN 1610-2940 R&D Projects: GA AV ČR KAN400720701 Institutional research plan: CEZ:AV0Z40500505 Keywords : polaron * polaron binding energy * polysilane Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.984, year: 2012

  3. 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

  4. Full-f XGC1 gyrokinetic study of improved ion energy confinement from impurity stabilization of ITG turbulence

    Science.gov (United States)

    Kim, Kyuho; Kwon, Jae-Min; Chang, C. S.; Seo, Janghoon; Ku, S.; Choe, W.

    2017-06-01

    Flux-driven full-f gyrokinetic simulations are performed to study carbon impurity effects on the ion temperature gradient (ITG) turbulence and ion thermal transport in a toroidal geometry. Employing the full-f gyrokinetic code XGC1, both main ions and impurities are evolved self-consistently including turbulence and neoclassical physics. It is found that the carbon impurity profile self-organizes to form an inwardly peaked density profile, which weakens the ITG instabilities and reduces the overall fluctuations and ion thermal transport. A stronger reduction appears in the low frequency components of the fluctuations. The global structure of E × B flow also changes, resulting in the reduction of global avalanche like transport events in the impure plasma. Detailed properties of impurity transport are also studied, and it is revealed that both the inward neoclassical pinch and the outward turbulent transport are equally important in the formation of the steady state impurity profile.

  5. Alternate Energy Sources for Thermalplastic Binding Agent Consolidation

    Energy Technology Data Exchange (ETDEWEB)

    Frame, B.J.

    1999-01-01

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

  6. Intense laser effects on donor impurity in a cylindrical single and vertically coupled quantum dots under combined effects of hydrostatic pressure and applied electric field

    International Nuclear Information System (INIS)

    Duque, C.A.; Kasapoglu, E.; Sakiroglu, S.; Sari, H.; Soekmen, I.

    2010-01-01

    Using the effective mass and parabolic band approximations and a variational procedure we have calculated the combined effects of intense laser radiation, hydrostatic pressure, and applied electric field on shallow-donor impurity confined in cylindrical-shaped single and double GaAs-Ga 1-x Al x As QD. Several impurity positions and inputs of the heterostructure dimensions, hydrostatic pressure, and applied electric field have been considered. The laser effects have been introduced by a perturbative scheme in which the Coulomb and the barrier potentials are modified to obtain dressed potentials. Our findings suggest that (1) for on-center impurities in single QD the binding energy is a decreasing function of the dressing parameter and for small dot dimensions of the structures (lengths and radius) the binding energy is more sensitive to the dressing parameter, (2) the binding energy is an increasing/decreasing function of the hydrostatic pressure/applied electric field, (3) the effects of the intense laser field and applied electric field on the binding energy are dominant over the hydrostatic pressure effects, (4) in vertically coupled QD the binding energy for donor impurity located in the barrier region is smaller than for impurities in the well regions and can be strongly modified by the laser radiation, and finally (5) in asymmetrical double QD heterostructures the binding energy as a function of the impurity positions follows a similar behavior to the observed for the amplitude of probability of the noncorrelated electron wave function.

  7. Binding Energy, Vapor Pressure and Melting Point of Semiconductor Nanoparticles

    International Nuclear Information System (INIS)

    H. H. Farrell; C. D. Van Siclen

    2007-01-01

    Current models for the cohesive energy of nanoparticles generally predict a linear dependence on the inverse particle diameter for spherical clusters, or, equivalently, on the inverse of the cube root of the number of atoms in the cluster. Although this is generally true for metals, we find that for the group IV semiconductors, C, Si and Ge, this linear dependence does not hold. Instead, using first principles, density functional theory calculations to calculate the binding energy of these materials, we find a quadratic dependence on the inverse of the particle size. Similar results have also been obtained for the metallic group IV elements Sn and Pb. This is in direct contradiction to current assumptions. Further, as a consequence of this quadratic behavior, the vapor pressure of semiconductor nanoparticles rises more slowly with decreasing size than would be expected. In addition, the melting point of these nanoparticles will experience less suppression than experienced by metal nanoparticles with comparable bulk binding energies. This non-linearity also affects sintering or Ostwald ripening behavior of these nanoparticles as well as other physical properties that depend on the nanoparticle binding energy. The reason for this variation in size dependence involves the covalent nature of the bonding in semiconductors, and even in the 'poor' metals. Therefore, it is expected that this result will hold for compound semiconductors as well as the elemental semiconductors

  8. Impurity control in TFTR

    International Nuclear Information System (INIS)

    Cecchi, J.L.

    1980-06-01

    The control of impurities in TFTR will be a particularly difficult problem due to the large energy and particle fluxes expected in the device. As part of the TFTR Flexibility Modification (TEM) project, a program has been implemented to address this problem. Transport code simulations are used to infer an impurity limit criterion as a function of the impurity atomic number. The configurational designs of the limiters and associated protective plates are discussed along with the consideration of thermal and mechanical loads due to normal plasma operation, neutral beams, and plasma disruptions. A summary is given of the materials-related research, which has been a collaborative effort involving groups at Argonne National Laboratory, Sandia Laboratories, and Princeton Plasma Physics Laboratory. Conceptual designs are shown for getterng systems capable of regenerating absorbed tritium. Research on this topic by groups at the previously mentioned laboratories and SAES Research Laboratory is reviewed

  9. Evaluation of binding energies by using quantum mechanical methods

    International Nuclear Information System (INIS)

    Postolache, Cristian; Matei, Lidia; Postolache, Carmen

    2002-01-01

    Evaluation of binding energies (BE) in molecular structure is needed for modelling chemical and radiochemical processes by quantum-chemical methods. An important field of application is evaluation of radiolysis and autoradiolysis stability of organic and inorganic compounds as well as macromolecular structures. The current methods of calculation do not allow direct determination of BE but only of total binding energies (TBE) and enthalpies. BEs were evaluated indirectly by determining the homolytic dissociation energies. The molecular structures were built and geometrically optimized by the molecular mechanics methods MM+ and AMBER. The energy minimizations were refined by semi-empirical methods. Depending on the chosen molecular structure, the CNDO, INDO, PM3 and AM1 methods were used. To reach a high confidence level the minimizations were done for gradients lower than 10 -3 RMS. The energy values obtained by the difference of the fragment TBLs, of the transition states and initial molecular structures, respectively, were associated to the hemolytic fragmentation energy and BE, respectively. In order to evaluate the method's accuracy and to establish the application fields of the evaluation methods, the obtained values of BEs were compared with the experimental data taken from literature. To this goal there were built, geometrically optimized by semi-empirical methods and evaluated the BEs for 74 organic and inorganic compounds (alkanes, alkene, alkynes, halogenated derivatives, alcohols, aldehydes, ketones, carboxylic acids, nitrogen and sulfur compounds, water, hydrogen peroxide, ammonia, hydrazine, etc. (authors)

  10. 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

  11. Hydrostatic pressure and temperature effects on the binding energy and optical absorption of a multilayered quantum dot with a parabolic confinement

    International Nuclear Information System (INIS)

    Ortakaya, Sami; Kirak, Muharrem

    2016-01-01

    The influence of hydrostatic pressure, temperature, and impurity on the electronic and optical properties of spherical core/shell/well/shell (CSWS) nanostructure with parabolic confinement potential is investigated theoretically. The energy levels and wave functions of the structure are calculated by using shooting method within the effective-mass approximation. The numerical results show that the ground state donor binding energy as a function layer thickness very sensitively depends on the magnitude of pressure and temperature. Also, we investigate the probability distributions to understand clearly electronic properties. The obtained results show that the existence of the pressure and temperature has great influence on the electronic and optical properties. (paper)

  12. A = 4 0+ - 1+ binding-energy difference

    International Nuclear Information System (INIS)

    Gibson, B.F.; Lehman, D.R.

    1982-01-01

    The A = 4 Λ-hypernuclei provide a rich source of information about the s-wave properties of the fundamental hyperon-nucleon (YN) force as well as offer a unique opportunity to investigate the complications that arise in calculations of the properties of bound systems in which one baryon (here the Λ) with a given isospin couples strongly to another (the Σ) with a different isospin. The Λ 4 H - Λ 4 He isodoublet ground-state energies are not consistent with a charge symmetry hypothesis for the YN interaction. The (spin-flip) excitation energies are quite sensitive to the ΛN - ΣN coupling of the YN interaction. In particular, when one represents the free YN interaction in terms of one-channel effective ΛN potentials, the resulting 0 + (ground) state and 1 + (excited) spin-flip state are inversely ordered in terms of binding energies, the 1 + state being more bound. It is the Σ suppression that results from the reduced strength of the ΛN - ΣN off-diagonal coupling potential when the trinucleon core is restricted to isospin-1/2 which we study here. We find this spin-isospin suppression of the Λ-Σ conversion, which is due to the composite nature of the nuclear cores of the Λ 4 H and Λ 4 He hypernuclei, to be a significant factor in understanding the 0 + - 1 + binding energy relationship

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. Charge compensation and binding energy referencing in XPS analysis

    International Nuclear Information System (INIS)

    Metson, J.B.

    1999-01-01

    Full text: The past decade has seen a number of significant advances in the capabilities of commercial X-ray Photoelectron spectrometers. Of note have been the near universal adoption of monochromatised X-ray sources, very useful advances in spatial resolution, particularly in spectroscopy, and radical developments in sample handling and automation. However one of the most significant advances has been the development of several relatively new concepts in charge compensation. Throughout the evolution of XPS, the ability to compensate for surface charging and accurately determine binding energies, particularly with electrically inhomogenous samples, has remained one of the most intractable problems. Beginning perhaps with the Kratos, 'in the lens' electrostatic mirror/electron source coupled with a magnetic snorkel lens, a number of concepts have been advanced which take a quite different conceptual approach to charge compensation. They differ in a number of quite fundamental ways to the electron flood type compensators widely used and absolutely essential with instruments based on monochromatised sources. The concept of the local return of secondary electrons to their point of emission, largely negates the problems associated with differential charging across different regions of the surface, and suggests the possibility of overcoming one of the central limitations of XPS, that is the inability to compare absolute binding energies of species in different electrical as well as chemical environments. The general status of charge compensation and the use of internal binding energy references in XPS will be reviewed, along with some practical examples of where these techniques work, and where there is clearly still room for further development. Copyright (1999) Australian X-ray Analytical Association Inc

  19. Integrating water exclusion theory into βcontacts to predict binding free energy changes and binding hot spots

    Science.gov (United States)

    2014-01-01

    Background Binding free energy and binding hot spots at protein-protein interfaces are two important research areas for understanding protein interactions. Computational methods have been developed previously for accurate prediction of binding free energy change upon mutation for interfacial residues. However, a large number of interrupted and unimportant atomic contacts are used in the training phase which caused accuracy loss. Results This work proposes a new method, βACV ASA , to predict the change of binding free energy after alanine mutations. βACV ASA integrates accessible surface area (ASA) and our newly defined β contacts together into an atomic contact vector (ACV). A β contact between two atoms is a direct contact without being interrupted by any other atom between them. A β contact’s potential contribution to protein binding is also supposed to be inversely proportional to its ASA to follow the water exclusion hypothesis of binding hot spots. Tested on a dataset of 396 alanine mutations, our method is found to be superior in classification performance to many other methods, including Robetta, FoldX, HotPOINT, an ACV method of β contacts without ASA integration, and ACV ASA methods (similar to βACV ASA but based on distance-cutoff contacts). Based on our data analysis and results, we can draw conclusions that: (i) our method is powerful in the prediction of binding free energy change after alanine mutation; (ii) β contacts are better than distance-cutoff contacts for modeling the well-organized protein-binding interfaces; (iii) β contacts usually are only a small fraction number of the distance-based contacts; and (iv) water exclusion is a necessary condition for a residue to become a binding hot spot. Conclusions βACV ASA is designed using the advantages of both β contacts and water exclusion. It is an excellent tool to predict binding free energy changes and binding hot spots after alanine mutation. PMID:24568581

  20. Microdistribution of Impurities in Semiconductors and its Influence on Photovoltaic Energy Conversion.

    Science.gov (United States)

    Rava, Paolo

    electrically inert complex. The presence of unactivated areas close to the crystal periphery was attributed to a lower concentration of available vacancies due to the presence of the B-defects (vacancy clusters); a 650(DEGREES)C heat treatment changed their structure, possibly releasing vacancies which then participated in donor formation. On the other hand, the areas activated the first time at 450(DEGREES)C have fewer vacancies available the second time for donor formation and therefore are less activated. It was shown that the vacancy-oxygen complex must be the first step in the formation of multivacancy or any multioxygen donor complexes. The role of a factor other than oxygen in donor activation can be revealed only by a microscale analysis such as the one presented here. In fact, the areas in which donor formation is enhanced by 650(DEGREES)C heat treatment are completely undetected in a macroscale analysis, which therefore would lead to a proportionality between oxygen concentration and activated donors. This work shows that the accepted premise that the concentration of oxygen donors is proportional to the oxygen concentration is not generally valid. Multiple p-n junctions have been prepared in b -doped Si through overcompensation near the oxygen periodic concentration maxima by thermal donors generated during an appropriate heat treatment at 450(DEGREES)C. Application of this structure to photovoltaic energy conversion has been investigated. A new solar cell structure based on multiple p-n junctions was developed and tested. An increase in short circuit current was achieved, but at the same time a degradation in open circuit voltage occurred. An interpretation of the experimental data in the light of the results of a computer simulation showed that an overall increase in efficiency can be achieved in this structure with a small and regular junction spacing. The effect of carrier density inhomogeneities in InP and GaAs samples was then investigated. The same scanning

  1. 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}-...

  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. Non-abelian binding energies from the lightcone bootstrap

    Energy Technology Data Exchange (ETDEWEB)

    Li, Daliang [Department of Physics, Yale University,New Haven, CT 06511 (United States); Department of Physics and Astronomy, Johns Hopkins University,Baltimore, MD 21218 (United States); Meltzer, David [Department of Physics, Yale University,New Haven, CT 06511 (United States); Poland, David [Department of Physics, Yale University,New Haven, CT 06511 (United States); School of Natural Sciences, Institute for Advanced Study,Princeton, NJ 08540 (United States)

    2016-02-23

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

  4. Mobile impurities in ferromagnetic liquids

    Science.gov (United States)

    Kantian, Adrian; Schollwoeck, Ulrich; Giamarchi, Thierry

    2011-03-01

    Recent work has shown that mobile impurities in one dimensional interacting systems may exhibit behaviour that differs strongly from that predicted by standard Tomonaga-Luttinger liquid theory, with the appearance of power-law divergences in the spectral function signifying sublinear diffusion of the impurity. Using time-dependent matrix product states, we investigate a range of cases of mobile impurities in systems beyond the analytically accessible examples to assess the existence of a new universality class of low-energy physics in one-dimensional systems. Correspondence: Adrian.Kantian@unige.ch This work was supported in part by the Swiss SNF under MaNEP and division II.

  5. Impurity-related optical properties in rectangular-transverse section GaAs-Ga{sub 1-x}Al{sub x}As quantum well wires: Hydrostatic pressure and electric field effects

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, J.W.; 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); Rodriguez, A.H. [Instituto de Fisica, Universidad Nacional Autonoma de Mexico (UNAM), Apdo. Postal 20-364, San Angel 01000, Mexico DF (Mexico); Porras-Montenegro, N. [Departamento de Fisica, Universidad del Valle, AA 25360, Cali (Colombia)

    2007-01-15

    Using a variational procedure within the effective mass approximation, we have calculated the influence of an applied electric field and hydrostatic pressure on the shallow-impurity-related optical properties in a rectangular-transverse section GaAs-Ga{sub 1-x}Al{sub x}As quantum well wire. The electric field is applied in the plane of the transverse section of the wire and different angular directions have been considered. The results presented are for the impurity binding energy, its corresponding density of impurity states, and impurity-related transition energy and polarizability. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  6. Hydrogenic donor impurity in parallel-triangular quantum wires: Hydrostatic pressure and applied electric field effects

    International Nuclear Information System (INIS)

    Restrepo, R.L.; Giraldo, E.; Miranda, G.L.; Ospina, W.; Duque, C.A.

    2009-01-01

    The combined effects of the hydrostatic pressure and in-growth direction applied electric field on the binding energy of hydrogenic shallow-donor impurity states in parallel-coupled-GaAs-Ga 1-x Al x As-quantum-well wires are calculated using a variational procedure within the effective-mass and parabolic-band approximations. Results are obtained for several dimensions of the structure, shallow-donor impurity positions, hydrostatic pressure, and applied electric field. Our results suggest that external inputs such us hydrostatic pressure and in-growth direction electric field are two useful tools in order to modify the binding energy of a donor impurity in parallel-coupled-quantum-well wires.

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

    International Nuclear Information System (INIS)

    Srirangarajan, Aarti; Datta, Aditi; Gandi, Appala Naidu; Ramamurty, U; Waghmare, U V

    2014-01-01

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

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

    Science.gov (United States)

    Srirangarajan, Aarti; Datta, Aditi; Gandi, Appala Naidu; Ramamurty, U; Waghmare, U V

    2014-02-05

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

  9. An accurate redetermination of the 118Sn binding energy

    International Nuclear Information System (INIS)

    Borzakov, S.B.; Panteleev, Ts.Ts.; Telezhnikov, S.A.; Chrien, R.E.; Faikow-Stanczyk, H.; Grigor'ev, Yu.V.; Pospisil, S.; Smotritskij, L.M.

    2001-01-01

    The energy of well-known strong γ-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,γ)-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 was taken into account by a Monte Carlo simulation. The procedure was used in obtaining of B n for 118 Sn and 64 Cu. The γ-ray spectrum from thermal neutron radiative capture by 117 Sn has been measured on the IBR-2 pulsed reactor. γ-rays were detected by a 72 cm 2 HPGe-detector. B n for 64 Cu was obtained from two γ-spectra. One spectrum was measured on the IBR-2 by the same detector. The other spectrum was measured with a pair spectrometer at the Brookhaven High Flux Beam Reactor. From these two spectra B n for 64 Cu was determined equal to 7915.52(8) keV. The mean value of two most precise results of B n for 118 Sn was determined to be 9326.35(9) keV. The B n for 57Fe was determined to be 7646.08(9) keV

  10. Role of codeposited impurities during growth. I. Explaining distinctive experimental morphology on Cu(0 0 1)

    Science.gov (United States)

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

    2011-01-01

    A unified explanation of the physics underlying all the distinctive features of the growth instabilities observed on Cu vicinals has long eluded theorists. Recently, kinetic Monte Carlo studies showed that codeposition of impurities during growth could account for the key distinctive experimental observations [Hamouda , Phys. Rev. BPLRBAQ0556-280510.1103/PhysRevB.77.245430 77, 245430 (2008)]. To identify the responsible impurity atom, we compute the nearest-neighbor binding energies (ENN) and terrace diffusion barriers (Ed) for several candidate impurity atoms on Cu(0 0 1) using DFT-based VASP. Our calculations show that codeposition (with Cu) of midtransition elements, such as Fe, Mn, and W, could—in conjunction with substantial Ehrlich-Schwoebel barriers—cause the observed instabilities; when the experimental setup is considered, W emerges to be the most likely candidate. We discuss the role of impurities in nanostructuring of surfaces.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-07-01

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

  12. Impurity diffusion in transition-metal oxides

    International Nuclear Information System (INIS)

    Peterson, N.L.

    1982-06-01

    Intrinsic tracer impurity diffusion measurements in ceramic oxides have been primarily confined to CoO, NiO, and Fe 3 O 4 . Tracer impurity diffusion in these materials and TiO 2 , together with measurements of the effect of impurities on tracer diffusion (Co in NiO and Cr in CoO), are reviewed and discussed in terms of impurity-defect interactions and mechanisms of diffusion. Divalent impurities in divalent solvents seem to have a weak interaction with vacancies whereas trivalent impurities in divalent solvents strongly influence the vacancy concentrations and significantly reduce solvent jump frequencies near a trivalent impurity. Impurities with small ionic radii diffuse more slowly with a larger activation energy than impurities with larger ionic radii for all systems considered in this review. Cobalt ions (a moderate size impurity) diffuse rapidly along the open channels parallel to the c-axis in TiO 2 whereas chromium ions (a smaller-sized impurity) do not. 60 references, 11 figures

  13. Measurement of impurity ion densities and energies in the divertor and edge regions of Alcator C-Mod tokamak

    International Nuclear Information System (INIS)

    Griem, H.R.; Moreno, J.; Welch, B.L.

    1992-01-01

    A study to investigate impurity production and transport in the divertor and edge regions of the Alcator C-Mod tokamak through spectroscopic techniques is described. A 0.75-meter Czerny-Turner spectrometer with a 1200-g/mm grating and a 35-meter quartz optic bundle transmission line were tested. A high-resolution 2-meter spectrometer will be ordered. Data acquisition considerations are being addressed

  14. The impurity transport in HT-6M tokamak

    International Nuclear Information System (INIS)

    Xu Wei; Wan Baonian; Xie Jikang

    2003-01-01

    The space-time profile of impurities has been measured with a multichannel visible spectroscopic detect system and UV rotation-mirror system in the HT-6M tokamak. An ideal impurity transport code has been used to simulate impurities (carbon and oxygen) behaviour during the OHM discharge. The profiles of impurities diffusion and convection coefficient, impurities ion densities in different ionized state, loss power density and effective charge number have been derived. The impurity behaviour during low-hybrid current drive has also been analyzed, the results show that the confinement of particles, impurities and energy has been improved, and emission power and effective charge number have been reduced

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

    International Nuclear Information System (INIS)

    Haddad, S.

    2011-04-01

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

  16. 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

  17. Semiphenomenological studies of the ground state binding energies of hypernuclei

    International Nuclear Information System (INIS)

    Mian, M.

    1987-01-01

    We show that the binding energies of /sub Λ/ 5 He and p-shell hypernuclei can be satisfactorily explained in the folding model approach using a density dependent effective ΛN interaction. Our analysis predicts a very reasonable value of the range of the ΛN interaction. The calculated value of B/sub Λ/ of /sub Λ/ 7 Li using the cluster model density for 6 Li and the best fit parameters of this potential supports the view that 6 Li possesses an α-d cluster structure. Using this potential we also determine the average size parameter (a 0 ) of the oscillator shell model density of nucleons in Nnot =Z core nuclei from fitting the B/sub Λ/ values of the corresponding hypernuclei. The effect of different forms of density distribution of core nuclei on the values of potential parameters is investigated and is found to be very small. As regards the form of density dependence, a rho/sup 2/3/ form is found to be the most appropriate for this purpose and is used throughout this work. Other forms do not give a satisfactory account of the data

  18. Optical-absorption spectra associated with shallow donor impurities in GaAs-(Ga,Al)As quantum-dots

    International Nuclear Information System (INIS)

    Silva Valencia, J.

    1995-08-01

    The binding energy of a hydrogenic donor impurity and the optical-absorption spectra associated with transitions between the n=1 valence level and the donor-impurity band were calculated for infinite barrier-well spherical GaAs-(Ga,Al)As quantum-dots of different radii, using the effective mass approximation within a variational scheme. An absorption peak associated with transitions involving impurities at the center of the well and a peak related with impurities at the edge of the dot were the main features observed for the different radii of the dots considered in the calculations. Also as a result of the higher electronic confinement in a quantum- dot, we found a much wider energy range of the absorption spectra when compared to infinite GaAs-(Ga,Al)As quantum-wells and quantum-well wires of width and diameter comparable to the diameter of the quantum dot. (author). 13 refs, 3 figs

  19. Electronic structures and magnetic properties of 3d and 4d transition-metal impurities in ferromagnetic Fe

    CERN Document Server

    Park, J H; Min, B I; Cho, H S

    2000-01-01

    Employing the self-consistent local approach, the tight-binding linear-muffin-tin orbital recursion method, we have investigated the electronic structures and the magnetic properties of 3d and 4d transition-metal (TM) impurities in ferromagnetic bcc Fe. In both 3d and 4d TM impurities, virtual bound states appear and are characterized by a high density of states in the energy spectrum. The characters of the states are studied by calculating the bond order between interaction orbitals. For early TM impurities, the states at the impurity sites have more antibonding characters, while the states at neighboring Fe sites have more bonding characters. For late TM impurities, the situation is reversed. late TM impurities of both the 3d and the 4d TM series have the same magnetic ordering as the host Fe atoms whereas early TM impurities have magnetic moments antiparallel to that of the host. As for the Mn impurity, an inward relaxation of neighboring Fe atoms stabilizes the antiferromagnetic ordering with respect to t...

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

    Science.gov (United States)

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

    2016-04-15

    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.

  1. 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.

  2. Effect of P impurity on mechanical properties of NiAl Σ5 grain boundary: From perspectives of stress and energy

    Science.gov (United States)

    Hu, Xue-Lan; Zhao, Ruo-Xi; Deng, Jiang-Ge; Hu, Yan-Min; Song, Qing-Gong

    2018-03-01

    In this paper, we employ the first-principle total energy method to investigate the effect of P impurity on mechanical properties of NiAl grain boundary (GB). According to “energy”, the segregation of P atom in NiAlΣ5 GB reduces the cleavage energy and embrittlement potential, demonstrating that P impurity embrittles NiAlΣ5 GB. The first-principle computational tensile test is conducted to determine the theoretical tensile strength of NiAlΣ5 GB. It is demonstrated that the maximum ideal tensile strength of NiAlΣ5 GB with P atom segregation is 144.5 GPa, which is lower than that of the pure NiAlΣ5 GB (164.7 GPa). It is indicated that the segregation of P weakens the theoretical strength of NiAlΣ5 GB. The analysis of atomic configuration shows that the GB fracture is caused by the interfacial bond breaking. Moreover, P is identified to weaken the interactions between Al–Al bonds and enhance Ni–Ni bonds. Project supported by the National Natural Science Foundation of China (Grant Nos. 11404396 and 51201181) and the Subject Construction Fund of Civil Aviation University of China (Grant No. 000032041102).

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

    KAUST Repository

    Evoli, Stefania; Mobley, David L.; Guzzi, Rita; Rizzuti, Bruno

    2016-01-01

    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

  4. 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.

  5. 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.

  6. Complexity of Quantum Impurity Problems

    Science.gov (United States)

    Bravyi, Sergey; Gosset, David

    2017-12-01

    We give a quasi-polynomial time classical algorithm for estimating the ground state energy and for computing low energy states of quantum impurity models. Such models describe a bath of free fermions coupled to a small interacting subsystem called an impurity. The full system consists of n fermionic modes and has a Hamiltonian {H=H_0+H_{imp}}, where H 0 is quadratic in creation-annihilation operators and H imp is an arbitrary Hamiltonian acting on a subset of O(1) modes. We show that the ground energy of H can be approximated with an additive error {2^{-b}} in time {n^3 \\exp{[O(b^3)]}}. Our algorithm also finds a low energy state that achieves this approximation. The low energy state is represented as a superposition of {\\exp{[O(b^3)]}} fermionic Gaussian states. To arrive at this result we prove several theorems concerning exact ground states of impurity models. In particular, we show that eigenvalues of the ground state covariance matrix decay exponentially with the exponent depending very mildly on the spectral gap of H 0. A key ingredient of our proof is Zolotarev's rational approximation to the {√{x}} function. We anticipate that our algorithms may be used in hybrid quantum-classical simulations of strongly correlated materials based on dynamical mean field theory. We implemented a simplified practical version of our algorithm and benchmarked it using the single impurity Anderson model.

  7. Photoelectron spectroscopy on the charge reorganization energy and small polaron binding energy of molecular film

    Energy Technology Data Exchange (ETDEWEB)

    Kera, Satoshi, E-mail: kera@ims.ac.jp [Institute for Molecular Science, Myodaiji, Okazaki 444-8585 (Japan); Department of Nanomaterial Science, Graduate School of Advanced Integration Science, Chiba University, Inage-ku, Chiba 263-8522 (Japan); Ueno, Nobuo [Department of Nanomaterial Science, Graduate School of Advanced Integration Science, Chiba University, Inage-ku, Chiba 263-8522 (Japan)

    2015-10-01

    Understanding of electron-phonon coupling as well as intermolecular interaction is required to discuss the mobility of charge carrier in functional molecular solids. This article summarizes recent progress in direct measurements of valence hole-vibration coupling in ultrathin films of organic semiconductors by using ultraviolet photoelectron spectroscopy (UPS). The experimental study of hole-vibration coupling of the highest occupied molecular orbital (HOMO) state in ordered monolayer film by UPS is essential to comprehend hole-hopping transport and small-polaron related transport in organic semiconductors. Only careful measurements can attain the high-resolution spectra and provide key parameters in hole-transport dynamics, namely the charge reorganization energy and small polaron binding energy. Analyses methods of the UPS HOMO fine feature and resulting charge reorganization energy and small polaron binding energy are described for pentacene and perfluoropentacene films. Difference between thin-film and gas-phase results is discussed by using newly measured high-quality gas-phase spectra of pentacene. Methodology for achieving high-resolution UPS measurements for molecular films is also described.

  8. Atom-solid binding energy shifts for K 2p and Rb 3d sublevels

    International Nuclear Information System (INIS)

    Holappa, M.; Aksela, S.; Patanen, M.; Urpelainen, S.; Aksela, H.

    2011-01-01

    Highlights: → Binding energy shifts between atom and solid. K 2p and Rb 3d sublevels were studied. → Simultaneous measurements give accurate results. → Results can be used as a reference for cluster studies. - Abstract: Binding energy shifts between free and solid state atoms for K 2p and Rb 3d photolines have been determined by measuring the vapor and solid state spectra simultaneously in similar experimental conditions applying synchrotron radiation excited photoelectron spectroscopy. This method has the important benefit that the work function is not needed to correct for different reference energy levels, therefore much more accurate values for binding energy shifts are obtained.

  9. Effect of binding in cyclic phosphorylation-dephosphorylation process and in energy transformation.

    Science.gov (United States)

    Sarkar, A; Beard, D A; Franza, B R

    2006-07-01

    The effects of binding on the phosphorylation-dephosphorylation cycle (PDPC) - one of the key components of the signal transduction processes - is analyzed based on a mathematical model. The model shows that binding of proteins, forming a complex, diminishes the ultrasensitivity of the PDPC to the differences in activity between kinase and phosphatase in the cycle. It is also found that signal amplification depends upon the strength of the binding affinity of the protein (phosphorylated or dephosphorylated) to other proteins . It is also observed that the amplification of signal is not only dependent on phosphorylation potential but also on binding properties and resulting adjustments in binding energies.

  10. The fractional acoustoelectric current plateau induced by the energy-dependent tunnelling from dynamic quantum dots into an impurity dot

    Science.gov (United States)

    Chen, S. W.; Song, L.

    2016-08-01

    The fractional acoustoelectric (AE) current plateau in surface-acoustic-waves (SAW) single-electron transport devices is studied by measuring the current plateau as a function of the SAW power and gate bias as well as a function of perpendicular magnetic filed. Our investigation indicates that the fractional plateau is induced by the tunnelling effect from the dynamic quantum dots (QDs) into a static impurity dot. Rate equations are used to extract the tunnelling rates, which change a lot with the number of electrons in the dynamic QDs, the SAW power and gate bias. In addition, the current plateau evolves into a fractional structure, when a strong perpendicular magnetic field is applied to the system.

  11. Impurities or a neutral Fermi surface? A further examination of the low-energy ac optical conductivity of SmB6

    Science.gov (United States)

    Laurita, N. J.; Morris, C. M.; Koohpayeh, S. M.; Phelan, W. A.; McQueen, T. M.; Armitage, N. P.

    2018-05-01

    Recent experiments have uncovered evidence of low energy excitations in the bulk of SmB6 that are perhaps associated with unconventional quasiparticles, bringing into question whether this Kondo "insulator" is truly insulating in the bulk. Recently, we demonstrated that SmB6 possesses significant in-gap bulk ac conduction far in excess of typical disordered semiconductors. Whether such conduction is an intrinsic feature of SmB6, suggesting the formation of an exotic state, or residual conduction from impurities continues to be a topic of debate. Here, we further examine the origin of the ac optical conductivity of SmB6 in light of recent experimental and theoretical developments. The optical conductivity of SmB6 is shown to possess distinct regimes of either dominant free carrier or localized response contributions. The free carrier response is found to be in good qualitative agreement with previous literature, although quantitative differences are revealed and discussed. The localized response, which dominates at the lowest temperatures, is analyzed in the context of models of either in-gap impurity states or an exotic neutral Fermi surface. The charge density or effective mass of this low temperature in-gap conductivity is extracted through a conductivity sum rule analysis and found to be in general alignment with both models in the appropriate limits. Our results shed further light on the nature of the in-gap states of SmB6.

  12. Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations

    Science.gov (United States)

    Mey, Antonia S. J. S.; Jiménez, Jordi Juárez; Michel, Julien

    2018-01-01

    The Drug Design Data Resource (D3R) consortium organises blinded challenges to address the latest advances in computational methods for ligand pose prediction, affinity ranking, and free energy calculations. Within the context of the second D3R Grand Challenge several blinded binding free energies predictions were made for two congeneric series of Farsenoid X Receptor (FXR) inhibitors with a semi-automated alchemical free energy calculation workflow featuring FESetup and SOMD software tools. Reasonable performance was observed in retrospective analyses of literature datasets. Nevertheless, blinded predictions on the full D3R datasets were poor due to difficulties encountered with the ranking of compounds that vary in their net-charge. Performance increased for predictions that were restricted to subsets of compounds carrying the same net-charge. Disclosure of X-ray crystallography derived binding modes maintained or improved the correlation with experiment in a subsequent rounds of predictions. The best performing protocols on D3R set1 and set2 were comparable or superior to predictions made on the basis of analysis of literature structure activity relationships (SAR)s only, and comparable or slightly inferior, to the best submissions from other groups.

  13. Observations of long impurity confinement times in the ISX tokamak

    Energy Technology Data Exchange (ETDEWEB)

    Burrell, K H; Wong, S K; Muller, III, C H; Hacker, M P [General Atomic Co., San Diego, CA (USA); Ketterer, H E; Isler, R C; Lazarus, E A [Oak Ridge National Lab., TN (USA)

    1981-08-01

    The transport of small amounts of silicon and aluminium injected into plasmas in the Impurity Study Experiment (ISX) tokamak is studied. By monitoring the time behaviour of ultra-violet spectral lines emitted by various charge states of those impurities and comparing this behaviour to the predictions of a multi-species impurity transport code, it is found that both impurity penetration times and impurity containment times are consistent with neoclassical predictions. The observed impurity containment times, which are greater than three times the energy containment time, are consistent with the inward convection predicted by neoclassical theory.

  14. Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site

    Science.gov (United States)

    Dolenc, Jožica; Oostenbrink, Chris; Koller, Jože; van Gunsteren, Wilfred F.

    2005-01-01

    Molecular dynamics simulations have been performed on netropsin in two different charge states and on distamycin binding to the minor groove of the DNA duplex d(CGCGAAAAACGCG)·d(CGCGTTTTTCGCG). The relative free energy of binding of the two non-covalently interacting ligands was calculated using the thermodynamic integration method and reflects the experimental result. From 2 ns simulations of the ligands free in solution and when bound to DNA, the mobility and the hydrogen-bonding patterns of the ligands were studied, as well as their hydration. It is shown that even though distamycin is less hydrated than netropsin, the loss of ligand–solvent interactions is very similar for both ligands. The relative mobilities of the ligands in their bound and free forms indicate a larger entropic penalty for distamycin when binding to the minor groove compared with netropsin, partially explaining the lower binding affinity of the distamycin molecule. The detailed structural and energetic insights obtained from the molecular dynamics simulations allow for a better understanding of the factors determining ligand–DNA binding. PMID:15687382

  15. Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site.

    Science.gov (United States)

    Dolenc, Jozica; Oostenbrink, Chris; Koller, Joze; van Gunsteren, Wilfred F

    2005-01-01

    Molecular dynamics simulations have been performed on netropsin in two different charge states and on distamycin binding to the minor groove of the DNA duplex d(CGCGAAAAACGCG).d(CGCGTTTTTCGCG). The relative free energy of binding of the two non-covalently interacting ligands was calculated using the thermodynamic integration method and reflects the experimental result. From 2 ns simulations of the ligands free in solution and when bound to DNA, the mobility and the hydrogen-bonding patterns of the ligands were studied, as well as their hydration. It is shown that even though distamycin is less hydrated than netropsin, the loss of ligand-solvent interactions is very similar for both ligands. The relative mobilities of the ligands in their bound and free forms indicate a larger entropic penalty for distamycin when binding to the minor groove compared with netropsin, partially explaining the lower binding affinity of the distamycin molecule. The detailed structural and energetic insights obtained from the molecular dynamics simulations allow for a better understanding of the factors determining ligand-DNA binding.

  16. Exciton binding energy in GaAsBiN spherical quantum dot heterostructures

    Science.gov (United States)

    Das, Subhasis; Dhar, S.

    2017-03-01

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

  17. Electronic structure and optical properties of triangular GaAs/AlGaAs quantum dots: Exciton and impurity states

    Energy Technology Data Exchange (ETDEWEB)

    Tiutiunnyk, A. [Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Department of Physics, Donbass State Engineering Academy, Shkadinova 72, 84313 Kramatorsk (Ukraine); Akimov, V. [Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Department of Physics, Donbass State Engineering Academy, Shkadinova 72, 84313 Kramatorsk (Ukraine); Universidad de Medellín, Carrera 87 No 30-65 Medellín (Colombia); Tulupenko, V. [Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Department of Physics, Donbass State Engineering Academy, Shkadinova 72, 84313 Kramatorsk (Ukraine); Mora-Ramos, M.E. [Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, CP 62209 Cuernavaca, Morelos (Mexico); Kasapoglu, E. [Cumhuriyet University, Physics Department, 58140 Sivas (Turkey); Ungan, F. [Cumhuriyet University, Faculty of Technology, Deparment of Optical Engineering, 58140 Sivas (Turkey); Sökmen, I. [Department of Physics, Dokuz Eylül University, 35160 Buca, İzmir (Turkey); and others

    2016-03-01

    Electronic structure and optical properties in equilateral triangular GaAs/Al{sub 0.3}Ga{sub 0.7}As quantum dots are studied extensively. The effects of donor and acceptor impurity atoms positioned in the orthocenter of the triangle, as well as of the external DC electric field are taken into account. Binding energies of the impurity, exciton energies, interband photoluminescence peak positions as well as linear and non-linear optical properties in THz range caused by transitions between excitonic states are calculated and discussed.

  18. Electronic structure and optical properties of triangular GaAs/AlGaAs quantum dots: Exciton and impurity states

    International Nuclear Information System (INIS)

    Tiutiunnyk, A.; Akimov, V.; Tulupenko, V.; Mora-Ramos, M.E.; Kasapoglu, E.; Ungan, F.; Sökmen, I.

    2016-01-01

    Electronic structure and optical properties in equilateral triangular GaAs/Al_0_._3Ga_0_._7As quantum dots are studied extensively. The effects of donor and acceptor impurity atoms positioned in the orthocenter of the triangle, as well as of the external DC electric field are taken into account. Binding energies of the impurity, exciton energies, interband photoluminescence peak positions as well as linear and non-linear optical properties in THz range caused by transitions between excitonic states are calculated and discussed.

  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. Systematic studies of binding energy dependence of neutron-proton momentum correlation function

    International Nuclear Information System (INIS)

    Wei, Y B; Ma, Y G; Shen, W Q; Ma, G L; Wang, K; Cai, X Z; Zhong, C; Guo, W; Chen, J G; Fang, D Q; Tian, W D; Zhou, X F

    2004-01-01

    Hanbury Brown-Twiss (HBT) results of the neutron-proton correlation function have been systematically investigated for a series of nuclear reactions with light projectiles with the help of the isospin-dependent quantum molecular dynamics model. The relationship between the binding energy per nucleon of the projectiles and the strength of the neutron-proton HBT at small relative momentum has been obtained. Results show that neutron-proton HBT results are sensitive to the binding energy per nucleon

  1. Impurity-related nonlinear optical properties in delta-doped quantum rings: Electric field effects

    Energy Technology Data Exchange (ETDEWEB)

    Restrepo, R.L., E-mail: rrestre@gmail.com [Escuela de Ingeniería de Antioquia-EIA, Medellín (Colombia); Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Morales, A.L. [Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Martínez-Orozco, J.C. [Unidad Académica de Física, Universidad Autónoma de Zacatecas, CP 98060, Zacatecas (Mexico); Baghramyan, H.M.; Barseghyan, M.G. [Department of Solid State Physics, Yerevan State University, Al. Manookian 1, 0025 Yerevan (Armenia); Mora-Ramos, M.E. [Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Ave. Universidad 1001, CP 62209, Cuernavaca, Morelos (Mexico); Duque, C.A. [Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia)

    2014-11-15

    Using a variational procedure within the effective mass approximation, we have calculated the donor impurity binding energy for the ground (1s-like) and the excited (2p{sub z}-like) states as well as the impurity-related nonlinear optical absorption and relative changes in the refraction index in a GaAs single quantum ring with axial n-type delta-doping. The delta-like potential along the z-direction is an approximate model analytically described using a Lorentzian function with two parameters. Additionally we consider the application of an electric field along the z-direction. It is found that the changes in the geometry of the quantum ring, the change in the 2D impurity density of the delta-like doping, and different values of the electric field lead to a shifting of the resonant peaks of the optical responses spectrum.

  2. Impurity-related nonlinear optical properties in delta-doped quantum rings: Electric field effects

    International Nuclear Information System (INIS)

    Restrepo, R.L.; Morales, A.L.; Martínez-Orozco, J.C.; Baghramyan, H.M.; Barseghyan, M.G.; Mora-Ramos, M.E.; Duque, C.A.

    2014-01-01

    Using a variational procedure within the effective mass approximation, we have calculated the donor impurity binding energy for the ground (1s-like) and the excited (2p z -like) states as well as the impurity-related nonlinear optical absorption and relative changes in the refraction index in a GaAs single quantum ring with axial n-type delta-doping. The delta-like potential along the z-direction is an approximate model analytically described using a Lorentzian function with two parameters. Additionally we consider the application of an electric field along the z-direction. It is found that the changes in the geometry of the quantum ring, the change in the 2D impurity density of the delta-like doping, and different values of the electric field lead to a shifting of the resonant peaks of the optical responses spectrum

  3. 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/.

  4. Ion Binding Energies Determining Functional Transport of ClC Proteins

    Science.gov (United States)

    Yu, Tao; Guo, Xu; Zou, Xian-Wu; Sang, Jian-Ping

    2014-06-01

    The ClC-type proteins, a large family of chloride transport proteins ubiquitously expressed in biological organisms, have been extensively studied for decades. Biological function of ClC proteins can be reflected by analyzing the binding situation of Cl- ions. We investigate ion binding properties of ClC-ec1 protein with the atomic molecular dynamics simulation approach. The calculated electrostatic binding energy results indicate that Cl- at the central binding site Scen has more binding stability than the internal binding site Sint. Quantitative comparison between the latest experimental heat release data isothermal titration calorimetry (ITC) and our calculated results demonstrates that chloride ions prefer to bind at Scen than Sint in the wild-type ClC-ec1 structure and prefer to bind at Sext and Scen than Sint in mutant E148A/E148Q structures. Even though the chloride ions make less contribution to heat release when binding to Sint and are relatively unstable in the Cl- pathway, they are still part contributors for the Cl- functional transport. This work provides a guide rule to estimate the importance of Cl- at the binding sites and how chloride ions have influences on the function of ClC proteins.

  5. Integrable quantum impurity models

    International Nuclear Information System (INIS)

    Eckle, H.P.

    1998-01-01

    By modifying some of the local L operators of the algebraic form of the Bethe Ansatz inhomogeneous one dimensional quantum lattice models can be constructed. This fact has recently attracted new attention, the inhomogeneities being interpreted as local impurities. The Hamiltonians of the so constructed one-dimensional quantum models have a nearest neighbour structure except in the vicinity of the local impurities which involve three-site interactions. The pertinent feature of these models is the absence of backscattering at the impurities: the impurities are transparent. (Copyright (1998) World Scientific Publishing Co. Pte. Ltd)

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

    Science.gov (United States)

    Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

    2014-02-01

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

  7. Donor impurity in nanotube with two GaAs/GaAlAs quantum wells: Magnetic field effects

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, J D; Escorcia, R; Sierra-Ortega, J, E-mail: jdavid0831@gmail.co [Grupo de Investigacion en teorIa de la Materia Condensada, Universidad del Magdalena, A.A. 731, Santa Marta (Colombia)

    2009-05-01

    Micro-tubes containing two GaAs/GaAlAs quantum wells (QWs) in a section of the tube layer has been fabricated and optical properties of the embedded QWs has been studied. The ground state binding energy of an off-axis donor in a cylindrical nanotube, containing two GaAs/GaAlAs quantum wells (QWs) in the presence of a uniform magnetic field is calculated as a function of the donor location as well as the density of states. A trial function for describing the asymmetric electron charge distribution is taken as a product of the combination of 1s and 2p{sub x,y} subband wave functions and an unknown function that depends only on electron-ion separation. We found that the increasing the magnetic field the increasing the binding energy while the impurity is located in the QW1, whereas the opposite occurs when the impurity is located in the QW2. Two peaks in the curves of the binding energy, as a function of the impurity position, are also found as well as in the density of impurity states.

  8. Impurity Induced Phase Competition and Supersolidity

    Science.gov (United States)

    Karmakar, Madhuparna; Ganesh, R.

    2017-12-01

    Several material families show competition between superconductivity and other orders. When such competition is driven by doping, it invariably involves spatial inhomogeneities which can seed competing orders. We study impurity-induced charge order in the attractive Hubbard model, a prototypical model for competition between superconductivity and charge density wave order. We show that a single impurity induces a charge-ordered texture over a length scale set by the energy cost of the competing phase. Our results are consistent with a strong-coupling field theory proposed earlier in which superconducting and charge order parameters form components of an SO(3) vector field. To discuss the effects of multiple impurities, we focus on two cases: correlated and random distributions. In the correlated case, the CDW puddles around each impurity overlap coherently leading to a "supersolid" phase with coexisting pairing and charge order. In contrast, a random distribution of impurities does not lead to coherent CDW formation. We argue that the energy lowering from coherent ordering can have a feedback effect, driving correlations between impurities. This can be understood as arising from an RKKY-like interaction, mediated by impurity textures. We discuss implications for charge order in the cuprates and doped CDW materials such as NbSe2.

  9. Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape.

    Science.gov (United States)

    Ghaemi, Zhaleh; Guzman, Irisbel; Gnutt, David; Luthey-Schulten, Zaida; Gruebele, Martin

    2017-09-14

    U1A protein-stem loop 2 RNA association is a basic step in the assembly of the spliceosomal U1 small nuclear ribonucleoprotein. Long-range electrostatic interactions due to the positive charge of U1A are thought to provide high binding affinity for the negatively charged RNA. Short range interactions, such as hydrogen bonds and contacts between RNA bases and protein side chains, favor a specific binding site. Here, we propose that electrostatic interactions are as important as local contacts in biasing the protein-RNA energy landscape toward a specific binding site. We show by using molecular dynamics simulations that deletion of two long-range electrostatic interactions (K22Q and K50Q) leads to mutant-specific alternative RNA bound states. One of these states preserves short-range interactions with aromatic residues in the original binding site, while the other one does not. We test the computational prediction with experimental temperature-jump kinetics using a tryptophan probe in the U1A-RNA binding site. The two mutants show the distinct predicted kinetic behaviors. Thus, the stem loop 2 RNA has multiple binding sites on a rough RNA-protein binding landscape. We speculate that the rough protein-RNA binding landscape, when biased to different local minima by electrostatics, could be one way that protein-RNA interactions evolve toward new binding sites and novel function.

  10. Impurity bound states in mesoscopic topological superconducting loops

    Science.gov (United States)

    Jin, Yan-Yan; Zha, Guo-Qiao; Zhou, Shi-Ping

    2018-06-01

    We study numerically the effect induced by magnetic impurities in topological s-wave superconducting loops with spin-orbit interaction based on spin-generalized Bogoliubov-de Gennes equations. In the case of a single magnetic impurity, it is found that the midgap bound states can cross the Fermi level at an appropriate impurity strength and the circulating spin current jumps at the crossing point. The evolution of the zero-energy mode can be effectively tuned by the located site of a single magnetic impurity. For the effect of many magnetic impurities, two independent midway or edge impurities cannot lead to the overlap of zero modes. The multiple zero-energy modes can be effectively realized by embedding a single Josephson junction with impurity scattering into the system, and the spin current displays oscillatory feature with increasing the layer thickness.

  11. Contribution of charge symmetry breaking interactions in binding energy difference of mirror nuclei

    International Nuclear Information System (INIS)

    Asghari, M.

    2006-01-01

    Nolen-Schiffer Anomaly in mirror nuclei due to the NN interactions with isospin mixing between T=0 and T=1 mesons of the same spin and parity are investigated. With the computation of coulomb energy along with the charge symmetry breaking effects provide a reasonably accurate description of binding energy differences between 39 Ca- 39 K , 41 Sc- 41 Ca mirror nuclei

  12. Excited-states of hydrogenic-like impurities in InGaN–GaN spherical QD: Electric field effect

    Energy Technology Data Exchange (ETDEWEB)

    El Ghazi, Haddou, E-mail: hadghazi@gmail.com [LPS, Faculty of Sciences, Dhar EL Mehrez, B.P 1796 Atlas Fez (Morocco); Special Mathematics, CPGE Kénitra (Morocco); Jorio, Anouar [LPS, Faculty of Sciences, Dhar EL Mehrez, B.P 1796 Atlas Fez (Morocco)

    2013-12-01

    By means of a traditional Ritz variational method within the effective-mass and single parabolic band approximations, the excited-states energy with and without the existence of the impurity is performed. Externally applied electric field and system radius effects are considered in wurtzite (In,Ga)N–GaN spherical quantum dot with finite potential barrier. The normalized binding energy is also reported. Compared to the previous theoretical findings, a good agreement is shown.

  13. Excited-states of hydrogenic-like impurities in InGaN–GaN spherical QD: Electric field effect

    International Nuclear Information System (INIS)

    El Ghazi, Haddou; Jorio, Anouar

    2013-01-01

    By means of a traditional Ritz variational method within the effective-mass and single parabolic band approximations, the excited-states energy with and without the existence of the impurity is performed. Externally applied electric field and system radius effects are considered in wurtzite (In,Ga)N–GaN spherical quantum dot with finite potential barrier. The normalized binding energy is also reported. Compared to the previous theoretical findings, a good agreement is shown

  14. Trace impurity analyzer

    International Nuclear Information System (INIS)

    Schneider, W.J.; Edwards, D. Jr.

    1979-01-01

    The desirability for long-term reliability of large scale helium refrigerator systems used on superconducting accelerator magnets has necessitated detection of impurities to levels of a few ppM. An analyzer that measures trace impurity levels of condensable contaminants in concentrations of less than a ppM in 15 atm of He is described. The instrument makes use of the desorption temperature at an indicated pressure of the various impurities to determine the type of contaminant. The pressure rise at that temperature yields a measure of the contaminant level of the impurity. A LN 2 cryogenic charcoal trap is also employed to measure air impurities (nitrogen and oxygen) to obtain the full range of contaminant possibilities. The results of this detector which will be in use on the research and development helium refrigerator of the ISABELLE First-Cell is described

  15. Effect of magnetic field on the donor impurity in CdTe/Cd1-xMnxTe quantum well wire

    Science.gov (United States)

    Kalpana, P.; Reuben, A. Merwyn Jasper D.; Nithiananthi, P.; Jayakumar, K.

    2016-05-01

    The donor impurity binding energy in CdTe / Cd1-xMnxTe QWW with square well confinement along x - direction and parabolic confinement along y - direction under the influence of externally applied magnetic field has been computed using variational principle in the effective mass approximation. The spin polaronic shift has also been computed. The results are presented and discussed.

  16. Local order dependent impurity levels in alloy semiconductors

    International Nuclear Information System (INIS)

    Silva, C.E.T.G. da; Ecole Normale Superieure, 75 - Paris

    1981-01-01

    We develop a one band/may sites model for an isoelectronic impurity in a semiconductor alloy. The cluster-Bethe-lattice approximation is used to study the dependence of the impurity energy level upon the short range order (SRO) of the alloy. The Kikuchi parametrization is used to describe the latter. We take into account diagonal disorder only, with possible off-diagonal relaxation around the impurity site. All the inequivalent clusters of the impurity site and its first nearest neighbours are considered, thus including the important short range alloy potential fluctuations. Results are presented for the local density of impurity states, for different degrees of SRO in the alloy. (Author) [pt

  17. Shallow donor impurities in different shaped double quantum wells under the hydrostatic pressure and applied electric field

    International Nuclear Information System (INIS)

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

    2005-01-01

    The combined electric field and hydrostatic pressure effects on the binding energy of the donor impurity in double triangle quantum well (DTQW), double graded (DGQW) and double square (DSQW) GaAs-(Ga,Al)As quantum wells are calculated by using a variational technique within the effective-mass approximation. The results have been obtained in the presence of an electric field applied along the growth direction as a function of hydrostatic pressure, the impurity position, barrier width and the geometric shape of the double quantum wells

  18. 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.

  19. Polaron binding energy and effective mass in the GaAs film

    International Nuclear Information System (INIS)

    Wu Zhenhua; Yan Liangxing; Tian Qiang; Li Hua; Liu Bingcan

    2012-01-01

    The binding energy and effective mass of a polaron in a GaAs film deposited on the Al 0.3 Ga 0.7 As substrate are studied theoretically by using the fractional-dimensional space approach. Our calculations show that the polaron binding energy and mass shift decrease monotonously with increasing the film thickness. For the film thicknesses with L w ≤ 70Å and the substrate thicknesses with L b ≤ 200Å, the different values of the substrate thickness influence the polaron binding energy and mass shift in the GaAs film. The polaron binding energy and mass shift increase monotonously with increasing the substrate thickness. For the film thickness with L w ≥ 70Å or the substrate thicknesses with L b ≤ 200Å, the different values of the substrate thickness have no significant influence on the polaron binding energy and mass shift in the GaAs film deposited on the Al 0.3 Ga 0.7 As substrate.

  20. BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.

    Science.gov (United States)

    Fu, Haohao; Gumbart, James C; Chen, Haochuan; Shao, Xueguang; Cai, Wensheng; Chipot, Christophe

    2018-03-26

    Quantifying protein-ligand binding has attracted the attention of both theorists and experimentalists for decades. Many methods for estimating binding free energies in silico have been reported in recent years. Proper use of the proposed strategies requires, however, adequate knowledge of the protein-ligand complex, the mathematical background for deriving the underlying theory, and time for setting up the simulations, bookkeeping, and postprocessing. Here, to minimize human intervention, we propose a toolkit aimed at facilitating the accurate estimation of standard binding free energies using a geometrical route, coined the binding free-energy estimator (BFEE), and introduced it as a plug-in of the popular visualization program VMD. Benefitting from recent developments in new collective variables, BFEE can be used to generate the simulation input files, based solely on the structure of the complex. Once the simulations are completed, BFEE can also be utilized to perform the post-treatment of the free-energy calculations, allowing the absolute binding free energy to be estimated directly from the one-dimensional potentials of mean force in simulation outputs. The minimal amount of human intervention required during the whole process combined with the ergonomic graphical interface makes BFEE a very effective and practical tool for the end-user.

  1. 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

  2. Stark shift and photoionization cross section of on-center and off-center donor impurity in a core/shell ellipsoidal quantum dot

    Science.gov (United States)

    Shi, L.; Yan, Z. W.

    2018-04-01

    Within the framework of the effective-mass approximation and by using a variational method, the Stark shift of on-center and off-center donor impurity binding energies and photoionization cross section under a z-direction electric field in a prolate (oblate) core/shell ellipsoidal quantum dot has been studied. We have calculated the Stark shift as a function of the core and shell sizes and shapes, electric field, and impurity position. We also discuss the photoionization cross section as a function of photon energy with different core and shell sizes and shapes, electric field strengths, and impurity positions. The results show that the Stark shift depends strongly on the impurity position, it could be positive or negative. The core and shell sizes and shapes also have a pronounce influence on the Stark shift, and the Stark shift changes with them is non-monotonic, especially when the impurity is located at the -z-axis, the situation will become complicated. In addition, the core and shell sizes and shapes, impurity position, and electric field also have an important influence on the photoionization cross section. In particular, the photoionization cross section will vanish when the impurity is located at center of spherical core with spherical or prolate shell case at zero field.

  3. Estimating Atomic Contributions to Hydration and Binding Using Free Energy Perturbation.

    Science.gov (United States)

    Irwin, Benedict W J; Huggins, David J

    2018-05-08

    We present a general method called atom-wise free energy perturbation (AFEP), which extends a conventional molecular dynamics free energy perturbation (FEP) simulation to give the contribution to a free energy change from each atom. AFEP is derived from an expansion of the Zwanzig equation used in the exponential averaging method by defining that the system total energy can be partitioned into contributions from each atom. A partitioning method is assumed and used to group terms in the expansion to correspond to individual atoms. AFEP is applied to six example free energy changes to demonstrate the method. Firstly, the hydration free energies of methane, methanol, methylamine, methanethiol, and caffeine in water. AFEP highlights the atoms in the molecules that interact favorably or unfavorably with water. Finally AFEP is applied to the binding free energy of human immunodeficiency virus type 1 protease to lopinavir, and AFEP reveals the contribution of each atom to the binding free energy, indicating candidate areas of the molecule to improve to produce a more strongly binding inhibitor. FEP gives a single value for the free energy change and is already a very useful method. AFEP gives a free energy change for each "part" of the system being simulated, where part can mean individual atoms, chemical groups, amino acids, or larger partitions depending on what the user is trying to measure. This method should have various applications in molecular dynamics studies of physical, chemical, or biochemical phenomena, specifically in the field of computational drug discovery.

  4. Binding energies of hypernuclei and Λ-nuclear interactions

    International Nuclear Information System (INIS)

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

    1984-01-01

    Variational calculations indicate that a reasonable description of Λp scattering and of Λ separation energies can be obtained in terms of ΛN plus dispersive and TPE ΛNN forces. Results for the ΛΛ interaction and for 6 /sub Λ/He obtained from an analysis of 10 /sub ΛΛ/Be are discussed. Coulomb and ΛN charge symmetry breaking effects in the A = 4 hypernuclei are discussed

  5. Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach

    Directory of Open Access Journals (Sweden)

    C. Ruben Vosmeer

    2014-01-01

    Full Text Available Binding affinity prediction of potential drugs to target and off-target proteins is an essential asset in drug development. These predictions require the calculation of binding free energies. In such calculations, it is a major challenge to properly account for both the dynamic nature of the protein and the possible variety of ligand-binding orientations, while keeping computational costs tractable. Recently, an iterative Linear Interaction Energy (LIE approach was introduced, in which results from multiple simulations of a protein-ligand complex are combined into a single binding free energy using a Boltzmann weighting-based scheme. This method was shown to reach experimental accuracy for flexible proteins while retaining the computational efficiency of the general LIE approach. Here, we show that the iterative LIE approach can be used to predict binding affinities in an automated way. A workflow was designed using preselected protein conformations, automated ligand docking and clustering, and a (semi-automated molecular dynamics simulation setup. We show that using this workflow, binding affinities of aryloxypropanolamines to the malleable Cytochrome P450 2D6 enzyme can be predicted without a priori knowledge of dominant protein-ligand conformations. In addition, we provide an outlook for an approach to assess the quality of the LIE predictions, based on simulation outcomes only.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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...... for well widths less than 8 nm. In the quantum wires an increase of 30% is found in the smallest quantum wire structures compared to the corresponding quantum well value. A simple analytical model taking into account the quantum confinement in these low-dimensional systems is used to explain...

  11. Simple method for determining binding energies of fullerene and complex atomic negative ions

    Science.gov (United States)

    Felfli, Zineb; Msezane, Alfred

    2017-04-01

    A robust potential which embeds fully the vital core polarization interaction has been used in the Regge pole method to explore low-energy electron scattering from C60, Eu and Nb through the total cross sections (TCSs) calculations. From the characteristic dramatically sharp resonances in the TCSs manifesting negative ion formation in these systems, we extracted the binding energies for the C60, Euand Nbanions they are found to be in outstanding agreement with the measured electron affinities of C60, Eu and Nb. Common among these considered systems, including the standard atomic Au is the formation of their ground state negative ions at the second Ramsauer-Townsend (R-T) minima of their TCSs. Indeed, this is a signature of all the fullerenes and complex atoms considered thus far. Shape resonances, R-T minima and binding energies of the resultant anions are presented. This work was supported by U.S. DOE, Basic Energy Sciences, Office of Energy Research.

  12. Structure-based prediction of free energy changes of binding of PTP1B inhibitors

    Science.gov (United States)

    Wang, Jing; Ling Chan, Shek; Ramnarayan, Kal

    2003-08-01

    The goals were (1) to understand the driving forces in the binding of small molecule inhibitors to the active site of PTP1B and (2) to develop a molecular mechanics-based empirical free energy function for compound potency prediction. A set of compounds with known activities was docked onto the active site. The related energy components and molecular surface areas were calculated. The bridging water molecules were identified and their contributions were considered. Linear relationships were explored between the above terms and the binding free energies of compounds derived based on experimental inhibition constants. We found that minimally three terms are required to give rise to a good correlation (0.86) with predictive power in five-group cross-validation test (q2 = 0.70). The dominant terms are the electrostatic energy and non-electrostatic energy stemming from the intra- and intermolecular interactions of solutes and from those of bridging water molecules in complexes.

  13. Variational method for magnetic impurities in metals: impurity pairs

    Energy Technology Data Exchange (ETDEWEB)

    Oles, A M [Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany, F.R.); Chao, K A [Linkoeping Univ. (Sweden). Dept. of Physics and Measurement Technology

    1980-01-01

    Applying a variational method to the generalized Wolff model, we have investigated the effect of impurity-impurity interaction on the formation of local moments in the ground state. The direct coupling between the impurities is found to be more important than the interaction between the impurities and the host conduction electrons, as far as the formation of local moments is concerned. Under certain conditions we also observe different valences on different impurities.

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

    International Nuclear Information System (INIS)

    Zheng, Y.; Brion, C.E.; Brunger, M.J.; Zhao, K.; Grisogono, A.M.; Braidwood, S.; Weigold, E.; Chakravorty, S.J.; Davidson, E.R.; Sgamellotti, A.; von Niessen, W.

    1996-01-01

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

  15. Effect of Γ-X band mixing on the donor binding energy in a Quantum Wire

    Science.gov (United States)

    Vijaya Shanthi, R.; Jayakumar, K.; Nithiananthi, P.

    2015-02-01

    To invoke the technological applications of heterostructure semiconductors like Quantum Well (QW), Quantum Well Wire (QWW) and Quantum Dot (QD), it is important to understand the property of impurity energy which is responsible for the peculiar electronic & optical behavior of the Low Dimensional Semiconductor Systems (LDSS). Application of hydrostatic pressure P>35kbar drastically alters the band offsets leading to the crossover of Γ band of the well & X band of the barrier resulting in an indirect transition of the carrier and this effect has been studied experimentally and theoretically in a QW structure. In this paper, we have investigated the effect of Γ-X band mixing due to the application of hydrostatic pressure in a GaAs/AlxGa1-xAs QWW system. The results are presented and discussed for various widths of the wire.

  16. Metastable decay and binding energies of van der Waals cluster ions

    International Nuclear Information System (INIS)

    Ernstberger, B.; Krause, H.; Neusser, H.J.

    1991-01-01

    In this work the appearance potentials for the metastable decay channel of a series of van der Waals dimer ions are presented. Ionization and metastable dissociation is achieved by resonance-enhanced two-photon absorption in a linear reflectron time-of-flight mass spectrometer. From the appearance potentials the binding energy of the neutral dimers is obtained and from the additionally measured ionization potentials binding energies of the dimer cations are achieved. The contribution of charge transfer resonance interaction to the binding in cluster ions is evaluated by investigation of several homo- and heterodimers of aromatic components and the heterodimer benzene/cyclohexane as an example for a dimer consisting of an aromatic and a nonaromatic component. (orig.)

  17. 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

  18. Core electron binding energy shifts of AlBr3 and Al2Br6 vapor

    International Nuclear Information System (INIS)

    Mueller, Astrid M.; Plenge, Juergen; Leone, Stephen R.; Canton, Sophie E.; Rude, Bruce S.; Bozek, John D.

    2006-01-01

    The Al 2p and Br 3d inner-shell photoelectron spectra of aluminum tribromide monomer and dimer vapor were measured at 90 and 95 eV photon energy, respectively, to determine the core electron binding energies of the atoms in the two molecular species. While AlBr 3 has three identical Br atoms, Al 2 Br 6 exhibits four terminal and two bridging Br atoms. The species are identified by their distinct valence photoelectron spectra. Comparison of the observed Al 2p 1/2 and Al 2p 3/2 electron binding energies of AlBr 3 with those of Al 2 Br 6 shows that there is a chemical shift of (0.15 ± 0.03) eV to lower energy in the dimer. In Al 2 Br 6 , an assignment is proposed in which the Br 3d 3/2 and Br 3d 5/2 binding energies of terminal Br atoms are (1.18 ± 0.03) eV lower than those of bridging Br atoms. This assignment assumes that both types of Br atoms have similar cross-sections for ionization. With this result, the Br 3d 3/2 and Br 3d 5/2 binding energies of Br atoms in AlBr 3 are (0.81 ± 0.03) eV lower than those of bridging Br atoms of the dimer but (0.37 ± 0.03) eV higher than those of terminal Br atoms of the dimer. The obtained chemical shifts are considered in terms of the binding relations and electron density distributions in both molecules. Chemical shifts that are larger than a few hundred millielectron volts, as observed in the Al 2 Br 6 /AlBr 3 system, offer potential to study the dissociation dynamics of the dimer in a femtosecond visible or ultraviolet-pump/XUV-probe experiment

  19. Comparison of experimental and theoretical binding and transition energies in the actinide region

    International Nuclear Information System (INIS)

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

    1977-01-01

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

  20. 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 ...

  1. A test of Wigner's spin-isospin symmetry from double binding energy differences

    International Nuclear Information System (INIS)

    Van Isacker, P.; Warner, D.D.; Brenner, D.S.

    1995-01-01

    It is shown that the anomalously large double binding energy differences for even-even N = Z nuclei are a consequence of Wigner's SU(4) symmetry. These, and similar quantities for odd-mass and odd-odd nuclei, provide a simple and distinct signature of this symmetry in N ≅ Z nuclei. (authors). 16 refs., 2 figs., 1 tab

  2. Exciton binding energy in wurtzite InGaN/GaN quantum wells

    International Nuclear Information System (INIS)

    Park, Seoung-Hwan; Kim, Jong-Jae; Kim, Hwa-Min

    2004-01-01

    The internal field and carrier density effects on the exciton binding energies in wurtzite (WZ) InGaN/GaN quantum-well (QW) structures are investigated using the multiband effective-mass theory, and are compared with those obtained from the at-band model and with those of GaN/AlGaN QW structures. The exciton binding energy is significantly reduced with increasing sheet carrier density, suggesting that excitons are nearly bleached at densities around 10 12 cm -2 for both InGaN/GaN and GaN/AlGaN QW structures. With the inclusion of the internal field, the exciton binding energy is substantialy reduced compared to that of the at-band model in the investigated region of the wells. This can be explained by a decrease in the momentum matrix element and an increase in the inverse screening length due to the internal field. The exciton binding energy of the InGaN/GaN structure is smaller than that of the GaN/AlGaN structure because InGaN/GaN structures have a smaller momentum matrix element and a larger inverse screening length than GaN/AlGaN structures.

  3. Impurity-induced states in superconducting heterostructures

    Science.gov (United States)

    Liu, Dong E.; Rossi, Enrico; Lutchyn, Roman M.

    2018-04-01

    Heterostructures allow the realization of electronic states that are difficult to obtain in isolated uniform systems. Exemplary is the case of quasi-one-dimensional heterostructures formed by a superconductor and a semiconductor with spin-orbit coupling in which Majorana zero-energy modes can be realized. We study the effect of a single impurity on the energy spectrum of superconducting heterostructures. We find that the coupling between the superconductor and the semiconductor can strongly affect the impurity-induced states and may induce additional subgap bound states that are not present in isolated uniform superconductors. For the case of quasi-one-dimensional superconductor/semiconductor heterostructures we obtain the conditions for which the low-energy impurity-induced bound states appear.

  4. Towards accurate free energy calculations in ligand protein-binding studies.

    Science.gov (United States)

    Steinbrecher, Thomas; Labahn, Andreas

    2010-01-01

    Cells contain a multitude of different chemical reaction paths running simultaneously and quite independently next to each other. This amazing feat is enabled by molecular recognition, the ability of biomolecules to form stable and specific complexes with each other and with their substrates. A better understanding of this process, i.e. of the kinetics, structures and thermodynamic properties of biomolecule binding, would be invaluable in the study of biological systems. In addition, as the mode of action of many pharmaceuticals is based upon their inhibition or activation of biomolecule targets, predictive models of small molecule receptor binding are very helpful tools in rational drug design. Since the goal here is normally to design a new compound with a high inhibition strength, one of the most important thermodynamic properties is the binding free energy DeltaG(0). The prediction of binding constants has always been one of the major goals in the field of computational chemistry, because the ability to reliably assess a hypothetical compound's binding properties without having to synthesize it first would save a tremendous amount of work. The different approaches to this question range from fast and simple empirical descriptor methods to elaborate simulation protocols aimed at putting the computation of free energies onto a solid foundation of statistical thermodynamics. While the later methods are still not suited for the screenings of thousands of compounds that are routinely performed in computational drug design studies, they are increasingly put to use for the detailed study of protein ligand interactions. This review will focus on molecular mechanics force field based free energy calculations and their application to the study of protein ligand interactions. After a brief overview of other popular methods for the calculation of free energies, we will describe recent advances in methodology and a variety of exemplary studies of molecular dynamics

  5. Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.

    Science.gov (United States)

    Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton

    2013-08-15

    Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.

  6. Impurity gettering in semiconductors

    Science.gov (United States)

    Sopori, Bhushan L.

    1995-01-01

    A process for impurity gettering in a semiconductor substrate or device such as a silicon substrate or device. The process comprises hydrogenating the substrate or device at the back side thereof with sufficient intensity and for a time period sufficient to produce a damaged back side. Thereafter, the substrate or device is illuminated with electromagnetic radiation at an intensity and for a time period sufficient to cause the impurities to diffuse to the back side and alloy with a metal there present to form a contact and capture the impurities. The impurity gettering process also can function to simultaneously passivate defects within the substrate or device, with the defects likewise diffusing to the back side for simultaneous passivation. Simultaneously, substantially all hydrogen-induced damage on the back side of the substrate or device is likewise annihilated. Also taught is an alternate process comprising thermal treatment after hydrogenation of the substrate or device at a temperature of from about 500.degree. C. to about 700.degree. C. for a time period sufficient to cause the impurities to diffuse to the damaged back side thereof for subsequent capture by an alloying metal.

  7. Cooper-pair size and binding energy for unconventional superconducting systems

    Science.gov (United States)

    Dinóla Neto, F.; Neto, Minos A.; Salmon, Octavio D. Rodriguez

    2018-06-01

    The main proposal of this paper is to analyze the size of the Cooper pairs composed by unbalanced mass fermions from different electronic bands along the BCS-BEC crossover and study the binding energy of the pairs. We are considering an interaction between fermions with different masses leading to an inter-band pairing. In addiction to the attractive interaction we have an hybridization term to couple both bands, which in general acts unfavorable for the pairing between the electrons. We get first order phase transitions as the hybridization breaks the Cooper pairs for the s-wave symmetry of the gap amplitude. The results show the dependence of the Cooper-pair size as a function of the hybridization for T = 0 . We also propose the structure of the binding energy of the inter-band system as a function of the two-bands quasi-particle energies.

  8. 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.

  9. Converging ligand‐binding free energies obtained with free‐energy perturbations at the quantum mechanical level

    Science.gov (United States)

    Olsson, Martin A.; Söderhjelm, Pär

    2016-01-01

    In this article, the convergence of quantum mechanical (QM) free‐energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa‐acid deep‐cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158–224 atoms). We use single‐step exponential averaging (ssEA) and the non‐Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi‐empirical PM6‐DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free‐energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27117350

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

    DEFF Research Database (Denmark)

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

    1997-01-01

    We report a systematic study of exciton binding energies and lifetimes in InGaAs/GaAs quantum wells. The experimental binding energies have been deduced from photoluminescence excitation measurements taking into account the contribution of the 2s state of the exciton and the line broadening...

  11. Effect of impurity radiation on tokamak equilibrium

    International Nuclear Information System (INIS)

    Rebut, P.H.; Green, B.J.

    1977-01-01

    The energy loss from a tokamak plasma due to the radiation from impurities is of great importance in the overall energy balance. Taking the temperature dependence of this loss for two impurities characteristic of those present in existing tokamak plasmas, the condition for radial power balance is derived. For the impurities considered (oxygen and iron) it is found that the radiation losses are concentrated in a thin outer layer of the plasma and the equilibrium condition places an upper limit on the plasma paraticle number density in this region. This limiting density scales with mean current density in the same manner as is experimentally observed for the peak number density of tokamak plasmas. The stability of such equilibria is also discussed. (author)

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

    Science.gov (United States)

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

    2018-05-01

    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.

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

    Science.gov (United States)

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

    2018-05-01

    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.

  14. Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach.

    Science.gov (United States)

    Pan, Yuliang; Wang, Zixiang; Zhan, Weihua; Deng, Lei

    2018-05-01

    Identifying RNA-binding residues, especially energetically favored hot spots, can provide valuable clues for understanding the mechanisms and functional importance of protein-RNA interactions. Yet, limited availability of experimentally recognized energy hot spots in protein-RNA crystal structures leads to the difficulties in developing empirical identification approaches. Computational prediction of RNA-binding hot spot residues is still in its infant stage. Here, we describe a computational method, PrabHot (Prediction of protein-RNA binding hot spots), that can effectively detect hot spot residues on protein-RNA binding interfaces using an ensemble of conceptually different machine learning classifiers. Residue interaction network features and new solvent exposure characteristics are combined together and selected for classification with the Boruta algorithm. In particular, two new reference datasets (benchmark and independent) have been generated containing 107 hot spots from 47 known protein-RNA complex structures. In 10-fold cross-validation on the training dataset, PrabHot achieves promising performances with an AUC score of 0.86 and a sensitivity of 0.78, which are significantly better than that of the pioneer RNA-binding hot spot prediction method HotSPRing. We also demonstrate the capability of our proposed method on the independent test dataset and gain a competitive advantage as a result. The PrabHot webserver is freely available at http://denglab.org/PrabHot/. leideng@csu.edu.cn. Supplementary data are available at Bioinformatics online.

  15. 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.

  16. Analysis of oxygen binding-energy variations for BaO on W

    Science.gov (United States)

    Haas, G. A.; Shih, A.; Mueller, D.; Thomas, R. E.

    Interatomic Auger analyses have been made of different forms of BaO layers on W substrates. Variations in Auger spectroscopy energies of the Ba4dBa5pO2p interatomic Auger transition were found to be largely governed by the O2p binding energy of the BaO adsorbate. This was illustrated by comparing results of the Auger data values with values derived from O2p binding energies using ultraviolet photoelectron spectroscopy. Very good agreement was observed not only for the W substrate but also for the W substrate which showed two oxygen-induced electronics state. Variations in binding energy were noted for different states of BaO lattice formation and for different amounts of oxidation, ranging from the transition of Ba to BaO and continuing to the BaO 2 stoichiometry and beyond. Effects were also reported for adsorbate alignment and thermal activation (i.e., reduction) of the oxidized state. An empirical relationship was found suggesting that the more tightly bound the O2p states of the BaO adsorbate were, the lower its work function would be. This link between binding energy and work function was observed to be valid not only for cases of poisoning by oxidation, but held as well during reactivation by the subsequent reduction of the oxide. In addition, this relationship also appeared to predict the low work function obtained through the introduction of substances such as Sc to the BaO-W system. Possible qualitative reasons which might contribute to this are discussed in terms of enhanced dipole effects and shifts in band structure.

  17. 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.

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

    International Nuclear Information System (INIS)

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

    2014-01-01

    We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ∼0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach

  19. Impurities and conductivity in a D-wave superconductor

    International Nuclear Information System (INIS)

    Balatsky, A.V.

    1994-01-01

    Impurity scattering in the unitary limit produces low energy quasiparticles with anisotropic spectrum in a two-dimensional d-wave superconductor. The authors describe a new quasi-one-dimensional limit of the quasiparticle scattering, which might occur in a superconductor with short coherence length and with finite impurity potential range. The dc conductivity in a d-wave superconductor is predicted to be proportional to the normal state scattering rate and is impurity-dependent. They show that quasi-one-dimensional regime might occur in high-T c superconductors with Zn impurities at low temperatures T approx-lt 10 K

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-01-01

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

  1. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations.

    Science.gov (United States)

    Cournia, Zoe; Allen, Bryce; Sherman, Woody

    2017-12-26

    Accurate in silico prediction of protein-ligand binding affinities has been a primary objective of structure-based drug design for decades due to the putative value it would bring to the drug discovery process. However, computational methods have historically failed to deliver value in real-world drug discovery applications due to a variety of scientific, technical, and practical challenges. Recently, a family of approaches commonly referred to as relative binding free energy (RBFE) calculations, which rely on physics-based molecular simulations and statistical mechanics, have shown promise in reliably generating accurate predictions in the context of drug discovery projects. This advance arises from accumulating developments in the underlying scientific methods (decades of research on force fields and sampling algorithms) coupled with vast increases in computational resources (graphics processing units and cloud infrastructures). Mounting evidence from retrospective validation studies, blind challenge predictions, and prospective applications suggests that RBFE simulations can now predict the affinity differences for congeneric ligands with sufficient accuracy and throughput to deliver considerable value in hit-to-lead and lead optimization efforts. Here, we present an overview of current RBFE implementations, highlighting recent advances and remaining challenges, along with examples that emphasize practical considerations for obtaining reliable RBFE results. We focus specifically on relative binding free energies because the calculations are less computationally intensive than absolute binding free energy (ABFE) calculations and map directly onto the hit-to-lead and lead optimization processes, where the prediction of relative binding energies between a reference molecule and new ideas (virtual molecules) can be used to prioritize molecules for synthesis. We describe the critical aspects of running RBFE calculations, from both theoretical and applied perspectives

  2. 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.

  3. Relativistic deformed mean-field calculation of binding energy differences of mirror nuclei

    International Nuclear Information System (INIS)

    Koepf, W.; Barreiro, L.A.

    1996-01-01

    Binding energy differences of mirror nuclei for A=15, 17, 27, 29, 31, 33, 39 and 41 are calculated in the framework of relativistic deformed mean-field theory. The spatial components of the vector meson fields and the photon are fully taken into account in a self-consistent manner. The calculated binding energy differences are systematically smaller than the experimental values and lend support to the existence of the Okamoto-Nolen-Schiffer anomaly found decades ago in nonrelativistic calculations. For the majority of the nuclei studied, however, the results are such that the anomaly is significantly smaller than the one obtained within state-of-the-art nonrelativistic calculations. (author). 35 refs

  4. Binding energies of double-Λ hypernuclei and ΛΛ G-matrix

    International Nuclear Information System (INIS)

    Himeno, Hiroyuki; Sakuda, Toshimi; Nagata, Sinobu; Yamamoto, Yasuo.

    1993-01-01

    Binding energies of double-Λ hypernuclei ΛΛ 10 Be, ΛΛ 13 B and ΛΛ 6 He are calculated on the basis of G-matrix theory in finite nuclei. The core + Λ + Λ three-body model is adopted and the G-matrix for ΛΛ interaction is treated consistently with the model space. As the bare interaction the Nijmegen model D and model F are used. It is discussed that the consistency of the interaction with the model space is very important to calculate reliably the binding energies. It is shown that if the new event of double-Λ hypernuclei is interpreted as ΛΛ 13 B, model D reproduces the experimental data very well, whereas model F does not. (author)

  5. Dynamical impurity problems

    International Nuclear Information System (INIS)

    Emery, V.J.; Kivelson, S.A.

    1993-01-01

    In the past few years there has been a resurgence of interest in dynamical impurity problems, as a result of developments in the theory of correlated electron systems. The general dynamical impurity problem is a set of conduction electrons interacting with an impurity which has internal degrees of freedom. The simplest and earliest example, the Kondo problem, has attracted interest since the mid-sixties not only because of its physical importance but also as an example of a model displaying logarithmic divergences order by order in perturbation theory. It provided one of the earliest applications of the renormalization group method, which is designed to deal with just such a situation. As we shall see, the antiferromagnetic Kondo model is controlled by a strong-coupling fixed point, and the essence of the renormalization group solution is to carry out the global renormalization numerically starting from the original (weak-coupling) Hamiltonian. In these lectures, we shall describe an alternative route in which we identify an exactly solvable model which renormalizes to the same fixed point as the original dynamical impurity problem. This approach is akin to determining the critical behavior at a second order phase transition point by solving any model in a given universality class

  6. Dynamical impurity problems

    Energy Technology Data Exchange (ETDEWEB)

    Emery, V.J. [Brookhaven National Lab., Upton, NY (United States); Kivelson, S.A. [California Univ., Los Angeles, CA (United States). Dept. of Physics

    1993-12-31

    In the past few years there has been a resurgence of interest in dynamical impurity problems, as a result of developments in the theory of correlated electron systems. The general dynamical impurity problem is a set of conduction electrons interacting with an impurity which has internal degrees of freedom. The simplest and earliest example, the Kondo problem, has attracted interest since the mid-sixties not only because of its physical importance but also as an example of a model displaying logarithmic divergences order by order in perturbation theory. It provided one of the earliest applications of the renormalization group method, which is designed to deal with just such a situation. As we shall see, the antiferromagnetic Kondo model is controlled by a strong-coupling fixed point, and the essence of the renormalization group solution is to carry out the global renormalization numerically starting from the original (weak-coupling) Hamiltonian. In these lectures, we shall describe an alternative route in which we identify an exactly solvable model which renormalizes to the same fixed point as the original dynamical impurity problem. This approach is akin to determining the critical behavior at a second order phase transition point by solving any model in a given universality class.

  7. Binding energies of sd-shell nuclei with a realistic effective Hamiltonian

    International Nuclear Information System (INIS)

    Dalton, B.J.; Vary, J.P.; Baldridge, W.J.

    1977-01-01

    The nuclear shell model with a second-order effective Hamiltonian derived within Brueckner theory from the free nucleon-nucleon interaction is shown to yield accurate binding energies of nuclei with 16 < A < 40. This agreement is obtained by choosing the spectrum of low-lying unoccupied orbitals in a justified manner and, when necessary, by employing a statistical method to approximate the lowest eigenvalue of very large shell-model diagonalizations

  8. 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.

  9. Effect of the dielectric constant of mesoscopic particle on the exciton binding energy

    International Nuclear Information System (INIS)

    Lai Zuyou; Gu Shiwei

    1991-09-01

    For materials with big exciton reduced mass and big dielectric constant, such as TiO 2 , the variation of dielectric constant with the radius of an ultrafine particle (UFP) is important for determining the exciton binding energy. For the first time a phenomenological formula of the dielectric constant of a UFP with its radius in mesoscopic range is put forward in order to explain the optical properties of TiO 2 UFP. (author). 22 refs, 3 figs, 1 tab

  10. On the photo-ionization of impurity centres in semiconductors

    International Nuclear Information System (INIS)

    Tomak, M.

    1982-10-01

    The dependence of the photo-ionization cross-section on photon energy is calculated. The impurity potential is assumed to be of the Hulthen potential type and bound state wave function is calculated variationally. The results show that, at least in some cases, the Hulthen potential may describe the impurity better than the hydrogen or delta function potentials. (author)

  11. Impurity levels: corrections to the effective mass approximation

    International Nuclear Information System (INIS)

    Bentosela, F.

    1977-07-01

    Some rigorous results concerning the effective mass approximation used for the calculation of the impurity levels in semiconductors are presented. Each energy level is expressed as an asymptotic series in the inverse of the dielectric constant K, in the case where the impurity potential is 1/μ

  12. Polaronic effects on the off-center donor impurity in AlAs/GaAs/SiO2 spherical core/shell quantum dots

    Science.gov (United States)

    El Haouari, M.; Feddi, E.; Dujardin, F.; Restrepo, R. L.; Mora-Ramos, M. E.; Duque, C. A.

    2017-11-01

    The ground state of a conduction electron coupled to an off-center impurity donor in a AlAS/GaAs spherical core/shell quantum dot is investigated theoretically. The image-charge effect and the influence of the electron-polar-LO-phonon interaction are considered. The electron-impurity binding energy is calculated via a variational procedure and is reported both as a function of the shell width and of the radial position of the donor atom. The polaronic effects on this quantity are particularly discussed.

  13. 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.

  14. 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

  15. 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.

  16. Momentum distributions and binding energies for the valence orbitals of methanol

    International Nuclear Information System (INIS)

    Minchinton, A.; Brion, C.E.; Weigold, E.

    1981-06-01

    Methanol has been studied by binary (e,2e) coincidence spectroscopy at 1200 eV using symmetric non-coplanar geometry. The binding energy spectrum has been determined in the energy range up to 46eV at azimuthal angles of 0 deg. and 7 deg. Momentum distributions measured for the valence orbitals are compared with calculations using the wave functions (essentially double-zeta quality) reported by Snyder and Basch. Agreement is generally quite good except for the outermost orbitals and the 5a' orbital which all show somewhat larger low momentum components than predicted by the calculations. This is indicative of a more spatially extended orbital than is predicted

  17. Impurity solitons with quadratic nonlinearities

    DEFF Research Database (Denmark)

    Clausen, Carl A. Balslev; Torres, Juan P-; Torner, Lluis

    1998-01-01

    We fmd families of solitary waves mediated by parametric mixing in quadratic nonlinear media that are localized at point-defect impurities. Solitons localized at attractive impurities are found to be dynamically stable. It is shown that localization at the impurity modifies strongly the soliton...

  18. Impurity studies in the advanced toroidal facility

    International Nuclear Information System (INIS)

    Isler, R.C.; Horton, L.D.; Crume, E.C.; Howe, H.C.; Voronov, G.S.

    1989-01-01

    Impurities have played an important role in the initial stages of operation of the Advanced Toroidal Facility. Cleanup practices have been adequate enough that plasmas heated by ECH only can be operated in a quasi-steady state; however, neutral beam injected plasmas always collapse to a low temperature. It is not clear whether impurity radiation is actually responsible for initiating the collapse, but at the time the stored energy reaches a maximum, there are indications of poloidal asymmetries in radiation from low ionization stages, such as observed in marfes, which could play a dominant role in the plasma evolution. 3 refs., 5 figs

  19. Benchmark calculations with correlated molecular wave functions. VII. Binding energy and structure of the HF dimer

    International Nuclear Information System (INIS)

    Peterson, K.A.; Dunning, T.H. Jr.

    1995-01-01

    The hydrogen bond energy and geometry of the HF dimer have been investigated using the series of correlation consistent basis sets from aug-cc-pVDZ to aug-cc-pVQZ and several theoretical methods including Moller--Plesset perturbation and coupled cluster theories. Estimates of the complete basis set (CBS) limit have been derived for the binding energy of (HF) 2 at each level of theory by utilizing the regular convergence characteristics of the correlation consistent basis sets. CBS limit hydrogen bond energies of 3.72, 4.53, 4.55, and 4.60 kcal/mol are estimated at the SCF, MP2, MP4, and CCSD(T) levels of theory, respectively. CBS limits for the intermolecular F--F distance are estimated to be 2.82, 2.74, 2.73, and 2.73 A, respectively, for the same correlation methods. The effects of basis set superposition error (BSSE) on both the binding energies and structures have also been investigated for each basis set using the standard function counterpoise (CP) method. While BSSE has a negligible effect on the intramolecular geometries, the CP-corrected F--F distance and binding energy differ significantly from the uncorrected values for the aug-cc-pVDZ basis set; these differences decrease regularly with increasing basis set size, yielding the same limits in the CBS limit. Best estimates for the equilibrium properties of the HF dimer from CCSD(T) calculations are D e =4.60 kcal/mol, R FF =2.73 A, r 1 =0.922 A, r 2 =0.920 A, Θ 1 =7 degree, and Θ 2 =111 degree

  20. 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.

  1. Magnetic impurity coupled to interacting conduction electrons

    International Nuclear Information System (INIS)

    Schork, T.

    1996-01-01

    We consider a magnetic impurity which interacts by hybridization with a system of weakly correlated electrons and determine the energy of the ground state by means of a 1/N f expansion. The correlations among the conduction electrons are described by a Hubbard Hamiltonian and are treated to the lowest order in the interaction strength. We find that their effect on the Kondo temperature, T K , in the Kondo limit is twofold: first, the position of the impurity level is shifted due to the reduction of charge fluctuations, which reduces T K . Secondly, the bare Kondo exchange coupling is enhanced as spin fluctuations are enlarged. In total, T K increases. Both corrections require intermediate states beyond the standard Varma-Yafet ansatz. This shows that the Hubbard interaction does not just provide quasiparticles, which hybridize with the impurity, but also renormalizes the Kondo coupling. copyright 1996 The American Physical Society

  2. Photoionization cross-section of donor impurity in spherical quantum dots under electric and intense laser fields

    International Nuclear Information System (INIS)

    Burileanu, L.M.

    2014-01-01

    Using a perturbative method we have investigated the behavior of the binding energy and photoionization cross-section of a donor impurity in spherical GaAs–GaAlAs quantum dots under the influence of electric and intense high-frequency laser fields. The dependencies of the binding energy and photoionization cross-section on electric and laser field strength, dot radius and impurity position were investigated. Our results show that the amplitude of photoionization cross-section grows with the dot radius increase and the peak of the cross-section blue shifts with the laser intensity increment. We have found that the binding energy is not a monotonically function of laser intensity: it decreases or increases depending on electric field regime. The studied effects are even more pronounced as the quantum dot radius is smaller. -- Highlights: • A photoionization cross-section study in quantum dots under laser and electric fields. • The photoionization cross-section peaks are red shifted by the electric field. • The photoionization cross-section peaks are blue shifted by the laser field. • The combined effects of applied fields strongly affect the binding energy

  3. Hydrostatic Pressure and Built-In Electric Field Effects on the Donor Impurity States in Cylindrical Wurtzite GaN/AlxGa1−xN Quantum Rings

    Directory of Open Access Journals (Sweden)

    Guangxin Wang

    2015-01-01

    Full Text Available Within the framework of the effective mass approximation, the ground-state binding energy of a hydrogenic impurity is investigated in cylindrical wurtzite GaN/AlxGa1-xN strained quantum ring (QR by means of a variational approach, considering the influence of the applied hydrostatic pressure along the QR growth direction and the strong built-in electric field (BEF due to the piezoelectricity and spontaneous polarization. Numerical results show that the donor binding energy for a central impurity increases inchmeal firstly as the QR radial thickness (ΔR decreases gradually and then begins to drop quickly. In addition, the donor binding energy is an increasing (a decreasing function of the inner radius (height. It is also found that the donor binding energy increases almost linearly with the increment of the applied hydrostatic pressure. Moreover, we also found that impurity positions have an important influence on the donor binding energy. The physical reasons have been analyzed in detail.

  4. 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.

  5. On the binding energy of double Λ hypernuclei in the relativistic mean field theory

    International Nuclear Information System (INIS)

    Marcos, S.; Lombard, R.J.

    1997-01-01

    The binding energy of two Λ hyperons bound to a nuclear core is calculated within the relativistic mean field theory. The starting point is a two body relativistic equation of the Breit type suggested by the RMFT, and corrected for the two-particle interaction. The 2 Λ correlation energy is evaluated and the contribution of the δ and φ mesons, acting solely between hyperons, to the bond energy σB ΛΛ of ( ΛΛ ) 6 He, ( ΛΛ ) 10 Be and ( ΛΛ ) 13 B is calculated. Predictions of the ΔB ΛΛ A dependence are made for heavier Λ-hypernuclei. (K.A.)

  6. An extension of the fenske-hall LCAO method for approximate calculations of inner-shell binding energies of molecules

    Science.gov (United States)

    Zwanziger, Ch.; Reinhold, J.

    1980-02-01

    The approximate LCAO MO method of Fenske and Hall has been extended to an all-election method allowing the calculation of inner-shell binding energies of molecules and their chemical shifts. Preliminary results are given.

  7. Anisotropic Lithium Insertion Behavior in Silicon Nanowires: Binding Energy, Diffusion Barrier, and Strain Effect

    KAUST Repository

    Zhang, Qianfan; Cui, Yi; Wang, Enge

    2011-01-01

    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.

  8. 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.

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

    Science.gov (United States)

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

    2008-03-01

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

  10. Evolution of Structure in Nuclei: Meditation by Sub-Shell Modifications and Relation to Binding Energies

    Science.gov (United States)

    Casten, R. F.; Cakirli, R. B.

    2009-03-01

    Understanding the development of configuration mixing, coherence, collectivity, and deformation in nuclei is one of the crucial challenges in nuclear structure physics, and one which has become all the more important with the advent of next generation facilities for the study of exotic nuclei. We will discuss recent work on phase/shape transitional behavior in nuclei, and the role of changes in sub-shell structure in mediating such transitional regions. We will also discuss a newly found, much deeper, link between nuclear structure and nuclear binding energies.

  11. Simulation of core-level binding energy shifts in germanium-doped lead telluride crystals

    International Nuclear Information System (INIS)

    Zyubin, A.S.; Dedyulin, S.N.; Yashina, L.V.; Shtanov, V.I.

    2007-01-01

    To simulate the changes in core-level binding energies in germanium-doped lead telluride, cluster calculations of the changes in the electrostatic potential at the corresponding centers have been performed. Different locations of the Ge atom in the crystal bulk have been considered: near vacancies, near another dopant site, and near the surface. For calculating the potential in the clusters that model the bulk and the surface of the lead telluride crystal (c-PbTe), the electron density obtained in the framework of the Hartree-Fock and hybrid density functional theory (DFT) methods has been used [ru

  12. Accurate core-electron binding energy shifts from density functional theory

    International Nuclear Information System (INIS)

    Takahata, Yuji; Marques, Alberto Dos Santos

    2010-01-01

    Current review covers description of density functional methods of calculation of accurate core-electron binding energy (CEBE) of second and third row atoms; applications of calculated CEBEs and CEBE shifts (ΔCEBEs) in elucidation of topics such as: hydrogen-bonding, peptide bond, polymers, DNA bases, Hammett substituent (σ) constants, inductive and resonance effects, quantitative structure activity relationship (QSAR), and solid state effect (WD). This review limits itself to works of mainly Chong and his coworkers for the period post-2002. It is not a fully comprehensive account of the current state of the art.

  13. Free energy calculations on Transthyretin dissociation and ligand binding from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew

    experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated......Many questions about the nature of aggregation and the proteins that are involved in these events are still left unanswered. One of the proteins that is known to form amyloids is Transthyretine (TTR), the secondary transporter of thyroxine and transporter of retinol-binding-protein. Several...

  14. Folding model analysis of Λ binding energies and three-body ΛNN force

    International Nuclear Information System (INIS)

    Mian, M.; Rahman Khan, M.Z.

    1988-02-01

    Working within the framework of the folding model, we analyze the Λ binding energy data of light hypernuclei with effective two-body ΛN plus three-body ΛNN interaction. The two-body density for the core nucleus required for evaluating the three-body force contribution is obtained in terms of the centre of mass pair correlation. It is found that except for Λ 5 He the data are fairly well explained. The three-body force seems to account for the density dependence of the effective two-body ΛN interaction proposed earlier. (author). 13 refs, 2 tabs

  15. Impurity effects on ionic-liquid-based supercapacitors

    International Nuclear Information System (INIS)

    Liu, Kun; Lian, Cheng; Henderson, Douglas; Wu, Jianzhong

    2016-01-01

    Small amounts of an impurity may affect the key properties of an ionic liquid and such effects can be dramatically amplified when the electrolyte is under confinement. Here the classical density functional theory is employed to investigate the impurity effects on the microscopic structure and the performance of ionic-liquid-based electrical double-layer capacitors, also known as supercapacitors. Using a primitive model for ionic species, we study the effects of an impurity on the double layer structure and the integral capacitance of a room temperature ionic liquid in model electrode pores and find that an impurity strongly binding to the surface of a porous electrode can significantly alter the electric double layer structure and dampen the oscillatory dependence of the capacitance with the pore size of the electrode. Meanwhile, a strong affinity of the impurity with the ionic species affects the dependence of the integral capacitance on the pore size. Up to 30% increase in the integral capacitance can be achieved even at a very low impurity bulk concentration. As a result, by comparing with an ionic liquid mixture containing modified ionic species, we find that the cooperative effect of the bounded impurities is mainly responsible for the significant enhancement of the supercapacitor performance.

  16. Impurity effects on ionic-liquid-based supercapacitors

    Science.gov (United States)

    Liu, Kun; Lian, Cheng; Henderson, Douglas; Wu, Jianzhong

    2017-02-01

    Small amounts of an impurity may affect the key properties of an ionic liquid and such effects can be dramatically amplified when the electrolyte is under confinement. Here the classical density functional theory is employed to investigate the impurity effects on the microscopic structure and the performance of ionic-liquid-based electrical double-layer capacitors, also known as supercapacitors. Using a primitive model for ionic species, we study the effects of an impurity on the double layer structure and the integral capacitance of a room temperature ionic liquid in model electrode pores and find that an impurity strongly binding to the surface of a porous electrode can significantly alter the electric double layer structure and dampen the oscillatory dependence of the capacitance with the pore size of the electrode. Meanwhile, a strong affinity of the impurity with the ionic species affects the dependence of the integral capacitance on the pore size. Up to 30% increase in the integral capacitance can be achieved even at a very low impurity bulk concentration. By comparing with an ionic liquid mixture containing modified ionic species, we find that the cooperative effect of the bounded impurities is mainly responsible for the significant enhancement of the supercapacitor performance.

  17. Reaction of hydrogen with Ag(111): binding states, minimum energy paths, and kinetics.

    Science.gov (United States)

    Montoya, Alejandro; Schlunke, Anna; Haynes, Brian S

    2006-08-31

    The interaction of atomic and molecular hydrogen with the Ag(111) surface is studied using periodic density functional total-energy calculations. This paper focuses on the site preference for adsorption, ordered structures, and energy barriers for H diffusion and H recombination. Chemisorbed H atoms are unstable with respect to the H(2) molecule in all adsorption sites below monolayer coverage. The three-hollow sites are energetically the most favorable for H chemisorption. The binding energy of H to the surface decreases slightly up to one monolayer, suggesting a small repulsive H-H interaction on nonadjacent sites. Subsurface and vacancy sites are energetically less favorable for H adsorption than on-top sites. Recombination of chemisorbed H atoms leads to the formation of gas-phase H(2) with no molecular chemisorbed state. Recombination is an exothermic process and occurs on the bridge site with a pronounced energy barrier. This energy barrier is significantly higher than that inferred from experimental temperature-programmed desorption (TPD) studies. However, there is significant permeability of H atoms through the recombination energy barrier at low temperatures, thus increasing the rate constant for H(2) desorption due to quantum tunneling effects, and improving the agreement between experiment and theory.

  18. Spectroscopical studies of impurities in the belt pinch HECTOR

    International Nuclear Information System (INIS)

    Singethan, J.

    1981-04-01

    In this paper UV-line-intensity measurements of impurities are presented, which have been performed in the belt-pinch HECTOR. From the line-intensities impurity concentrations and information on the radiation losses is be obtained. At temperatures below 100 eV, the energy loss due to line emission of oxygen and carbon impurities is one of the most important electron energy loss mechanisms. Thus the measurement and calculation of the radiation losses is of particular relevance. Furthermore the electron temperature time dependence can be obtained by comparing the line intensity time dependence with the solution of the respective rate equations. (orig./HT) [de

  19. Excited states of hydrogen shallow impurities in GaAs-Ga Al As quantum wells

    International Nuclear Information System (INIS)

    Neves Carneiro, Gleise das

    1994-01-01

    The study of shallow impurities in semiconductor heterostructures, such as quantum and superlattices, has been of continuous interest over the last years. Successful comparisons between experimental results photoluminescence: N.N Ledentsov et al., Appl. Phys. A 54, 261 (1992) and theoretical calculations [L.E. Oliveira and G.D. Mahan, Phys. Rev. B 47, 2406 (1993)] constitute a strong motivation for an in-depth theoretical study. We present a variational calculation of the binding energies of shallow donors in a Ga-As-AlGaAs quantum well. The energies and variational wave functions associated to the ground state (1s-like) as well as some excited states (2s, 2p xy , 2p xy , 3s, 3p xy , and 3p like) are obtained as functions of the position of the impurity (z i ) in the well. The density of impurity states, intra-donor transition strengths and the infrared absorption spectra are calculated for some of these excited states and results compared with previous theoretical [S. Fraizzoli, F. Bassani, and R. Buczko, Phys. rev. B 41, 5096 (1990)] and experimental works [N.C. Jarosik et al., Phys. Rev. Lett. 54, 1283 (1985). (author)

  20. 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

  1. 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

  2. 4He binding energy calculation including full tensor-force effects

    Science.gov (United States)

    Fonseca, A. C.

    1989-09-01

    The four-body equations of Alt, Grassberger, and Sandhas are solved in the version where the (2)+(2) subamplitudes are treated exactly by convolution, using one-term separable Yamaguchy nucleon-nucleon potentials in the 1S0 and 3S1-3D1 channels. The resulting jp=1/2+ and (3/2+ three-body subamplitudes are represented in a separable form using the energy-dependent pole expansion. Converged bound-state results are calculated for the first time using the full interaction, and are compared with those obtained from a simplified treatment of the tensor force. The Tjon line that correlates three-nucleon and four-nucleon binding energies is shown using different nucleon-nucleon potentials. In all calculations the Coulomb force has been neglected.

  3. 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.

  4. 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...

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

    Science.gov (United States)

    Liu, Hui; Hou, Tingjun

    2016-07-15

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

  6. 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

  7. Impurities in uranium process solutions

    International Nuclear Information System (INIS)

    Boydell, D.W.

    1980-01-01

    Several uranium purification circuits are presented in tabular form together with the average major impurity levels associated with each. The more common unit operations in these circuits, namely strong- and weak-base ion-exchange, solvent extraction and the precipitation of impurities are then discussed individually. Particular attention is paid to the effect and removal of impurities in each of these four unit operations. (author)

  8. Effect of magnetic field on the donor impurity in CdTe/Cd{sub 1-x}Mn{sub x}Te quantum well wire

    Energy Technology Data Exchange (ETDEWEB)

    Kalpana, P.; Nithiananthi, P.; Jayakumar, K., E-mail: kjkumar-gri@rediffmail.com [Nanostructure Lab, Department of Physics, Gandhigram Rural University, Gandhigram – 624 302, Tamilnadu (India); Reuben, A. Merwyn Jasper D. [Department of Physics, School of Engineering, Saveetha University, Thandalam, Chennai-600104, TamilNadu (India)

    2016-05-23

    The donor impurity binding energy in CdTe / Cd{sub 1-x}Mn{sub x}Te QWW with square well confinement along x – direction and parabolic confinement along y – direction under the influence of externally applied magnetic field has been computed using variational principle in the effective mass approximation. The spin polaronic shift has also been computed. The results are presented and discussed.

  9. 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

  10. Impurity sources in TEXTOR

    Energy Technology Data Exchange (ETDEWEB)

    Pospieszczyk, A; Bay, H L; Bogen, P; Hartwig, H; Hintz, E; Koenen, L; Ross, G G; Rusbueldt, D; Samm, U; Schweer, B

    1987-02-01

    The deuterium, oxygen and carbon fluxes from the main limiter and the deuterium fluxes from the wall are measured in TEXTOR for an 'all carbon' surrounding as a function of central density n/sub e/, of applied ICRH-power and of different wall conditions (carbonization). For this purpose, emission spectroscopy both with filter systems and spectrometers has been used. It is found that a major release mechanism for light impurities is via the formation of molecules. Oxygen seems to enter the discharge from the liner via O-D containing molecules, whereas the limiter acts as the main carbon source by the release of hydro-carbons as indicated by the observed CD-band spectra. Both oxygen and carbon fluxes are reduced by about a factor of two after a fresh carbonization. Above a certain critical density the plasma detaches from the limiter and forms a stable discharge with a radiation cooled boundary layer and with a major fraction of particles now reaching the wall instead of the limiter. The critical density rises with decreasing impurity fluxes or with increasing heating powers.

  11. Impurity sources in TEXTOR

    International Nuclear Information System (INIS)

    Pospieszczyk, A.; Bay, H.L.; Bogen, P.; Hartwig, H.; Hintz, E.; Koenen, L.; Ross, G.G.; Rusbueldt, D.; Samm, U.; Schweer, B.

    1987-01-01

    The deuterium, oxygen and carbon fluxes from the main limiter and the deuterium fluxes from the wall are measured in TEXTOR for an 'all carbon' surrounding as a function of central density n e , of applied ICRH-power and of different wall conditions (carbonization). For this purpose, emission spectroscopy both with filter systems and spectrometers has been used. It is found that a major release mechanism for light impurities is via the formation of molecules. Oxygen seems to enter the discharge from the liner via O-D containing molecules, whereas the limiter acts as the main carbon source by the release of hydro-carbons as indicated by the observed CD-band spectra. Both oxygen and carbon fluxes are reduced by about a factor of two after a fresh carbonization. Above a certain critical density the plasma detaches from the limiter and forms a stable discharge with a radiation cooled boundary layer and with a major fraction of particles now reaching the wall instead of the limiter. The critical density rises with decreasing impurity fluxes or with increasing heating powers. (orig.)

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

    Science.gov (United States)

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

    2016-05-04

    Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect.

  13. Influence of impurities on the evolution of vacancy-type defects in neutron-irradiated nickel

    International Nuclear Information System (INIS)

    Druzhkov, A.P.; Perminov, D.A.; Arbuzov, V.L.

    2012-01-01

    Highlights: ► We study, by means of PAS, the effects of purity on damage evolution in neutron-irradiated Ni at 330 K. ► Impurity carbon atoms in solution decrease the cascade efficiency during irradiation. ► C–V complexes are formed on the recovery stage III in impure Ni irradiated with 10 −4 dpa. ► The formation of V-loops and SFTs dominate on stage III with increasing dose level. ► The thermal stability of SFTs in impure Ni is similar to that in pure Ni. - Abstract: In order to investigate the effect of impurities on vacancy defect evolution in nickel, specimens with high (5N) and technical (3N) purity were neutron-irradiated at ∼330 K in the IVV-2M reactor (Russia) to fluencies in the range of 1 × 10 21 –1 × 10 23 n/m 2 (E > 0.1 MeV) corresponding to displacement dose levels in the range of about 0.0001–0.01 dpa and subsequently stepwise annealed to about 900 K. The specimens of Ni with different purities were characterized both in as-irradiated state as well as after post-irradiation annealing by positron annihilation spectroscopy. The formation of three-dimensional vacancy clusters (3D-VCs) in cascades was observed under neutron irradiation. The density and size of 3D-VCs depended not only on dose level, but also on purity. The population of 3D-VCs in the technical Ni is lower than that in the high-purity Ni. 3D-VCs collapse into secondary-type clusters (stacking fault tetrahedra (SFTs) and vacancy loops) during stepwise annealing at 350–450 K (stage III in Ni). The suppression of secondary cluster formation in 3N Ni is attributed to an effective vacancy interaction with impurity carbon atoms, which based on a relatively large vacancy–carbon atom binding energy (0.32–0.35 eV). The trapping of vacancies released at the collapse of 3D-VCs by the interstitial impurity atoms dominates at low irradiation dose level (10 −4 dpa). Thus, we found that carbon impurity atoms have strong effects both on the primary vacancy-type defect

  14. Microscopic models of impurities in silicon

    International Nuclear Information System (INIS)

    Assali, L.V.C.

    1985-01-01

    The study of electronic structure of insulated and complex puntual impurities in silicon responsible by the appearing of deep energy levels in the forbiden band of semiconductor, is presented. The molecular cluster model with the treatment of surface orbitals by Watson sphere within the formalism of Xα multiple scattering method, was used. The electronic structures of three clusters representative of perfect silicon crystal, which were used for the impurity studies, are presented. The method was applied to analyse insulated impurities of substitutional and interstitial hydrogen (Si:H and Si:H i ), subtitutional and interstitial iron in neutral and positive charge states (Si:Fe 0 , + , Si:Fe 0 , + ) and substitutional gold in three charge states(Si,Au - , 0 , + ). The thetraedic interstitial defect of silicon (Si:Si i ) was also studied. The complex impurities: neighbour iron pair in the lattice (Si:Fe 2 ), substitutional gold-interstitial iron pair (Si:Au s Fe) and substitutional boron-interstitial hydrogen pair (Si:B s H i ), were analysed. (M.C.K.) [pt

  15. Calculation of absolute protein-ligand binding free energy using distributed replica sampling.

    Science.gov (United States)

    Rodinger, Tomas; Howell, P Lynne; Pomès, Régis

    2008-10-21

    Distributed replica sampling [T. Rodinger et al., J. Chem. Theory Comput. 2, 725 (2006)] is a simple and general scheme for Boltzmann sampling of conformational space by computer simulation in which multiple replicas of the system undergo a random walk in reaction coordinate or temperature space. Individual replicas are linked through a generalized Hamiltonian containing an extra potential energy term or bias which depends on the distribution of all replicas, thus enforcing the desired sampling distribution along the coordinate or parameter of interest regardless of free energy barriers. In contrast to replica exchange methods, efficient implementation of the algorithm does not require synchronicity of the individual simulations. The algorithm is inherently suited for large-scale simulations using shared or heterogeneous computing platforms such as a distributed network. In this work, we build on our original algorithm by introducing Boltzmann-weighted jumping, which allows moves of a larger magnitude and thus enhances sampling efficiency along the reaction coordinate. The approach is demonstrated using a realistic and biologically relevant application; we calculate the standard binding free energy of benzene to the L99A mutant of T4 lysozyme. Distributed replica sampling is used in conjunction with thermodynamic integration to compute the potential of mean force for extracting the ligand from protein and solvent along a nonphysical spatial coordinate. Dynamic treatment of the reaction coordinate leads to faster statistical convergence of the potential of mean force than a conventional static coordinate, which suffers from slow transitions on a rugged potential energy surface.

  16. Binding energies and chemical shifts of least bound core electron excitations in cubic Asub(N)Bsub(8-N) semiconductors

    International Nuclear Information System (INIS)

    Bechstedt, F.; Enderlein, R.; Wischnewski, R.

    1981-01-01

    Core electron binding energies Esup(B) with respect to the vacuum level and their chemical shifts are calculated for the least bound core levels of cations and anions of cubic Asub(N)Bsub(8-N) semiconductors. Starting from the HF-binding energy of the free atom absolute values of Esup(B) are obtained by adding core level shifts and relaxation energies. Core level shifts are calculated by means of an electrostatic model with ionic and bond charges according to Phillips' bond charge model. For the calculation of relaxation energies the linear dielectric theory of electronic polarization is applied. Valence and core electrons, and diagonal and non-diagonal screening are taken into account. The theoretical results for chemical shifts of binding energies are compared with experimental values from XPS-measurements corrected by work function data. Good agreement is obtained in all cases within the error limit of about one eV. Chemical and atomic trends of core level shifts, relaxation energies, and binding energies are discussed in terms of changes of atomic and solid state parameters. Chemical shifts and relaxation energies are predicted for various ternary Asub(N)Bsub(8-N) compounds. (author)

  17. 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.

  18. Exploring the binding energy profiles of full agonists, partial agonists, and antagonists of the α7 nicotinic acetylcholine receptor.

    Science.gov (United States)

    Tabassum, Nargis; Ma, Qianyun; Wu, Guanzhao; Jiang, Tao; Yu, Rilei

    2017-09-01

    Nicotinic acetylcholine receptors (nAChRs) belong to the Cys-loop receptor family and are important drug targets for the treatment of neurological diseases. However, the precise determinants of the binding efficacies of ligands for these receptors are unclear. Therefore, in this study, the binding energy profiles of various ligands (full agonists, partial agonists, and antagonists) were quantified by docking those ligands with structural ensembles of the α7 nAChR exhibiting different degrees of C-loop closure. This approximate treatment of interactions suggested that full agonists, partial agonists, and antagonists of the α7 nAChR possess distinctive binding energy profiles. Results from docking revealed that ligand binding efficacy may be related to the capacity of the ligand to stabilize conformational states with a closed C loop.

  19. Nonlinearity and disorder: Classification and stability of nonlinear impurity modes

    DEFF Research Database (Denmark)

    Sukhorukov, Andrey A.; Kivshar, Yuri S.; Bang, Ole

    2001-01-01

    We study the effects produced by competition of two physical mechanisms of energy localization in inhomogeneous nonlinear systems. As an example, we analyze spatially localized modes supported by a nonlinear impurity in the generalized nonlinear Schrödinger equation and describe three types of no...... the case of a power-law nonlinearity in detail. We discuss several scenarios of the instability-induced dynamics of the nonlinear impurity modes, including the mode decay or switching to a new stable state, and collapse at the impurity site....

  20. Neo-classical impurity transport

    International Nuclear Information System (INIS)

    Stringer, T.E.

    The neo-classical theory for impurity transport in a toroidal plasma is outlined, and the results discussed. A general account is given of the impurity behaviour and its dependence on collisionality. The underlying physics is described with special attention to the role of the poloidal rotation

  1. Impurity study experiment proposal

    International Nuclear Information System (INIS)

    1975-05-01

    ISX is a modest tokamak which emphasizes the production of a predictable test plasma, experimental flexibility, ease of assembly and disassembly, and good diagnostic access. Its plasma models the outer cooler layers in EPR like plasmas. In addition, provisions will be made for long discharge times which may be necessary to observe some impurity effects. These machine characteristics will enable one to study the collisional transport of impurities in the plasma, perform systematic studies of wall and limiter materials and geometries, study methods of cleaning the walls, and develop and test new diagnostic techniques. ISX will employ water-cooled copper coils to produce a maximum toroidal magnetic field of 20 kG at the plasma axis, which is 77 cm from the major axis. The plasma minor radius will be about 15 cm, and the maximum plasma current will be 100 kA which will be induced by an iron core transformer with a capability of up to 0.9 volt-sec for long discharges. An aspect ratio of five and the modest magnetic field permit a design with ample space for thick wall structures such as honeycomb walls. The ''picture frame'' toroidal field coil provides additional space, while removable coil top sections allow easy replacement of the vacuum chamber. The 72-turn toroidal field coil is grouped into 24 sections for increased access. Absence of a conducting shell and placement of the vertical field and transformer primary coils away from the plasma allow easy viewing of the plasma and good diagnostic access. (U.S.)

  2. 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

  3. Impurity magnetopolaron in a parabolic quantum dot: the squeezed-state variational approach

    International Nuclear Information System (INIS)

    Kandemir, B S; Cetin, A

    2005-01-01

    We present a calculation of the ground-state binding energy of an impurity magnetopolaron confined in a three-dimensional (3D) parabolic quantum dot potential, in the framework of a variational approach based on two successive canonical transformations. First, we apply a displaced-oscillator type unitary transformation to diagonalize the relevant Froehlich Hamiltonian. Second, a single-mode squeezed-state transformation is introduced to deal with bilinear terms arising from the first transformation. Finally, the parameters of these transformations together with the parameters included in the electronic trial wavefunction are determined variationally to obtain the ground-state binding energy of an impurity magnetopolaron confined in a 3D parabolic quantum dot potential. Our approach has two advantages: first, the displaced-oscillator transformation allows one to obtain results valid for whole range of electron-phonon coupling strength since it is a special combination of Lee-Low-Pines and Huybrechts (LLP-H) canonical transformations, and second, the later transformation improves all-coupling results. It has been shown that the effects of quadratic terms arising from the all-coupling approach are very important and should be taken into account in studying the size-dependent physical properties of nanostructured materials

  4. 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.

  5. 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.

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

    International Nuclear Information System (INIS)

    Zhao, Junhua; Lu, Lixin; Rabczuk, Timon

    2014-01-01

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

  7. 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.

  8. Improving density functional tight binding predictions of free energy surfaces for peptide condensation reactions in solution

    Science.gov (United States)

    Kroonblawd, Matthew; Goldman, Nir

    First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for chemistry that is fast relative to DFT simulation times (Contract DE-AC52-07NA27344.

  9. Improving Density Functional Tight Binding Predictions of Free Energy Surfaces for Slow Chemical Reactions in Solution

    Science.gov (United States)

    Kroonblawd, Matthew; Goldman, Nir

    2017-06-01

    First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for reactions that are fast relative to DFT simulation times (Contract DE-AC52-07NA27344.

  10. 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.

  11. 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.

  12. Core-level binding energy shifts in Pt Ru nanoparticles: A puzzle resolved

    Science.gov (United States)

    Lewera, Adam; Zhou, Wei Ping; Hunger, Ralf; Jaegermann, Wolfram; Wieckowski, Andrzej; Yockel, Scott; Bagus, Paul S.

    2007-10-01

    Synchrotron measurements of Pt and Ru core-level binding energies, BE's, in Pt-Ru nanoparticles, as a function of Pt content, quantify earlier indications that the Pt 4f BE shift is much larger than the Ru 3d BE shift. A complementary theoretical analysis relates the BE shifts to changes in the metal-metal distances as the composition of the nanoparticle changes. We establish that the large Pt and small Ru BE shifts arise from the different response of these metals to changes in the bond distances, an unexpected result. Our results give evidence that the magnitudes of the BE shifts depend on whether the d band is open, as for Ru, or essentially filled, as for Pt.

  13. Orbital momentum distribution and binding energies for the complete valence shell of molecular bromine

    International Nuclear Information System (INIS)

    Frost, L.; Grisogono, A.M.; Weigold, E.

    1987-08-01

    The binding energy spectrum of Br 2 has been recorded in both the outer and inner valence regions using electron momentum spectroscopy. The measurements are compared with the results of several Green's function calculations using different approximations and based on both polarized and unpolarized wave functions. The inner valence region, observed for the first time, is found to exhibit complex structure that is shown to be due to many-body effects, thus indicating a breakdown of the simple MO picture for ionization in this region. Momentum distributions for the three outer valence orbitals are also measured and compared with spherically averaged calculations using the target Hartree-Fock and plane wave impulse approximations. The effect of polarization functions in the basis set is investigated. Orbital density maps in both momentum and position space have been calculated and compared with the experimental measurements

  14. Orbital momentum distributions and binding energies for the complete valence shell of molecular iodine

    International Nuclear Information System (INIS)

    Grisogono, A.M.; Pascual, R.; Weigold, E.

    1988-03-01

    The complete valence shell binding energy spectrum (8-43eV) of I 2 has been measured by using electron momentum spectroscopy at 1000eV. The complete inner valence region, corresponding to ionization from the 10 σ u and 10 σ g orbitals, has been measured for the first time and shows extensive splitting of the ionization strength due to electron correlation effects in the ion. Many-body calculations using the Green's function method have been carried out and are compared with the data. Momentum distributions, measured in both the outer and inner valence regions, are compared with those given by SCF orbital wave functions calculated with a number of different basis sets. Computed orbital position and momentum density maps for oriented I 2 molecules are discussed in comparison with the measured and calculated spherically averaged momentum distributions

  15. Comparison of experimental and theoretical binding and transition energies in the actinide region

    Energy Technology Data Exchange (ETDEWEB)

    Krause, M. O.; NESTOR, JR., C. W. [OAK RIDGE NATIONAL LAB., TENN. (USA)

    1977-11-15

    The present status of experimental and theoretical binding and transition energy determinations is reviewed. Experimental data and the most recent theoretical predictions are compared for the energies of K..cap alpha../sub 1/ X-rays, M series X-rays, K-LL Auger electrons, K, L/sub 3/, M and N levels, and the 4f spin-orbit splitting. In addition, the K..cap alpha../sub 1/ and L/sub 3/ data are fitted by Moseley-type diagrams, and data on the shallow levels and the valence bands of actinide oxides are discussed. Comparison shows that the single-particle Dirac-Fock theory and the inclusion of quantum-electrodynamic contributions predicts energies of the innermost levels generally within the accuracy of data, that is in the order of magnitude of 1 eV. However, in the N, O... shells large deviations do occur presumably due to strong many-electron interactions. The inclusion of many-electron effects in the relativistic theory remains a challenge, as do experimental investigations affording an accuracy of better than 1 eV for the various electronic levels.

  16. First lattice calculation of the B-meson binding and kinetic energies

    CERN Document Server

    Crisafulli, M; Martinelli, G; Sachrajda, Christopher T C

    1995-01-01

    We present the first lattice calculation of the B-meson binding energy \\labar and of the kinetic energy -\\lambda_1/2 m_Q of the heavy-quark inside the pseudoscalar B-meson. This calculation has required the non-perturbative subtraction of the power divergences present in matrix elements of the Lagrangian operator \\bar h D_4 h and of the kinetic energy operator \\bar h \\vec D^2 h. The non-perturbative renormalisation of the relevant operators has been implemented by imposing suitable renormalisation conditions on quark matrix elements, in the Landau gauge. Our numerical results have been obtained from several independent numerical simulations at \\beta=6.0 and 6.2, and using, for the meson correlators, the results obtained by the APE group at the same values of \\beta. Our best estimate, obtained by combining results at different values of \\beta, is \\labar =190 \\err{50}{30} MeV. For the \\overline{MS} running mass, we obtain \\overline {m}_b(\\overline {m}_b) =4.17 \\pm 0.06 GeV, in reasonable agreement with previous...

  17. Effects of impurities on radiation damage in InP

    International Nuclear Information System (INIS)

    Yamaguchi, M.; Ando, K.

    1986-01-01

    Strong impurity effects upon introduction and annealing behavior of radiation-induced defects in InP irradiated with 1-MeV electrons have been found. The main defect center of 0.37-eV hole trap H4 in p-InP, which must be due to a point defect, is annealed even at room temperature. Its annealing rate is found to be proportional to the 2/3 power of the preirradiation carrier concentration in InP. Moreover, the density of the hole trap H5 (E/sub v/+0.52 eV) in p-InP, which must be due to a point defect--impurity complex, increases with increase in the InP carrier concentration. These results suggest that the radiation-induced defects in InP must recover through long-range diffusion mediated by impurity atoms. A model is proposed in which point defects diffuse to sinks through impurities so as to disappear or bind impurities so as to form point defect--impurity complexes. In addition to the long-range diffusion mechanism, the possibility of charge-state effects responsible for the thermal annealing of radiation-induced defects in InP is also discussed

  18. 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...

  19. Impurity modes in the one-dimensional XXZ Heisenberg model

    International Nuclear Information System (INIS)

    Sousa, J.M.; Leite, R.V.; Landim, R.R.; Costa Filho, R.N.

    2014-01-01

    A Green's function formalism is used to calculate the energy of impurity modes associated with one and/or two magnetic impurities in the one-dimensional Heisenberg XXZ magnetic chain. The system can be tuned from the Heisenberg to the Ising model varying a parameter λ. A numerical study is performed showing two types of localized modes (s and p). The modes depend on λ and the degeneracy of the acoustic modes is broken.

  20. Engineering and material aspects of impurity control systems

    International Nuclear Information System (INIS)

    Koski, J.A.

    1985-01-01

    The design of impurity control devices for fusion energy devices is discussed from the engineering and materials viewpoint. First, examples of impurity control devices are presented, and the plasma edge environment for which they are designed is briefly described. Materials concerns related to the design of the components are discussed and some currently proposed designs presented. Engineering tools available to the designer are listed, and some commonly encountered engineering analysis problems described

  1. 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

  2. Spin-1 two-impurity Kondo problem on a lattice

    Science.gov (United States)

    Allerdt, A.; Žitko, R.; Feiguin, A. E.

    2018-01-01

    We present an extensive study of the two-impurity Kondo problem for spin-1 adatoms on a square lattice using an exact canonical transformation to map the problem onto an effective one-dimensional system that can be numerically solved using the density matrix renormalization group method. We provide a simple intuitive picture and identify the different regimes, depending on the distance between the two impurities, Kondo coupling JK, longitudinal anisotropy D , and transverse anisotropy E . In the isotropic case, two impurities on opposite (the same) sublattices have a singlet (triplet) ground state. However, the energy difference between the triplet ground state and the singlet excited state is very small and we expect an effectively fourfold-degenerate ground state, i.e., two decoupled impurities. For large enough JK the impurities are practically uncorrelated forming two independent underscreened states with the conduction electrons, a clear nonperturbative effect. When the impurities are entangled in an RKKY-like state, Kondo correlations persist and the two effects coexist: the impurities are underscreened, and the dangling spin-1 /2 degrees of freedom are responsible for the interimpurity entanglement. We analyze the effects of magnetic anisotropy in the development of quasiclassical correlations.

  3. Impurities block the alpha to omega martensitic transformation in titanium.

    Science.gov (United States)

    Hennig, Richard G; Trinkle, Dallas R; Bouchet, Johann; Srinivasan, Srivilliputhur G; Albers, Robert C; Wilkins, John W

    2005-02-01

    Impurities control phase stability and phase transformations in natural and man-made materials, from shape-memory alloys to steel to planetary cores. Experiments and empirical databases are still central to tuning the impurity effects. What is missing is a broad theoretical underpinning. Consider, for example, the titanium martensitic transformations: diffusionless structural transformations proceeding near the speed of sound. Pure titanium transforms from ductile alpha to brittle omega at 9 GPa, creating serious technological problems for beta-stabilized titanium alloys. Impurities in the titanium alloys A-70 and Ti-6Al-4V (wt%) suppress the transformation up to at least 35 GPa, increasing their technological utility as lightweight materials in aerospace applications. These and other empirical discoveries in technological materials call for broad theoretical understanding. Impurities pose two theoretical challenges: the effect on the relative phase stability, and the energy barrier of the transformation. Ab initio methods calculate both changes due to impurities. We show that interstitial oxygen, nitrogen and carbon retard the transformation whereas substitutional aluminium and vanadium influence the transformation by changing the d-electron concentration. The resulting microscopic picture explains the suppression of the transformation in commercial A-70 and Ti-6Al-4V alloys. In general, the effect of impurities on relative energies and energy barriers is central to understanding structural phase transformations.

  4. 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

  5. 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

  6. Trapping of He clusters by inert-gas impurities in tungsten: First-principles predictions and experimental validation

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen-Manh, Duc, E-mail: duc.nguyen@ccfe.ac.uk; Dudarev, S.L.

    2015-06-01

    Properties of point defects resulting from the incorporation of inert-gas atoms in bcc tungsten are investigated systematically using first-principles density functional theory (DFT) calculations. The most stable configuration for the interstitial neon, argon, krypton and xenon atoms is the tetrahedral site, similarly to what was found earlier for helium in W. The calculated formation energies for single inert-gas atoms at interstitial sites as well as at substitutional sites are much larger for Ne, Ar, Kr and Xe than for He. While the variation of the energy of insertion of inert-gas defects into interstitial configurations can be explained by a strong effect of their large atomic size, the trend exhibited by their substitutional energies is more likely related to the covalent interaction between the noble gas impurity atoms and the tungsten atoms. There is a remarkable variation exhibited by the energy of interaction between inert-gas impurities and vacancies, where a pronounced size effect is observed when going from He to Ne, Ar, Kr, Xe. The origin of this trend is explained by electronic structure calculations showing that p-orbitals play an important part in the formation of chemical bonds between a vacancy and an atom of any of the four inert-gas elements in comparison with helium, where the latter contains only 1s{sup 2} electrons in the outer shell. The binding energies of a helium atom trapped by five different defects (He-v, Ne-v, Ar-v, Kr-v, Xe-v, where v denotes a vacancy in bcc-W) are all in excellent agreement with experimental data derived from thermal desorption spectroscopy. Attachment of He clusters to inert gas impurity atom traps in tungsten is analysed as a function of the number of successive trapping helium atoms. Variation of the Young modulus due to inert-gas impurities is analysed on the basis of data derived from DFT calculations.

  7. Infrared Dielectric Screening Determines the Low Exciton Binding Energy of Metal-Halide Perovskites.

    Science.gov (United States)

    Umari, Paolo; Mosconi, Edoardo; De Angelis, Filippo

    2018-02-01

    The performance of lead-halide perovskites in optoelectronic devices is due to a unique combination of factors, including highly efficient generation, transport, and collection of photogenerated charge carriers. The mechanism behind efficient charge generation in lead-halide perovskites is still largely unknown. Here, we investigate the factors that influence the exciton binding energy (E b ) in a series of metal-halide perovskites using accurate first-principles calculations based on solution of the Bethe-Salpeter equation, coupled to ab initio molecular dynamics simulations. We find that E b is strongly modulated by screening from low-energy phonons, which account for a factor ∼2 E b reduction, while dynamic disorder and rotational motion of the organic cations play a minor role. We calculate E b = 15 meV for MAPbI 3 , in excellent agreement with recent experimental estimates. We then explore how different material combinations (e.g., replacing Pb → Pb:Sn→ Sn; and MA → FA → Cs) may lead to different E b values and highlight the mechanisms underlying E b tuning.

  8. Rearrangements under confinement lead to increased binding energy of Synaptotagmin-1 with anionic membranes in Mg2+ and Ca2.

    Science.gov (United States)

    Gruget, Clémence; Coleman, Jeff; Bello, Oscar; Krishnakumar, Shyam S; Perez, Eric; Rothman, James E; Pincet, Frederic; Donaldson, Stephen H

    2018-05-01

    Synaptotagmin-1 (Syt1) is the primary calcium sensor (Ca 2+ ) that mediates neurotransmitter release at the synapse. The tandem C2 domains (C2A and C2B) of Syt1 exhibit functionally critical, Ca 2+ -dependent interactions with the plasma membrane. With the surface forces apparatus, we directly measure the binding energy of membrane-anchored Syt1 to an anionic membrane and find that Syt1 binds with ~6 k B T in EGTA, ~10 k B T in Mg 2+ and ~18 k B T in Ca 2+ . Molecular rearrangements measured during confinement are more prevalent in Ca 2+ and Mg 2+ and suggest that Syt1 initially binds through C2B, then reorients the C2 domains into the preferred binding configuration. These results provide energetic and mechanistic details of the Syt1 Ca 2+ -activation process in synaptic transmission. © 2018 Federation of European Biochemical Societies.

  9. 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.

  10. 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.

  11. Application of secondary ion emission to impurity control in tokamaks

    International Nuclear Information System (INIS)

    Krauss, A.R.; Gruen, D.M.

    1979-01-01

    The extent to which high Z impurities enter the plasma of a magnetic confinement fusion device depends on the kinetic energy, angle of emission, and very importantly, the charge state of the ejected material. We have been studying both the fundamental process of secondary ion emission and possible techniques for producing surfaces which give rise to high ion fractions during sputtering, with a view to assessing the potential of this approach to impurity control in tokamaks. By carefully choosing materials exposed to fusion plasmas and by properly modifying the surface it may be possible to insure that nearly all the impurities are ejected as ions. As long as certain gas blanket configurations are avoided and especially if a divertor is used, it should then be possible to remove the impurities before they reach the plasma. The relative merits of a variety of materials are considered with regard to this application

  12. 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.

  13. Ab-initio study of C and O impurities in uranium nitride

    Energy Technology Data Exchange (ETDEWEB)

    Lopes, Denise Adorno; Claisse, Antoine; Olsson, Pär, E-mail: polsson@kth.se

    2016-09-15

    Uranium nitride (UN) has been considered a potential fuel for Generation IV (GEN-IV) nuclear reactors as well as a possible new fuel for Light Water Reactors (LWR), which would permit an extension of the fuel residence time in the reactor. Carbon and oxygen impurities play a key role in the UN microstructure, influencing important parameters such as creep, swelling, gas release under irradiation, compatibility with structural steel and coolants, and thermal stability. In this work, a systematic study of the electronic structure of UN containing C and O impurities using first-principles calculations by the Density Functional Theory (DFT) method is presented. In order to describe accurately the localized U 5f electrons, the DFT + U formalism was adopted. Moreover, to avoid convergence toward metastable states, the Occupation Matrix Control (OMC) methodology was applied. The incorporation of C and O in the N-vacancy is found to be energetically favorable. In addition, only for O, the incorporation in the interstitial position is energetically possible, showing some degree of solubility for this element in this site. The binding energies show that the pairs (C−N{sub vac}) and (O−N{sub vac}) interact much further than the other defects, which indicate the possible occurrence of vacancy drag phenomena and clustering of these impurities in grain boundaries, dislocations and free surfaces. The migration energy of an impurity by single N-vacancy show that C and O employ different paths during diffusion. Oxygen migration requires significantly lower energy than carbon. This fact is due to flexibility in the U−O chemical bonds, which bend during the diffusion forming a pseudo UO{sub 2} coordination. On the other hand, C and N have a directional and inflexible chemical bond with uranium; always requiring the octahedral coordination. These findings provide detailed insight into how these impurities behave in the UN matrix, and can be of great interest for assisting the

  14. Ab-initio study of C and O impurities in uranium nitride

    International Nuclear Information System (INIS)

    Lopes, Denise Adorno; Claisse, Antoine; Olsson, Pär

    2016-01-01

    Uranium nitride (UN) has been considered a potential fuel for Generation IV (GEN-IV) nuclear reactors as well as a possible new fuel for Light Water Reactors (LWR), which would permit an extension of the fuel residence time in the reactor. Carbon and oxygen impurities play a key role in the UN microstructure, influencing important parameters such as creep, swelling, gas release under irradiation, compatibility with structural steel and coolants, and thermal stability. In this work, a systematic study of the electronic structure of UN containing C and O impurities using first-principles calculations by the Density Functional Theory (DFT) method is presented. In order to describe accurately the localized U 5f electrons, the DFT + U formalism was adopted. Moreover, to avoid convergence toward metastable states, the Occupation Matrix Control (OMC) methodology was applied. The incorporation of C and O in the N-vacancy is found to be energetically favorable. In addition, only for O, the incorporation in the interstitial position is energetically possible, showing some degree of solubility for this element in this site. The binding energies show that the pairs (C−N_v_a_c) and (O−N_v_a_c) interact much further than the other defects, which indicate the possible occurrence of vacancy drag phenomena and clustering of these impurities in grain boundaries, dislocations and free surfaces. The migration energy of an impurity by single N-vacancy show that C and O employ different paths during diffusion. Oxygen migration requires significantly lower energy than carbon. This fact is due to flexibility in the U−O chemical bonds, which bend during the diffusion forming a pseudo UO_2 coordination. On the other hand, C and N have a directional and inflexible chemical bond with uranium; always requiring the octahedral coordination. These findings provide detailed insight into how these impurities behave in the UN matrix, and can be of great interest for assisting the development

  15. Coordination-resolved local bond relaxation, electron binding-energy shift, and Debye temperature of Ir solid skins

    Energy Technology Data Exchange (ETDEWEB)

    Bo, Maolin [Key Laboratory of Low-Dimensional Materials and Application Technologies, Ministry of Education, Xiangtan University, Xiangtan, Hunan 411105 (China); Wang, Yan [Key Laboratory of Low-Dimensional Materials and Application Technologies, Ministry of Education, Xiangtan University, Xiangtan, Hunan 411105 (China); School of Information and Electronic Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201 (China); Huang, Yongli, E-mail: huangyongli@xtu.edu.cn [Key Laboratory of Low-Dimensional Materials and Application Technologies, Ministry of Education, Xiangtan University, Xiangtan, Hunan 411105 (China); Yang, Xuexian [Department of Physics, Jishou University, Jishou, Hunan 416000 (China); Yang, Yezi [Key Laboratory of Low-Dimensional Materials and Application Technologies, Ministry of Education, Xiangtan University, Xiangtan, Hunan 411105 (China); Li, Can [Center for Coordination Bond Engineering, School of Materials Science and Engineering, China Jiliang University, Hangzhou 330018 (China); Sun, Chang Q., E-mail: ecqsun@ntu.edu.sg [Key Laboratory of Low-Dimensional Materials and Application Technologies, Ministry of Education, Xiangtan University, Xiangtan, Hunan 411105 (China); NOVITAS, School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 (Singapore)

    2014-11-30

    Highlights: • Cohesive energy of the representative bond determines the core-level shift. • XPS derives the energy level of an isolated atom and its bulk shift. • XPS derives the local bond length, bond energy, binding energy density. • Thermal XPS resolves the Debye temperature and atomic cohesive energy. - Abstract: Numerical reproduction of the measured 4f{sub 7/2} energy shift of Ir(1 0 0), (1 1 1), and (2 1 0) solid skins turns out the following: (i) the 4f{sub 7/2} level of an isolated Ir atom shifts from 56.367 eV to 60.332 eV by 3.965 eV upon bulk formation; (ii) the local energy density increases by up to 130% and the atomic cohesive energy decreases by 70% in the skin region compared with the bulk values. Numerical match to observation of the temperature dependent energy shift derives the Debye temperature that varies from 285.2 K (Surface) to 315.2 K (Bulk). We clarified that the shorter and stronger bonds between under-coordinated atoms cause local densification and quantum entrapment of electron binding energy, which perturbs the Hamiltonian and the core shifts in the skin region.

  16. Extended fenske-hall calculation of inner-shell binding energies using ( Z + 1)-bazis sets: Sulfur-containing molecules

    Science.gov (United States)

    Zwanziger, Ch.; Zwanziger, H.; Szargan, R.; Reinhold, J.

    1981-08-01

    It is shown that the S1s and S2p binding energies and their chemical shifts in the molecules H 2S, SO 2, SF 6 and COS obtained with hole-state calculations using an extended Fenske-Hall method are in good agreement with experimental values if mixed ( Z + 1)-basis sets are applied.

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

    NARCIS (Netherlands)

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

    2012-01-01

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

  18. Effect of non-parabolicity on the binding energy of a hydrogenic donor in quantum well with a magnetic field

    International Nuclear Information System (INIS)

    Jayakumar, K.; Balasubramanian, S.; Tomak, M.

    1985-08-01

    A hydrogenic donor in a quantum well in the presence of a magnetic field perpendicular to the barrier is considered in the effective mass approximation. The non-parabolicity of the subband is included in the Hamiltonian by an energy-dependent effective mass. The donor binding energy is calculated variationally for different well widths and the effect of non-parabolicity is discussed in the light of recent experimental results. (author)

  19. Influence of impurities on silicide contact formation

    International Nuclear Information System (INIS)

    Kazdaev, Kh.R.; Meermanov, G.B.; Kazdaev, R.Kh.

    2002-01-01

    Research objectives of this work are to investigate the influence of light impurities implantation on peculiarities of the silicides formation in molybdenum monocrystal implanted by silicon, and in molybdenum films sputtered on silicon substrate at subsequent annealing. Implantation of the molybdenum samples was performed with silicon ions (90 keV, 5x10 17 cm -2 ). Phase identification was performed by X ray analysis with photographic method of registration. Analysis of the results has shown the formation of the molybdenum silicide Mo 3 Si at 900 deg. C. To find out the influence of impurities present in the atmosphere (C,N,O) on investigated processes we have applied combined implantation. At first, molybdenum was implanted with ions of the basic component (silicon) and then -- with impurities ions. Acceleration energies (40keV for C, 45 keV for N and 50 keV for O) were chosen to obtain the same distribution profiles for basic and impurities ions. Ion doses were 5x10 17 cm -2 for Si-ions and 5x10 16 cm -2 - for impurities. The most important results are reported here. The first, for all three kinds of impurities the decreased formation temperatures of the phase Mo 3 Si were observed; in the case of C and N it was ∼100 deg. and in the case of nitrogen - ∼200 deg. Further, simultaneously with the Mo 3 Si phase, the appearance of the rich-metal phase Mo 5 Si 3 was registered (not observed in the samples without additional implantation). In case of Mo/Si-structure, the implantation of the impurities (N,O) was performed to create the peak concentration (∼4at/%) located in the middle of the molybdenum film (∼ 150nm) deposited on silicon substrate. Investigation carried out on unimplanted samples showed the formation of the silicide molybdenum MoSi 2 , observed after annealing at temperatures 900/1000 deg. C, higher than values 500-600 deg. C reported in other works. It is discovered that electrical conductivity of Mo 5 Si 3 -films synthesized after impurities

  20. Defect-impurity interactions in irradiated germanium

    International Nuclear Information System (INIS)

    Cleland, J.W.; James, F.J.; Westbrook, R.D.

    1975-07-01

    Results of experiments are used to formulate a better model for the structures of lattice defects and defect-impurity complexes in irradiated n-type Ge. Single crystals were grown by the Czochralski process from P, As, or Sb-doped melts, and less than or equal to 10 15 to greater than or equal to 10 17 oxygen cm -3 was added to the furnace chamber after approximately 1 / 3 of the crystal had been solidified. Hall coefficient and resistivity measurements (at 77 0 K) were used to determine the initial donor concentration due to the dopant and clustered oxygen, and infrared absorption measurements (at 11.7 μ) were used to determine the dissociated oxygen concentration. Certain impurity and defect-impurity interactions were then investigated that occurred as a consequence of selected annealing, quenching, Li diffusion, and irradiation experiments at approximately 300 0 K with 60 Co photons, 1.5 to 2.0 MeV electrons, or thermal energy neutrons. Particular attention was given to determining the electrical role of the irradiation produced interstitial and vacancy, and to look for any evidence from electrical and optical measurements of vacancy--oxygen, lithium--oxygen, and lithium--vacancy interactions. (U.S.)

  1. Evaluation of determinative methods for sodium impurities

    International Nuclear Information System (INIS)

    Molinari, Marcelo; Guido, Osvaldo; Botbol, Jose; Ares, Osvaldo

    1988-01-01

    Sodium, universally accepted as heat transfer fluid in fast breeder reactors, requires a special technology for every operation involved in any applicable methodology, due to its well known chemical reactivity. The purpose of this work is: a) to study the sources and effects of chemical species which, as traces, accompany sodium used in the nuclear field; b) to classify, taking into account, the present requirements and resources of the National Atomic Energy Commission (CNEA), the procedures found in the literature for determination of the most important impurities which exist in experimental liquid sodium systems and c) to describe the principles of the methods and to evaluate them in order to make a selection. It was concluded the convenience to develop, as a first stage, laboratory procedures to determine carbon, oxygen, hydrogen and non-volatile impurities, which besides serving present needs, will be referential for direct methods with undeferred response. The latter are needed in liquid sodium experimental loops and require, primarily, more complex and extended development. Additionally, a description is made of experimental work performed up-to-now in this laboratory, consisting of a transfer device for sodium sampling and a sodium distillation device, adapted from a previous design, with associated vacuum and inert gas systems. It is intended as a separative technique for indirect determination of oxygen and non-volatile impurities. (Author) [es

  2. Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities.

    Science.gov (United States)

    Dolenc, Jožica; Riniker, Sereina; Gaspari, Roberto; Daura, Xavier; van Gunsteren, Wilfred F

    2011-08-01

    Docking algorithms for computer-aided drug discovery and design often ignore or restrain the flexibility of the receptor, which may lead to a loss of accuracy of the relative free enthalpies of binding. In order to evaluate the contribution of receptor flexibility to relative binding free enthalpies, two host-guest systems have been examined: inclusion complexes of α-cyclodextrin (αCD) with 1-chlorobenzene (ClBn), 1-bromobenzene (BrBn) and toluene (MeBn), and complexes of DNA with the minor-groove binding ligands netropsin (Net) and distamycin (Dist). Molecular dynamics simulations and free energy calculations reveal that restraining of the flexibility of the receptor can have a significant influence on the estimated relative ligand-receptor binding affinities as well as on the predicted structures of the biomolecular complexes. The influence is particularly pronounced in the case of flexible receptors such as DNA, where a 50% contribution of DNA flexibility towards the relative ligand-DNA binding affinities is observed. The differences in the free enthalpy of binding do not arise only from the changes in ligand-DNA interactions but also from changes in ligand-solvent interactions as well as from the loss of DNA configurational entropy upon restraining.

  3. Asymptotic theory of charge exchange for relativistic velocities and binding energies

    International Nuclear Information System (INIS)

    Demkov, Yu.N.; Ostrovskij, V.N.; Shevchenko, S.I.

    1983-01-01

    The asymptotic theory of charge exchange (ATCE) at a large shock parameter rho is applied to the case of relativistic velocities and binding energies. The charge exchange reaction (1+e)+2 → 1+(e+2), when an electron from the bound 1Ssub(1/2) state on one particle transforms to the 1Ssub(1/2) state on the other, is considered. Oasic features of the method are as follows: 1) the representation of the transition amplitude in the form of multidimensional integral over some hypersurface; 2) the use of the saddle-point method for calculating necessary multidimensional integrals; 3) the refinement of wave functions as compared with the case of the absence of the interaction. The ATCE (at rho → infinity) makes it possible to obtain analytical results whose accuracy is determined solely with the shock parameter rho. A basic term of charge exchange amplitude asymptotics for 1Ssub(1/2) → 1Ssub(1/2) transitions has been calculated. It is possible to consider the ATCE as a peculiar reference with which theoretical and experimental results can be compared as well as to use the ATCE as boundary conditions during numerical calculations

  4. 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

  5. Changes in the Zero-Point Energy of the Protons as the Source of the Binding Energy of Water to A-Phase DNA

    International Nuclear Information System (INIS)

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2010-10-01

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

  7. 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

  8. Effects of alloying and transmutation impurities on stability and mobility of helium in tungsten under a fusion environment

    International Nuclear Information System (INIS)

    Wu Xuebang; Kong Xiangshan; You Yuwei; Liu, C.S.; Fang, Q.F.; Chen Junling; Luo, G.-N.; Wang Zhiguang

    2013-01-01

    The behaviour of helium in metals is particularly significant in fusion research due to the He-induced degradation of materials. A small amount of impurities introduced either by intentional alloying or by transmutation reactions, will interact with He and lead the microstructure and mechanical properties of materials to change. In this paper, we present the results of first-principles calculations on the interactions of He with impurities and He diffusion around them in tungsten (W), including the interstitials Be, C, N, O, and substitutional solutes Re, Ta, Tc, Nb, V, Os, Ti, Si, Zr, Y and Sc. We find that the trapping radii of interstitial atoms on He are much larger than those of substitutional solutes. The binding energies between the substitutional impurities and He increase linearly with the relative charge densities at the He occupation site, indicating that He atoms easily aggregate at the low charge density site. The sequence of diffusion energy barriers of He around the possible alloying elements is Ti > V > Os > Ta > Re. The present results suggest that Ta might be chosen as a relatively suitable alloying element compared with other possible ones. (paper)

  9. Stacking change in MoS2 bilayers induced by interstitial Mo impurities.

    Science.gov (United States)

    Cortés, Natalia; Rosales, Luis; Orellana, Pedro A; Ayuela, Andrés; González, Jhon W

    2018-02-01

    We use a theoretical approach to reveal the electronic and structural properties of molybdenum impurities between MoS 2 bilayers. We find that interstitial Mo impurities are able to reverse the well-known stability order of the pristine bilayer, because the most stable form of stacking changes from AA' (undoped) into AB' (doped). The occurrence of Mo impurities in different positions shows their split electronic levels in the energy gap, following octahedral and tetrahedral crystal fields. The energy stability is related to the accommodation of Mo impurities compacted in hollow sites between layers. Other less stable configurations for Mo dopants have larger interlayer distances and band gaps than those for the most stable stacking. Our findings suggest possible applications such as exciton trapping in layers around impurities, and the control of bilayer stacking by Mo impurities in the growth process.

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

    Science.gov (United States)

    Thermodynamic parameters for binding of a series of galacturonic acid oligomers to an exo-polygalacturonase, RPG16 from Rhizopus oryzae, were determined by isothermal titration calorimetry. Binding of oligomers varying in chain length from two to five galacturonic acid residues is an exothermic proc...

  11. Effects of ECRH power and safety factor on laser blow-off injected impurity confinement in TCV

    International Nuclear Information System (INIS)

    Scavino, E; Bakos, J; Weisen, H

    2004-01-01

    Evidence from injection into the TCV device of laser ablated, non-recycling silicon impurities shows that the transport of impurities confinement can be remarkably different from that of energy. The ratio of impurity to energy confinement times ranges from near unity in Ohmic discharges to 5 in the presence of high power ECCD. In Ohmic discharges in deuterium, above a threshold of density and of safety factor near q 95 = 4.5, the impurity confinement time increases abruptly by a factor of 2 and is sometimes accompanied by indefinite retention of non-recycling impurities within the sawtooth mixing radius

  12. Transformation of cooperative free energies between ligation systems of hemoglobin: resolution of the carbon monoxide binding intermediates.

    Science.gov (United States)

    Huang, Y; Ackers, G K

    1996-01-23

    A strategy has been developed for quantitatively "translating" the distributions of cooperative free energy between different oxygenation analogs of hemoglobin (Hb). The method was used to resolve the cooperative free energies of all eight carbon monoxide binding intermediates. These parameters of the FeCOHb system were determined by thermodynamic transformation of corresponding free energies obtained previously for all species of the Co/FeCO system, i.e., where cobalt-substituted hemes comprise the unligated sites [Speros, P. C., et al. (1991) Biochemistry 30, 7254-7262]. Using hybridized combinations of normal and cobalt-substituted Hb, ligation analog systems Co/FeX (X = CO, CN) were constructed and experimentally quantified. Energetics of cobalt-induced structural perturbation were determined for all species of both the "mixed metal" Co/Fe system and also the ligated Co/FeCN system. It was found that major energetic perturbations of the Co/Fe hybrid species originate from a pure cobalt substitution effect on the alpha subunits. These perturbations are transduced to the beta subunit within the same dimeric half-tetramer, resulting in alteration of the free energies for binding at the nonsubstituted (Fe) sites. Using the linkage strategy developed in this study along with the determined energetics of these couplings, the experimental assembly free energies for the Co/FeCO species were transformed into cooperative free energies of the 10 Fe/FeCO species. The resulting values were found to distribute according to predictions of a symmetry rule mechanism proposed previously [Ackers, G. K., et al. (1992) Science 255, 54-63]. Their distribution is consistent with accurate CO binding data of normal Hb [Perrella, M., et al. (1990b) Biophys. Chem. 37, 211-223] and also with accurate O2 binding data obtained under the same conditions [Chu, A. H., et al. (1984) Biochemistry 23, 604-617].

  13. Impurity dynamics in stellarator W7-AS plasmas

    International Nuclear Information System (INIS)

    Igitkhanov, Yuri; Beidler, Craig D.; Burhenn, Reiner; Polunovsky, Eduard; Yamazaki, Kozo

    2006-01-01

    Numerical efforts to understand the neoclassical transport of impurities in stellarator plasmas have been undertaken. The new code solves the radial continuity equations for each ionization stage of the impurity ions for given background plasma profiles and magnetic configuration. An analytic description of the neoclassical transport coefficients based on numerical results from the DKES (Drift Kinetic Equation Solver) code and monoenergetic Monte-Carlo calculation (C.D. Beidler et al., EPS 1994), is here applied for impurity transport coefficients. The transition between the different charge states due to the ionization and recombination in balance equation is described by using the ADAS (Atomic Data and Analysis Structure) database. The impurity behavior in some typical discharges from W7-AS with moderate (NC) and improved energy confinement (HDH) has been considered. It is shown that the spatial distribution results from the competition between the radial electric field and the thermal force (which together produce a convective flux), and the diffusive term, which flattens the radial impurity distribution. The impurity ions are localized at the radial position where the convective flux goes through zero. It is also shown that for typical stellarator discharges there is no pronounced temperature screening effect as in tokamak plasmas. (author)

  14. Quasiparticle Lagrangian for the binding energies and self-consistent fields of nuclei in the Fermi-liquid approach

    International Nuclear Information System (INIS)

    Sapershtein, E.E.; Khodel', V.A.

    1981-01-01

    The problem of calculating the binding energy and self-consistent field of a nucleus in terms of the effective interaction of quasiparticles at the Fermi surface is solved. It is shown that for this one can go over from the system of N Fermi particles to a system of N interacting quasiparticles described by an effective quasiparticle Lagrangian L/sub q/. It is shown that the corresponding quasiparticle energy is equal to the ground-state energy of the system. The connection between the parameters of the effective Lagrangian and the constants of the quasiparticle interaction introduced in the theory of finite Fermi systems is established

  15. Impurity bubbles in a BEC

    Science.gov (United States)

    Timmermans, Eddy; Blinova, Alina; Boshier, Malcolm

    2013-05-01

    Polarons (particles that interact with the self-consistent deformation of the host medium that contains them) self-localize when strongly coupled. Dilute Bose-Einstein condensates (BECs) doped with neutral distinguishable atoms (impurities) and armed with a Feshbach-tuned impurity-boson interaction provide a unique laboratory to study self-localized polarons. In nature, self-localized polarons come in two flavors that exhibit qualitatively different behavior: In lattice systems, the deformation is slight and the particle is accompanied by a cloud of collective excitations as in the case of the Landau-Pekar polarons of electrons in a dielectric lattice. In natural fluids and gases, the strongly coupled particle radically alters the medium, e.g. by expelling the host medium as in the case of the electron bubbles in superfluid helium. We show that BEC-impurities can self-localize in a bubble, as well as in a Landau-Pekar polaron state. The BEC-impurity system is fully characterized by only two dimensionless coupling constants. In the corresponding phase diagram the bubble and Landau-Pekar polaron limits correspond to large islands separated by a cross-over region. The same BEC-impurity species can be adiabatically Feshbach steered from the Landau-Pekar to the bubble regime. This work was funded by the Los Alamos LDRD program.

  16. Fused integrable lattice models with quantum impurities and open boundaries

    International Nuclear Information System (INIS)

    Doikou, Anastasia

    2003-01-01

    The alternating integrable spin chain and the RSOS(q 1 ,q 2 ;p) model in the presence of a quantum impurity are investigated. The boundary free energy due to the impurity is derived, the ratios of the corresponding g functions at low and high temperature are specified and their relevance to boundary flows in unitary minimal and generalized coset models is discussed. Finally, the alternating spin chain with diagonal and non-diagonal integrable boundaries is studied, and the corresponding boundary free energy and g functions are derived

  17. Effect of titanium impurities on helium bubble growth in nickel

    International Nuclear Information System (INIS)

    Amarendra, G.; Viswanathan, B.; Rajaraman, R.; Srinivasan, S.; Gopinathan, K.P.

    1992-01-01

    Positron lifetime measurements in He-implanted Ni and Ni-Ti alloys containing dilute concentrations of Ti, during isochronal annealing, are reported. In the initial annealing stage of Ni-Ti alloys, only a single lifetime ranging from 160 to 180 ps is observed, in contrast with the two lifetimes seen in pure Ni. This indicates saturation positron trapping at helium-bound Ti-vacancy complexes, formed in high concentrations. Lattice statics calculations of the He binding energy at various defect complexes in Ni-containing Ti give credence to the above interpretation. Above 800K, two lifetimes are resolved in Ni-Ti alloys, where the longer lifetime τ 2 increases with a sharp reduction in its intensity. This is indicative of He bubble growth. The bubble radius r B and bubble concentration C B are obtained from an analysis of positron lifetime parameters. These results indicate that, for a given annealing temperature, r B is smaller by a factor of two and C B higher by nearly an order of magnitude in Ni-Ti than the corresponding values in pure Ni. This is explained as due to significant retardation of bubble growth on the addition of Ti to Ni, where the Ti impurities cause an impediment to bubble migration and coalescence. (author)

  18. Self-consistent Green’s-function technique for bulk and surface impurity calculations: Surface core-level shifts by complete screening

    DEFF Research Database (Denmark)

    Aldén, M.; Abrikosov, I. A.; Johansson, B.

    1994-01-01

    of the frozen-core and atomic-sphere approximation but, in addition, includes the dipole contribution to the intersphere potential. Within the concept of complete screening, we identify the surface core-level binding-energy shift with the surface segregation energy of a core-ionized atom and use the Green......'s-function impurity technique in a comprehensive study of the surface core-level shifts (SCLS) of the 4d and 5d transition metals. In those cases, where observed data refer to single crystals, we obtain good agreement with experiment, whereas the calculations typically underestimate the measured shift obtained from...

  19. In-gap bound states induced by interstitial Fe impurities in iron-based superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Degang, E-mail: degangzhang@yahoo.com

    2015-12-15

    Highlights: • We provide an explanation for the interesting STM observation of the robust zero energy bound state on the interstitial Fe impurities in iron-based superconductors. - Abstract: Based on a two-orbit four-band tight binding model, we investigate the low-lying electronic states around the interstitial excess Fe ions in the iron-based superconductors by using T-matrix approach. It is shown that the local density of states at the interstitial Fe impurity (IFI) possesses a strong resonance inside the gap, which seems to be insensitive to the doping and the pairing symmetry in the Fe–Fe plane, while a single or two resonances appear at the nearest neighboring (NN) Fe sites. The location and height of the resonance peaks only depend on the hopping t and the pairing parameter Δ{sub I} between the IFI and the NN Fe sites. These in-gap resonances are originated in the Andreev’s bound states due to the quasiparticle tunneling through the IFI, leading to the change of the magnitude of the superconducting order parameter. When both t and Δ{sub I} are small, this robust zero-energy bound state near the IFI is consistent with recent scanning tunneling microscopy observations.

  20. 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)

  1. STM tunneling through a quantum wire with a side-attached impurity

    International Nuclear Information System (INIS)

    Kwapinski, T.; Krawiec, M.; Jalochowski, M.

    2008-01-01

    The STM tunneling through a quantum wire (QW) with a side-attached impurity (atom, island) is investigated using a tight-binding model and the non-equilibrium Keldysh Green function method. The impurity can be coupled to one or more QW atoms. The presence of the impurity strongly modifies the local density of states of the wire atoms, thus influences the STM tunneling through all the wire atoms. The transport properties of the impurity itself are also investigated mainly as a function of the wire length and the way it is coupled to the wire. It is shown that the properties of the impurity itself and the way it is coupled to the wire strongly influence the STM tunneling, the density of states and differential conductance

  2. Divertor experiment for impurity control in DIVA

    International Nuclear Information System (INIS)

    Nagami, Masayuki

    1979-04-01

    Divertor actions of controlling the impurities and the transport of impurity ions in the plasma have been investigated in the DIVA device. Following are the results: (1) The radial transport of impurity ions is not described only by neoclassical theory, but it is strongly influenced by anomalous process. Radial diffusion of impurity ions across the whole minor radius is well described by a neoclassical diffusion superposed by the anomalous diffusion for protons. Due to this anomalous process, which spreads the radial density profile of impurity ions, 80 to 90% of the impurity flux in the plasma outer edge is shielded even in a nondiverted discharge. (2) The divertor reduces the impurity flux entering the main plasma by a factor of 2 to 4. The impurity ions shielded by the scrape-off plasma are rapidly guided into the burial chamber with a poloidal excursion time roughly equal to that of the scrape-off plasma. (3) The divertor reduces the impurity ion flux onto the main vacuum chamber by guiding the impurity ions diffusing from the main plasma into the burial chamber, thereby reducing the plasma-wall interaction caused by diffusing impurity ions at the main vacuum chamber. The impurity ions produced in the burial chamber may flow back to the main plasma through the scrape-off layer. However, roughly only 0.3% of the impurity flux into the scrape-off plasma in the burial chamber penetrates into the main plasma due to the impurity backflow. (4) A slight cooling of the scrape-off plasma with light-impurity injection effectively reduces the metal impurity production at the first wall by reducing the potential difference between the plasma and the wall, thereby reducing the accumulation of the metal impurity in the discharge. Radiation cooling by low-Z impurities in the plasma outer edge, which may become an important feature in future large tokamaks both with and without divertor, is numerically evaluated for carbon, oxygen and neon. (author)

  3. Evaluation of B3LYP, X3LYP, and M06-class density functionals for predicting the binding energies of neutral, protonated, and deprotonated water clusters

    OpenAIRE

    Bryantsev, Vyacheslav S.; Diallo, Mamadou S.; van Duin, Adri C. T.; Goddard, William A., III

    2009-01-01

    In this paper we assess the accuracy of the B3LYP, X3LYP, and newly developed M06-L, M06-2X, and M06 functionals to predict the binding energies of neutral and charged water clusters including (H_2O)_n, n = 2−8, 20), H_3O+(H_2O_)n, n = 1−6, and OH−(H_2O)_n, n = 1−6. We also compare the predicted energies of two ion hydration and neutralization reactions on the basis of the calculated binding energies. In all cases, we use as benchmarks calculated binding energies of water clusters extrapolate...

  4. 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

  5. The effect of including tensor forces in nucleon-nucleon interaction on three-nucleon binding energy

    International Nuclear Information System (INIS)

    Osman, A.; Ramadan, S.

    1986-01-01

    Separable two-body interactions are used in considering the three-nucleon problem. The nucleon-nucleon potentials are taken to include attraction and repulsion as well as tensor forces. The separable approximation is used in order to investigate the effect of the tensor forces. The separable expansion is introduced in the three-nucleon problem, by which the Faddeev equations are reduced to a well-behaved set of coupled integral equations. Numerical calculations are carried out for the obtained integral equations using potential functions of the Yamaguchi, Gaussian, Takabin, Mongan and Reid forms. The present calculated values of the binding energies of the 3 H and 3 He nuclei are in good agreement with the experimental values. The effect of including the tensor forces in the nucleon-nucleon interactions is found to improve the three-nucleon binding energy by about 4.490% to 8.324%. 37 refs., 2 tabs. (author)

  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. Total-energy Assisted Tight-binding Method Based on Local Density Approximation of Density Functional Theory

    Science.gov (United States)

    Fujiwara, Takeo; Nishino, Shinya; Yamamoto, Susumu; Suzuki, Takashi; Ikeda, Minoru; Ohtani, Yasuaki

    2018-06-01

    A novel tight-binding method is developed, based on the extended Hückel approximation and charge self-consistency, with referring the band structure and the total energy of the local density approximation of the density functional theory. The parameters are so adjusted by computer that the result reproduces the band structure and the total energy, and the algorithm for determining parameters is established. The set of determined parameters is applicable to a variety of crystalline compounds and change of lattice constants, and, in other words, it is transferable. Examples are demonstrated for Si crystals of several crystalline structures varying lattice constants. Since the set of parameters is transferable, the present tight-binding method may be applicable also to molecular dynamics simulations of large-scale systems and long-time dynamical processes.

  8. 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.

  9. The effect of impurities on the electronic properties of MgO

    Energy Technology Data Exchange (ETDEWEB)

    Jalili, Seifollah [Department of Chemistry, K.N. Toosi University of Technology, P.O. Box 16315-1618, Tehran (Iran, Islamic Republic of); Computational Physical Sciences Research Laboratory, Department of Nano-Science, Institute for Studies in Theoretical Physics and Mathematics (IPM), P.O. Box 19395-5531, Tehran (Iran, Islamic Republic of)], E-mail: sjalili@nano.ipm.ac.ir; Majidi, Roya [Department of Physics, Shahid Beheshti University, Tehran (Iran, Islamic Republic of)

    2008-10-01

    The effect of impurities on the electronic properties of MgO is investigated using the full potential linearized augmented plane-wave plus local-orbitals method based on density functional theory. The electronic band structures and density of states of MgO in the presence of Ca, Li, and Na impurities were calculated. It is found that increasing the amount of Ca impurity decreases the energy band gap and increases the width of the upper part of the valence band. Some of the considered impurities (Li and Na) change the electronic properties of MgO extensively.

  10. The effect of impurities on the electronic properties of MgO

    International Nuclear Information System (INIS)

    Jalili, Seifollah; Majidi, Roya

    2008-01-01

    The effect of impurities on the electronic properties of MgO is investigated using the full potential linearized augmented plane-wave plus local-orbitals method based on density functional theory. The electronic band structures and density of states of MgO in the presence of Ca, Li, and Na impurities were calculated. It is found that increasing the amount of Ca impurity decreases the energy band gap and increases the width of the upper part of the valence band. Some of the considered impurities (Li and Na) change the electronic properties of MgO extensively

  11. Investigation of impurity defects in α-iron by molecular dynamics method

    International Nuclear Information System (INIS)

    Kevorkyan, Yu.R.

    1986-01-01

    Investigation of the configuration of impurity defects in α-iron by the molecular dynamics method is presented. The Jhonson model potential has been used to calculate the interaction of matrix atoms. The impurity-matrix atom interaction is described by the same form of the potential shifted along the axis of interatomic distances for a definite value. The correspondence between the shift value and change in the radius of the impurity defect is established on the basis of calculation of the relaxation volume. Possible configurations of the impurity - interstitial matrix atom complexes are obtained for the given model of the impurity defect, dimensional boundaries of possible transitions between different configurations are determined. Formation and bound energies, relaxation volumes of impurity defects are calculated

  12. Study on impurity screening in stochastic magnetic boundary of the Large Helical Device

    International Nuclear Information System (INIS)

    Kobayashi, M.; Morita, S.; Feng, Y.

    2008-10-01

    The impurity transport characteristics in the scrape-off layer associated with a stochastic magnetic boundary of LHD are analyzed. The remnant islands with very small internal field line pitch in the stochastic region play a key role in reducing the impurity influx. The thermal force driven impurity influx is significantly suppressed when the perpendicular energy flux exceeds the parallel one inside the islands due to the small pitch. Application of the 3D edge transport code, EMC3-EIRENE, confirmed the impurity retention (screening) effect in the edge region. It is also found that the edge surface layers are the most effective region to retain (screen) impurities because of the flow acceleration and plasma cooling via short flux tubes. The carbon emission obtained in experiments is in good agreement with the modelling results, showing the impurity retention (screening) potential of the stochastic magnetic boundary. (author)

  13. Impurity transport calculations for the limiter shadow region of a tokamak

    International Nuclear Information System (INIS)

    Claassen, H.A.; Repp, H.

    1981-01-01

    Impurity transport calculations are presented for the scrape-off layer of a tokamak with a poloidal ring limiter. The theory is based on the drift-kinetic equations for the impurity ions in their different ionization states. It is developed in the limit of low impurity concentrations under due consideration of electron impact ionization, Coulomb collisions with hydrogen ions streaming onto a neutralizing surface, a convection along the magnetic field, and a radial drift. The background plasma and the impurity sources at the walls enter the theory as input parameters. Numerical results are given for the radial profiles of density, temperature, particle flux, and energy flux of wall-released impurity ions as well as for the screening efficiency of the scrape-off layer neglecting impurity re-emission from the limiter. (author)

  14. Insulator-semimetallic transition in quasi-1D charged impurity-infected armchair boron-nitride nanoribbons

    Science.gov (United States)

    Dinh Hoi, Bui; Yarmohammadi, Mohsen

    2018-04-01

    We address control of electronic phase transition in charged impurity-infected armchair-edged boron-nitride nanoribbons (ABNNRs) with the local variation of Fermi energy. In particular, the density of states of disordered ribbons produces the main features in the context of pretty simple tight-binding model and Green's functions approach. To this end, the Born approximation has been implemented to find the effect of π-band electron-impurity interactions. A modulation of the π-band depending on the impurity concentrations and scattering potentials leads to the phase transition from insulator to semimetallic. We present here a detailed physical meaning of this transition by studying the treatment of massive Dirac fermions. From our findings, it is found that the ribbon width plays a crucial role in determining the electronic phase of disordered ABNNRs. The obtained results in controllable gap engineering are useful for future experiments. Also, the observations in this study have also fueled interest in the electronic properties of other 2D materials.

  15. Impurity doping processes in silicon

    CERN Document Server

    Wang, FFY

    1981-01-01

    This book introduces to non-experts several important processes of impurity doping in silicon and goes on to discuss the methods of determination of the concentration of dopants in silicon. The conventional method used is the discussion process, but, since it has been sufficiently covered in many texts, this work describes the double-diffusion method.

  16. Tokamak impurity-control techniques

    International Nuclear Information System (INIS)

    Schmidt, J.A.

    1980-01-01

    A brief review is given of the impurity-control functions in tokamaks, their relative merits and disadvantages and some prominent edge-interaction-control techniques, and there is a discussion of a new proposal, the particle scraper, and its potential advantages. (author)

  17. Nonmagnetic impurities in magnetic superconductors

    International Nuclear Information System (INIS)

    Mineev, V.P.

    1989-01-01

    The magnetization and magnetic field arising around the nonmagnetic impurity in magnetic superconductor with triplet pairing are found. The relationship of these results with the data of recent (gm)sR experiments in heavy fermionic superconductor U 1 - x Th x Be 13 is presented

  18. Quasiparticle Properties of a Mobile Impurity in a Bose-Einstein Condensate.

    Science.gov (United States)

    Christensen, Rasmus Søgaard; Levinsen, Jesper; Bruun, Georg M

    2015-10-16

    We develop a systematic perturbation theory for the quasiparticle properties of a single impurity immersed in a Bose-Einstein condensate. Analytical results are derived for the impurity energy, effective mass, and residue to third order in the impurity-boson scattering length. The energy is shown to depend logarithmically on the scattering length to third order, whereas the residue and the effective mass are given by analytical power series. When the boson-boson scattering length equals the boson-impurity scattering length, the energy has the same structure as that of a weakly interacting Bose gas, including terms of the Lee-Huang-Yang and fourth order logarithmic form. Our results, which cannot be obtained within the canonical Fröhlich model of an impurity interacting with phonons, provide valuable benchmarks for many-body theories and for experiments.

  19. Surface segregation of the metal impurity to the (1 0 0) surface of fcc ...

    Indian Academy of Sciences (India)

    good relation to the differences in surface energy between the impurity and host crystals ΔQ ..... mobile impurity are treated as movable discrete particles. ..... [64] J Siera, van Delft FCMJM, A D van Langeveld and B E Nieuwenhuys, Surf. Sci.

  20. Breatherlike impurity modes in discrete nonlinear lattices

    DEFF Research Database (Denmark)

    Hennig, D.; Rasmussen, Kim; Tsironis, G. P.

    1995-01-01

    We investigate the properties of a disordered generalized discrete nonlinear Schrodinger equation, containing both diagonal and nondiagonal nonlinear terms. The equation models a Linear host lattice doped with nonlinear impurities. We find different types of impurity states that form itinerant...

  1. Light impurity production in tokamaks

    International Nuclear Information System (INIS)

    Philipps, V.; Vietzke, E.; Erdweg, M.

    1989-01-01

    A review is given of the different erosion processes of carbon materials with special emphasis on conditions relevant to plasma surface interactions. New results on the chemical erosion and radiation enhanced sublimation of boron-carbon layers are presented. The chemical hydrocarbon formation produced by the interaction of the TEXTOR scrape-off plasma with a carbon target has been investigated up to temperatures of 1500K using a Sniffer probe. The chemical interaction of the plasma with the carbon walls in TEXTOR is also analysed by measuring the hydrocarbon and CO and CO 2 partial pressures built up on the surrounding walls during the discharges. The recycling of oxygen impurities in an all carbon surrounding occurs predominantly in the form of CO and Co 2 molecules and the analysis of both neutral pressures during the discharges has been used as an additional diagnostic for the oxygen impurity situation in TEXTOR. These data are discussed in view of spectroscopic measurements on the influx of carbon and oxygen atoms from the walls and impurity line radiation. CD-band spectroscopy in addition is employed to identify the hydrocarbon chemical carbon erosion. Our present understanding of the oxygen impurity recycling and the oxygen sources are described. Particle induced release of CO molecules from the entire first wall is believed to be the dominant influx process of oxygen in the SOL of plasmas with carbon facing materials. The influence of coating the TEXTOR first wall with a boron-carbon film (B/C ≅1) on the light impurity behaviour is shown. (author)

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

    DEFF Research Database (Denmark)

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

    1999-01-01

    Biexciton binding energies and biexciton dephasing in In0.18Ga0.82As/GaAs single quantum wells have been measured by time-integrated and spectrally resolved four-wave mixing. The biexciton binding energy increases from 1.5 to 2.6 meV for well widths increasing from 1 to 4 nm. The ratio between...... exciton and biexciton binding energy changes from 0.23 to 0.3 with increasing inhomogeneous broadening, corresponding to increasing well width. From the temperature dependence of the exciton and biexciton four-wave mixing signal decay, we have deduced the acoustic-phonon scattering of the exciton...

  3. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Karpov, V. Ya. [Bruk Institute of Electronic Control Machines (Russian Federation); Shpatakovskaya, G. V., E-mail: shpagalya@yandex.ru [Russian Academy of Sciences, Keldysh Institute of Applied Mathematics (Russian Federation)

    2017-03-15

    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.

  5. Impurities in silicon and their impact on solar cell performance

    NARCIS (Netherlands)

    Coletti, Gianluca

    2011-01-01

    Photovoltaic conversion of solar energy is a rapidly growing technology. More than 80% of global solar cell production is currently based on silicon. The aim of this thesis is to understand the complex relation between impurity content of silicon starting material (“feedstock”) and the resulting

  6. Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR.

    Science.gov (United States)

    Westermaier, Yvonne; Ruiz-Carmona, Sergio; Theret, Isabelle; Perron-Sierra, Françoise; Poissonnet, Guillaume; Dacquet, Catherine; Boutin, Jean A; Ducrot, Pierre; Barril, Xavier

    2017-08-01

    The knowledge of the free energy of binding of small molecules to a macromolecular target is crucial in drug design as is the ability to predict the functional consequences of binding. We highlight how a molecular dynamics (MD)-based approach can be used to predict the free energy of small molecules, and to provide priorities for the synthesis and the validation via in vitro tests. Here, we study the dynamics and energetics of the nuclear receptor REV-ERBα with its co-repressor NCoR and 35 novel agonists. Our in silico approach combines molecular docking, molecular dynamics (MD), solvent-accessible surface area (SASA) and molecular mechanics poisson boltzmann surface area (MMPBSA) calculations. While docking yielded initial hints on the binding modes, their stability was assessed by MD. The SASA calculations revealed that the presence of the ligand led to a higher exposure of hydrophobic REV-ERB residues for NCoR recruitment. MMPBSA was very successful in ranking ligands by potency in a retrospective and prospective manner. Particularly, the prospective MMPBSA ranking-based validations for four compounds, three predicted to be active and one weakly active, were confirmed experimentally.

  7. Deep impurity levels in n-type copper oxides

    International Nuclear Information System (INIS)

    Ovchinnikov, S.G.

    1994-01-01

    The density of Nd 2-x Ce x CuO 4 monoparticle states was calculated by the method of precise diagonalization of multielectron hamiltonian of 6-zone model for CuO cluster. Emergence of a deep impurity state of a symmetry in the middle of dielectric slit, which is a mixture of d z 2-states of copper and a 1 -molecular orbital of oxygen, is shown. Fluctuation of parameters of p-d jump and energies of charge transfer provide additional fine impurity levels near the bottom of conductivity zone and ceiling of valency zone. 30 refs., 4 figs

  8. 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

  9. Innovative sludge pretreatment technology for impurity separation using micromesh.

    Science.gov (United States)

    Mei, Xiaojie; Han, Xiaomeng; Zang, Lili; Wu, Zhichao

    2018-05-23

    In order to reduce the impacts on sludge treatment facilities caused by impurities such as fibers, hairs, plastic debris, and coarse sand, an innovative primary sludge pretreatment technology, sludge impurity separator (SIS), was proposed in this study. Non-woven micromesh with pore size of 0.40 mm was used to remove the impurities from primary sludge. Results of lab-scale tests showed that impurity concentration, aeration intensity, and channel gap were the key operation parameters, of which the optimized values were below 25 g/L, 0.8 m 3 /(m 2  min), and 2.5 cm, respectively. In the full-scale SIS with treatment capacity of 300 m 3 /day, over 88% of impurities could be removed from influent and the cleaning cycle of micromesh was more than 16 days. Economic analysis revealed that the average energy consumption was 1.06 kWh/m 3 treated sludge and operation cost was 0.6 yuan/m 3 treated sludge.

  10. Observation of impurity accumulation and concurrent impurity influx in PBX

    International Nuclear Information System (INIS)

    Sesnic, S.S.; Fonck, R.J.; Ida, K.; Couture, P.; Kaita, R.; Kaye, S.; Kugel, H.; LeBlanc, B.; Okabayashi, M.; Paul, S.; Powell, E.T.; Reusch, M.; Takahashi, H.; Gammel, G.; Morris, W.

    1987-01-01

    Impurity studies in L- and H-mode discharges in PBX have shown that both types of discharges can evolve into either an impurity accumulative or nonaccumulative case. In a typical accumulative discharge, Z eff peaks in the center to values of about 5. The central metallic densities can be high, n met /n e ≅ 0.01, resulting in central radiated power densities in excess of 1 W/cm 3 , consistent with bolometric estimates. The radial profiles of metals obtained independently from the line radiation in the soft X-ray and the VUV regions are very peaked. Concurrent with the peaking, an increase in the impurity influx coming from the edge of the plasma is observed. At the beginning of the accumulation phase the inward particle flux for titanium has values of 6x10 10 and 10x10 10 particles/cm 2 s at minor radii of 6 and 17 cm. At the end of the accumulation phase, this particle flux is strongly increased to values of 3x10 12 and 1x10 12 particles/cm 2 s. This increased flux is mainly due to influx from the edge of the plasma and to a lesser extent due to increased convective transport. Using the measured particle flux, an estimate of the diffusion coefficient D and the convective velocity v is obtained. (orig.)

  11. Coordination-resolved local bond contraction and electron binding-energy entrapment of Si atomic clusters and solid skins

    Energy Technology Data Exchange (ETDEWEB)

    Bo, Maolin; Huang, Yongli; Zhang, Ting [Key Laboratory of Low-Dimensional Materials and Application Technologies, Xiangtan University, Hunan 411105 (China); Wang, Yan, E-mail: ywang8@hnust.edu.cn, E-mail: ecqsun@ntu.edu.sg [Key Laboratory of Low-Dimensional Materials and Application Technologies, Xiangtan University, Hunan 411105 (China); School of Information and Electronic Engineering, Hunan University of Science and Technology, Hunan 411201 (China); Zhang, Xi [School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 (Singapore); Li, Can [Center for Coordination Bond Engineering, School of Materials Science and Engineering, China Jiliang University, Hangzhou 330018 (China); Sun, Chang Q., E-mail: ywang8@hnust.edu.cn, E-mail: ecqsun@ntu.edu.sg [Key Laboratory of Low-Dimensional Materials and Application Technologies, Xiangtan University, Hunan 411105 (China); School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 (Singapore); Center for Coordination Bond Engineering, School of Materials Science and Engineering, China Jiliang University, Hangzhou 330018 (China)

    2014-04-14

    Consistency between x-ray photoelectron spectroscopy measurements and density-function theory calculations confirms our bond order-length-strength notation-incorporated tight-binding theory predictions on the quantum entrapment of Si solid skin and atomic clusters. It has been revealed that bond-order deficiency shortens and strengthens the Si-Si bond, which results in the local densification and quantum entrapment of the core and valence electrons. Unifying Si clusters and Si(001) and (111) skins, this mechanism has led to quantification of the 2p binding energy of 96.089 eV for an isolated Si atom, and their bulk shifts of 2.461 eV. Findings evidence the significance of atomic undercoordination that is of great importance to device performance.

  12. Impurity effects on the magnetic ordering in chromium

    International Nuclear Information System (INIS)

    Fishman, R.S.

    1992-05-01

    It is well-known that impurities profoundly alter the magnetic properties of chromium. While vanadium impurities suppress the Neel temperature T N , manganese impurities enhanced T N substantially. As evidenced by neutron scattering experiments, doping with as little as 0.2% vanadium changes the transition from weakly first order to second order. Young and Sokoloff explained that the first-order transition in pure chromium is caused by a charge-density wave which is the second harmonic of the spin-density wave. By examining the subtle balance between the spin-density and charge- density wave terms in the mean-field free energy, we find that the first-order transition is destroyed when the vanadium concentration exceeds about 0.15%, in agreement with experiments

  13. A crystalline cluster method for deep impurities in insulators

    International Nuclear Information System (INIS)

    Guimaraes, P.S.

    1983-01-01

    An 'ab initio' self-consistent-field crystalline-cluster approach to the study of deep impurity states in insulators is proposed. It is shown that, in spite of being a cluster calculation, the interaction of the impurity with the crystal environment is fully taken into account. It is also shown that the present representation of the impurity states is, at least, as precise as the crystalline cluster representation of the pure crystal electronic structure. The procedure has been tested by performing the calculation of the electronic structure of the U center in a sodium chloride crystal, and it has been observed that the calculated GAMMA 1 - GAMMA 15 absorption energy is in good agreement with experiment. (Author) [pt

  14. A crystalline cluster method for deep impurities in insulators

    International Nuclear Information System (INIS)

    Guimaraes, P.S.

    1983-01-01

    An ''ab initio'' self-consistent-field crysttalline-cluster approach to the study of deep impurity states in insulators is proposed. It is shown that, in spite of being a cluster calculation, the interaction of the impurity with the crystal environment is fully taken into account. It is also shown that the present representation of the impurity states is, at least, as precise as the crystalline cluster representation of the pure crystal electronic structure. The procedure has been tested by performing the calculation of the electronic structure of the U center in a sodium chloride crystal, and it has been observed that the calculated γ 1 - γ 15 absorption energy is in good agreement with experiment. (author) [pt

  15. Models for impurity production and transport in tokamaks

    International Nuclear Information System (INIS)

    Hogan, J.T.

    1976-01-01

    Models for the edge conditions which are commonly used in tokamak transport codes have been kept simple partly because of a lack of data. A report is presented on an improved model for the particle and energy balance of e - , H 1 + , H 1 0 , H 2 + , H 2 0 , O 0 , O/sup (1 yields 8) + / in the plasma scrape-off region. Experiments should yield the needed data in the near future, and allow one to test the model. The diffusion of impurities has been studied with a neoclassical model. The role of 'anomalous spreading' of the impurity distribution has been studied for the case of Fe. A model is presented for the expulsion of low-Z (oxygen) impurities for cases where q(0) greater than 1, but in which a large shear-free region is produced in the plasma core

  16. Sodium sampling and impurities determination

    International Nuclear Information System (INIS)

    Docekal, J.; Kovar, C.; Stuchlik, S.

    1980-01-01

    Samples may be obtained from tubes in-built in the sodium facility and further processed or they are taken into crucibles, stored and processed later. Another sampling method is a method involving vacuum distillation of sodium, thus concentrating impurities. Oxygen is determined by malgamation, distillation or vanadium balance methods. Hydrogen is determined by the metal diaphragm extraction, direct extraction or amalgamation methods. Carbon is determined using dry techniques involving burning a sodium sample at 1100 degC or using wet techniques by dissolving the sample with an acid. Trace amounts of metal impurities are determined after dissolving sodium in ethanol. The trace metals are concentrated and sodium excess is removed. (M.S.)

  17. 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.

  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. Phonon scattering by isotopic impurities

    International Nuclear Information System (INIS)

    Dacol, D.K.

    1974-06-01

    The effects upon vibrations of a perfect crystal lattice due to the replacement of some of its atoms by isotopes of these atoms are studied. The approach consists in considering the isotopic impurities as scattering centres for the quanta of the elastic waves the objective is to obtain the scattering amplitudes. These amplitudes are obtained through a canonical transformation method which was introduced by Chevalier and Rideau in the study of the Wentzel's model in quantum field theory

  20. Low Z impurity transport in tokamaks

    International Nuclear Information System (INIS)

    Hawryluk, R.J.; Suckewer, S.; Hirshman, S.P.

    1978-10-01

    Low Z impurity transport in tokamaks was simulated with a one-dimensional impurity transport model including both neoclassical and anomalous transport. The neoclassical fluxes are due to collisions between the background plasma and impurity ions as well as collisions between the various ionization states. The evaluation of the neoclassical fluxes takes into account the different collisionality regimes of the background plasma and the impurity ions. A limiter scrapeoff model is used to define the boundary conditions for the impurity ions in the plasma periphery. In order to account for the spectroscopic measurements of power radiated by the lower ionization states, fluxes due to anomalous transport are included. The sensitivity of the results to uncertainties in rate coefficients and plasma parameters in the periphery are investigated. The implications of the transport model for spectroscopic evaluation of impurity concentrations, impurity fluxes, and radiated power from line emission measurements are discussed

  1. BWR water chemistry impurity studies

    International Nuclear Information System (INIS)

    Ljungberg, L.G.; Korhonen, S.; Renstroem, K.; Hofling, C.G.; Rebensdorff, B.

    1990-03-01

    Laboratory studies were made on the effect of water impurities on environmental cracking in simulated BWR water of stainless steel, low alloy steel and nickel-base alloys. Constant elongation rate tensile (CERT) tests were run in simulated normal water chemistry (NWC), hydrogen water chemistry (HWC), or start-up environment. Sulfate, chloride and copper with chloride added to the water at levels of a fraction of a ppM were found to be extremely deleterious to all kinds of materials except Type 316 NG. Other detrimental impurities were fluoride, silica and some organic acids, although acetic acid was beneficial. Nitrate and carbon dioxide were fairly inoccuous. Corrosion fatigue and constant load tests on compact tension specimens were run in simulated normal BWR water chemistry (NWC) or hydrogen water chemistry (HWC), without impurities or with added sulfate or carbon dioxide. For sensitized Type 304 SS in NWC, 0.1 ppM sulfate increased crack propagation rates in constant load tests by up to a factor of 100, and in fatigue tests up to a factor of 10. Also, cracking in Type 316 nuclear grade SS and Alloy 600 was enhanced, but to a smaller degree. Carbon dioxide was less detrimental than sulfate. 3 figs., 4 tabs

  2. 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.)

  3. 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.)

  4. The convergence of the binding energy expansion in the Brueckner-Bethe-Goldstone theory of nuclear matter

    International Nuclear Information System (INIS)

    Grange, P.; Lejeune, A.

    1979-01-01

    Two, three- and four-body contributions to the binding energy of nuclear matter are evaluated in the framework of the Bethe-Brueckner expansion. Special attention is devoted to the choice of the auxillary single particle field and to the potential diagrams at the level of three- and four-hole lines present when such a field is different from zero. Two nucleon-nucleon interactions are used: a model interaction V 1 and the Reid soft-core interaction. For V 1 our results are compared with those obtained from variational calculations; this comparison supports the reliability of the perturbative expansion. (Auth.)

  5. A study of core electron binding energies in technetium-99m complexes by internal conversion electron spectroscopy

    International Nuclear Information System (INIS)

    Burke, J.F.; Archer, C.M.; Wei Chiu, K.; Latham, I.A.; Egdell, R.G.

    1991-01-01

    Core electron binding energies in a series of 99m Tc complexes have been studied by internal conversion electron spectroscopy (ICES) in a conventional x-ray photoelectron spectrometer. In both 3d and 3p regions, a chemical shift of about 1 eV is observed per unit increase in oxidation state. The role of ICES in characterizing radiopharmaceutical agents is illustrated with studies of some novel 99m Tc-phosphine complexes that have been developed for myocardial perfusion imaging. (author)

  6. 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

  7. 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.

  8. Effects of mutants in bHLH region on structure stability and protein-DNA binding energy in DECs.

    Science.gov (United States)

    Kong, Yi; Wang, Zhen; Jia, Yanfei; Li, Ping; Hao, Shuhua; Wang, Yunshan

    2017-07-01

    The human DEC subfamily contains two highly conserved members belonging to basic helix-loop-helix (bHLH) transcription factors. This conserved family is spread widely among various species with the function of regulating various crucial molecular signaling pathways. Due to the significance of DECs for important biological processes, their relationship with diseases and the lack of experimentally proven structures, we have implemented a comparative modeling for the bHLH region of DECs as homodimers with themselves and heterodimers with HES-1. Three mutants with predicted roles in reducing intramolecular binding (H57A, R65A, and LL7879AA in DEC1 and LL7071AA in DEC2) were investigated on DEC monomers. Molecular dynamics (MD) simulations were also employed to evaluate the behavior of the mutant molecules in aqueous solution. The monomer was divided into subregions for accurate investigation. The fluctuation in the basic region of mutants was higher than that of wild-type molecules. The binding energy value between protein and DNA obviously increased in the homodimer harboring R65A mutants, which led to more unstable status between protein and DNA. Thus, the mutant R65A interfered DNA-binding affinity. A study on the spatial structures of wild-type and mutant DECs may facilitate functional prediction for mutation effects and dynamic behavior under various conditions and may ultimately help in targeted drug design.

  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. Effect of impurities on kinetic transport processes in fusion plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Braun, Stefanie

    2010-12-10

    Within the framework of this thesis, different problems arising in connection with impurities have been investigated. Collisional damping of zonal flows in tokamaks: Since the Coulomb collision frequency increases with increasing ion charge, heavy, highly charged impurities play an important role in this process. The effect of such impurities on the linear response of the plasma to an external potential perturbation, as caused by zonal flows, is calculated with analytical methods. In comparison with a pure plasma, the damping of the flows occurs, as expected, considerably faster; for experimentally relevant parameters, the enhancement exceeds the effective charge Z{sub eff} of the plasma. Impurity transport driven by microturbulence in tokamaks: With regard to impurities, it is especially important whether the resulting flows are directed inwards or outwards, since they are deleterious for core energy confinement on the one hand, but on the other hand help protecting plasma-facing components from too high energy fluxes in the edge region. A semi-analytical model is presented describing the resulting impurity fluxes and the stability boundary of the underlying mode. The main goal is to bridge the gap between, on the one hand, costly numerical simulations, which are applicable to a broad range of problems but yield scarcely traceable results, and, on the other hand, analytical theory, which might ease the interpretation of the results but is so far rather rudimentary. The model is based on analytical formulae whenever possible but resorts to a numerical treatment when the approximations necessary for an analytical solution would lead to a substantial distortion of the results. Both the direction of the impurity flux and the stability boundary are found to depend sensitively on the plasma parameters such as the impurity density and the temperature gradient. Pfirsch-Schlueter transport in stellarators: Due to geometry effects, collisional transport plays a much more

  11. Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation.

    Directory of Open Access Journals (Sweden)

    Luigi Capoferri

    Full Text Available Prediction of human Cytochrome P450 (CYP binding affinities of small ligands, i.e., substrates and inhibitors, represents an important task for predicting drug-drug interactions. A quantitative assessment of the ligand binding affinity towards different CYPs can provide an estimate of inhibitory activity or an indication of isoforms prone to interact with the substrate of inhibitors. However, the accuracy of global quantitative models for CYP substrate binding or inhibition based on traditional molecular descriptors can be limited, because of the lack of information on the structure and flexibility of the catalytic site of CYPs. Here we describe the application of a method that combines protein-ligand docking, Molecular Dynamics (MD simulations and Linear Interaction Energy (LIE theory, to allow for quantitative CYP affinity prediction. Using this combined approach, a LIE model for human CYP 1A2 was developed and evaluated, based on a structurally diverse dataset for which the estimated experimental uncertainty was 3.3 kJ mol-1. For the computed CYP 1A2 binding affinities, the model showed a root mean square error (RMSE of 4.1 kJ mol-1 and a standard error in prediction (SDEP in cross-validation of 4.3 kJ mol-1. A novel approach that includes information on both structural ligand description and protein-ligand interaction was developed for estimating the reliability of predictions, and was able to identify compounds from an external test set with a SDEP for the predicted affinities of 4.6 kJ mol-1 (corresponding to 0.8 pKi units.

  12. Atomistic modeling determination of placeholder binding energy of Ti, C, and N atoms on a-Fe (100) surfaces

    International Nuclear Information System (INIS)

    Wei, X J; Liu, Y P; Han, S P

    2015-01-01

    A Fe(100) surface containing Ti, C, and N was constructed and optimized to study the placeholder binding energy of the Ti, C, and N surface atoms; this was achieved by searching the transition state with the LST (linear synchronous transit) method of the CASTEP (Cambridge Serial Total Energy Package) module. Also, the authors analyzed electron structures to determine how Ti, C, and N atoms strengthen the Fe(100) surface. The results show that when Ti, C, or N atoms take placeholder alone, or simultaneously at the Fe(100) surface, the structure stability is at its best. When including Ti, C, and N as solid solutions on the Fe(100) surface, orbital electrons of Fe3d, Ti3d, C2p, and N2p hybridize near the Fermi level; the number of electronic bonding peaks increase and bonding capacity enhances. Also, a large amount of covalent bonds formed. Covalent bonds and metallic bond coexisted. (paper)

  13. 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 )

  14. Asymptotic elastic energy in simple metals

    International Nuclear Information System (INIS)

    Khalifeh, J.M.

    1983-07-01

    The asymptotic form of the elastic binding energy ΔEsup(as)(R) between two Mg atoms in Al is expressed as a product of a lattice Green function and the dipole force tensor P. The quantity P is obtained by a nearly free electron model in which the impurity effect is introduced by a screened Ashcroft pseudopotential characterized by an excess charge ΔZ and a core radius rsub(j). (author)

  15. Modeling impurity-assisted chain creation in noble-metal break junctions

    International Nuclear Information System (INIS)

    Di Napoli, S; Thiess, A; Blügel, S; Mokrousov, Y

    2012-01-01

    In this work we present the generalization of the model for chain formation in break junctions, introduced by Thiess et al (2008 Nano Lett. 8 2144), to zigzag transition-metal chains with s and p impurities. We apply this extended model to study the producibility trends for noble-metal chains with impurities, often present in break junction experiments, namely, Cu, Ag and Au chains with H, C, O and N adatoms. Providing the material-specific parameters for our model from systematic full-potential linearized augmented plane-wave first-principles calculations, we find that the presence of such impurities crucially affects the binding properties of the noble-metal chains. We reveal that both the impurity-induced bond strengthening and the formation of zigzag bonds can lead to a significantly enhanced probability for chain formation in break junctions. (paper)

  16. Impurity effects on electrical conductivity of doped bilayer graphene in the presence of a bias voltage

    International Nuclear Information System (INIS)

    Lotfi, E; Rezania, H; Arghavaninia, B; Yarmohammadi, M

    2016-01-01

    We address the electrical conductivity of bilayer graphene as a function of temperature, impurity concentration, and scattering strength in the presence of a finite bias voltage at finite doping, beginning with a description of the tight-binding model using the linear response theory and Green’s function approach. Our results show a linear behavior at high doping for the case of high bias voltage. The effects of electron doping on the electrical conductivity have been studied via changing the electronic chemical potential. We also discuss and analyze how the bias voltage affects the temperature behavior of the electrical conductivity. Finally, we study the behavior of the electrical conductivity as a function of the impurity concentration and scattering strength for different bias voltages and chemical potentials respectively. The electrical conductivity is found to be monotonically decreasing with impurity scattering strength due to the increased scattering among electrons at higher impurity scattering strength. (paper)

  17. 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.

  18. Binding Energy of Quantum Bound States in X-shaped Nanowire Intersection

    Science.gov (United States)

    2014-01-01

    α0)〉 = 3~2 mb2 ( 2α0 + 2 11 ) = 6~2 mb2 ( α0 + 1 11 ) = 1.058 ~2 ma2 ∆2 (111) The threshold energy is found to be Et = π2~2 2mw2 (112) Since the...energy (Eb) of the electron taking the threshold energy as zero level is given by Eb = −Emin = −1.058 ~2 ma2 ∆2 = −4.232 ~ 2 mw2 cos2(θ1 − θ2

  19. Noble gas atoms as chemical impurities in silicon

    International Nuclear Information System (INIS)

    Tkachev, V.D.; Mudryi, A.V.; Minaev, N.S.

    1984-01-01

    The behaviour of noble gas atoms implanted in silicon is studied by the luminescence method. The energy position of Moessbauer-type luminescence bands with zero-phonon lines 1.0148, 1.0120, 1.0097, 1.0048 eV and others connected with implanted atoms of neon, helium, argon, krypton, respectively, indicates the formation of deep energy levels in the forbidden gap of silicon. Implantation of the noble gas isotopes confirms their participation in formation processes of the luminescence centers in silicon. The temperature range of existence and the symmetry of defects incorporating the noble gas atoms are found. It is noted that noble gas atoms form impurity complexes with deep energy levels and their behaviour in crystals does not differ from that of main doped or residual technological impurity atoms. (author)

  20. Numerical comparison of atomic binding energies calculated by Thomas-Fermi like formulas

    International Nuclear Information System (INIS)

    Donnamaria, M.C.; Castro, E.A.; Fernandez, F.M.

    1985-01-01

    We apply in an exhaustive way formulas of Thomas-Fermi nature to determine atomic ground state energies. Results are compared with Hartree-Fock SCF data and the different methods are analysed in a comparative fashion. (authors)

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

    KAUST Repository

    Beke-Somfai, Tamás; Lincoln, Per; Nordén, Bengt

    2010-01-01

    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

  2. Impurity control in toroidal devices

    International Nuclear Information System (INIS)

    1990-01-01

    This summary report on the Technical Committee Meeting organized by the IAEA and held in Naka-Gun, Japan, 13-15 February 1989, provides an overview of the results presented. Of the twenty-three papers presented, sixteen were devoted to tokamak experiments. These presented data of plasma behavior in the scrape-off layer and divertor regions, as well as effects of impurities on the core plasma; these are summarized here. Other papers summarized deal with plasma-wall interactions, including wall material behavior. Still others deal with theoretical work on physics modelling in the edge region. Refs, figs and tabs

  3. 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

  4. 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)

  5. Void growth suppression by dislocation impurity atmospheres

    International Nuclear Information System (INIS)

    Weertman, J.; Green, W.V.

    1976-01-01

    A detailed calculation is given of the effect of an impurity atmosphere on void growth under irradiation damage conditions. Norris has proposed that such an atmosphere can suppress void growth. The hydrostatic stress field of a dislocation that is surrounded by an impurity atmosphere was found and used to calculate the change in the effective radius of a dislocation line as a sink for interstitials and vacancies. The calculation of the impurity concentration in a Cottrell cloud takes into account the change in hydrostatic pressure produced by the presence of the cloud itself. It is found that void growth is eliminated whenever dislocations are surrounded by a condensed atmosphere of either oversized substitutional impurity atoms or interstitial impurity atoms. A condensed atmosphere will form whenever the average impurity concentration is larger than a critical concentration

  6. Impurity-induced moments in underdoped cuprates

    International Nuclear Information System (INIS)

    Khaliullin, G.; Kilian, R.; Krivenko, S.; Fulde, P.

    1997-01-01

    We examine the effect of a nonmagnetic impurity in a two-dimensional spin liquid in the spin-gap phase, employing a drone-fermion representation of spin-1/2 operators. The properties of the local moment induced in the vicinity of the impurity are investigated and an expression for the nuclear-magnetic-resonance Knight shift is derived, which we compare with experimental results. Introducing a second impurity into the spin liquid an antiferromagnetic interaction between the moments is found when the two impurities are located on different sublattices. The presence of many impurities leads to a screening of this interaction as is shown by means of a coherent-potential approximation. Further, the Kondo screening of an impurity-induced local spin by charge carriers is discussed. copyright 1997 The American Physical Society

  7. Graphene plasmons: Impurities and nonlocal effects

    Science.gov (United States)

    Viola, Giovanni; Wenger, Tobias; Kinaret, Jari; Fogelström, Mikael

    2018-02-01

    This work analyzes how impurities and vacancies on the surface of a graphene sample affect its optical conductivity and plasmon excitations. The disorder is analyzed in the self-consistent Green's function formulation and nonlocal effects are fully taken into account. It is shown that impurities modify the linear spectrum and give rise to an impurity band whose position and width depend on the two parameters of our model, the density and the strength of impurities. The presence of the impurity band strongly influences the electromagnetic response and the plasmon losses. Furthermore, we discuss how the impurity-band position can be obtained experimentally from the plasmon dispersion relation and discuss this in the context of sensing.

  8. Moessbauer Studies of Implanted Impurities in Solids

    CERN Multimedia

    2002-01-01

    Moessbauer studies were performed on implanted radioactive impurities in semiconductors and metals. Radioactive isotopes (from the ISOLDE facility) decaying to a Moessbauer isotope were utilized to investigate electronic and vibrational properties of impurities and impurity-defect structures. This information is inferred from the measured impurity hyperfine interactions and Debye-Waller factor. In semiconductors isoelectronic, shallow and deep level impurities have been implanted. Complex impurity defects have been produced by the implantation process (correlated damage) or by recoil effects from the nuclear decay in both semiconductors and metals. Annealing mechanisms of the defects have been studied. \\\\ \\\\ In silicon amorphised implanted layers have been recrystallized epitaxially by rapid-thermal-annealing techniques yielding highly supersaturated, electrically-active donor concentrations. Their dissolution and migration mechanisms have been investigated in detail. The electronic configuration of Sb donors...

  9. 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).

  10. Tunneling spectroscopy of a phosphorus impurity atom on the Ge(111)-(2 × 1) surface

    Energy Technology Data Exchange (ETDEWEB)

    Savinov, S. V.; Oreshkin, A. I., E-mail: oreshkin@spmlab.phys.msu.su, E-mail: oreshkin@spmlab.ru [Moscow State University (Russian Federation); Oreshkin, S. I. [Moscow State University, Sternberg Astronomical Institute (Russian Federation); Haesendonck, C. van [Laboratorium voor Stoffysica en Magnetisme (Belgium)

    2015-06-15

    We numerically model the Ge(111)-(2 × 1) surface electronic properties in the vicinity of a P donor impurity atom located near the surface. We find a notable increase in the surface local density of states (LDOS) around the surface dopant near the bottom of the empty surface state band π*, which we call a split state due to its limited spatial extent and energetic position inside the band gap. We show that despite the well-established bulk donor impurity energy level position at the very bottom of the conduction band, a surface donor impurity on the Ge(111)-(2 × 1) surface might produce an energy level below the Fermi energy, depending on the impurity atom local environment. It is demonstrated that the impurity located in subsurface atomic layers is visible in a scanning tunneling microscope (STM) experiment on the Ge(111)-(2 × 1) surface. The quasi-1D character of the impurity image, observed in STM experiments, is confirmed by our computer simulations with a note that a few π-bonded dimer rows may be affected by the presence of the impurity atom. We elaborate a model that allows classifying atoms on the experimental low-temperature STM image. We show the presence of spatial oscillations of the LDOS by the density-functional theory method.

  11. Impurity study of TMX using ultraviolet spectroscopy

    International Nuclear Information System (INIS)

    Allen, S.L.; Strand, O.T.; Moos, H.W.; Fortner, R.J.; Nash, T.J.; Dietrich, D.D.

    1981-01-01

    An extreme ultraviolet (EUV) study of the emissions from intrinsic and injected impurities in TMX is presented. Two survey spectrographs were used to determine that the major impurities present were oxygen, nitrogen, carbon, and titanium. Three absolutely-calibrated monochromators were used to measure the time histories and radial profiles of these impurity emissions in the central cell and each plug. Two of these instruments were capable of obtaining radial profiles as a function of time in a single shot

  12. Demixing of impurities and hydrogen as deduced from Zeff profiles in the boronized ASDEX

    International Nuclear Information System (INIS)

    Steuer, K.H.; Roehr, H.; Engelhardt, W.; Fussmann, G.; Kallenbach, A.; Kurzan, B.; Murmann, H.D.

    1990-01-01

    Substantial progress towards fusion has been made in the confinement, stability and heating of tokamak plasmas. The transport behaviour of magnetically confined plasmas, however, is still an unsolved problem. The transport mechanisms of hydrogen and of impurities are known to be different, leading to phenomena such as impurity accumulation on axis, especially in good confinement regimes, and more generally to demixing of the various species. Besides energy losses from impurity radiation, one has to be concerned about dilution of the fuel-ion density, and about effects that impurities may have on the main ion and electron transport. To understand the transport behaviour of the different plasma species, one needs their spatial density profiles. It is convenient to represent the various impurities by a characteristic impurity ion with a density n z and a fictive charge Z (Z = Σn i Z i 2 / Σn i Z i ; i ≥ 2). A typical value for Z is 7, indicating that light impurities are dominating. Comparing the different profiles, we find characteristic differences in the electron, proton and impurity transport behaviour. (orig./AH)

  13. Self-consistent modeling of plasma response to impurity spreading from intense localized source

    International Nuclear Information System (INIS)

    Koltunov, Mikhail

    2012-07-01

    Non-hydrogen impurities unavoidably exist in hot plasmas of present fusion devices. They enter it intrinsically, due to plasma interaction with the wall of vacuum vessel, as well as are seeded for various purposes deliberately. Normally, the spots where injected particles enter the plasma are much smaller than its total surface. Under such conditions one has to expect a significant modification of local plasma parameters through various physical mechanisms, which, in turn, affect the impurity spreading. Self-consistent modeling of interaction between impurity and plasma is, therefore, not possible with linear approaches. A model based on the fluid description of electrons, main and impurity ions, and taking into account the plasma quasi-neutrality, Coulomb collisions of background and impurity charged particles, radiation losses, particle transport to bounding surfaces, is elaborated in this work. To describe the impurity spreading and the plasma response self-consistently, fluid equations for the particle, momentum and energy balances of various plasma components are solved by reducing them to ordinary differential equations for the time evolution of several parameters characterizing the solution in principal details: the magnitudes of plasma density and plasma temperatures in the regions of impurity localization and the spatial scales of these regions. The results of calculations for plasma conditions typical in tokamak experiments with impurity injection are presented. A new mechanism for the condensation phenomenon and formation of cold dense plasma structures is proposed.

  14. Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

    International Nuclear Information System (INIS)

    Henke, Paul S.; Mak, Chi H.

    2014-01-01

    The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg 2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure

  15. Regulation of insulin-like growth factor binding proteins in young growing animals by alteration of energy status.

    Science.gov (United States)

    Dauncey, M J; Rudd, B T; White, D A; Shakespear, R A

    1993-09-01

    The regulation of plasma insulin-like growth factor binding proteins (IGFBPs) by energy status has been assessed in 2-month-old pigs. Energy balance was modified by altering thermoregulatory demand and energy intake, with litter-mates being kept for several weeks at either 35 or 10 degrees C on a high (H) or low (L) level of food intake (where H = 2L); plasma samples were taken 20-24 h after the last meal. The two major forms of circulating IGFBP, as estimated by Western blot analysis, were identified putatively as IGFBP-2 and IGFBP-3 (relative molecular weights of 34 and 40-45 kDa respectively). There were significant differences in IGFBP profiles between the four treatment groups of 35H, 35L, 10H and 10L: the 40-45 kDa IGFBP (putative IGFBP-3) was elevated both in the warm and on a high food intake (P < 0.001), and there was a marked reciprocal relation between the 40-45 and 34 kDa IGFBPs. The relative concentration of the 34 kDa IGFBP (putative IGFBP-2) was greatest in the 10L and least in the 35H group. It is concluded that long-term alterations in energy balance, induced by changes in either intake or thermoregulatory demand, can significantly affect the plasma profile of IGFBPs during the first two months of life.

  16. Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

    Energy Technology Data Exchange (ETDEWEB)

    Henke, Paul S. [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Mak, Chi H., E-mail: cmak@usc.edu [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089 (United States)

    2014-08-14

    The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg{sup 2+} that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

  17. Binding free energy and counterion release for adsorption of the antimicrobial peptide lactoferricin B on a POPG membrane

    Science.gov (United States)

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

    2009-09-01

    Molecular dynamics (MD) simulations are used to study the interaction of an anionic palmitoyl-oleoyl-phosphatidylglycerol (POPG) bilayer with the cationic antimicrobial peptide bovine lactoferricin (LFCinB) in a 100 mM NaCl solution at 310 K. The interaction of LFCinB with a POPG bilayer is employed as a model system for studying the details of membrane adsorption selectivity of cationic antimicrobial peptides. Seventy eight 4 ns MD production run trajectories of the equilibrated system, with six restrained orientations of LFCinB at 13 different separations from the POPG membrane, are generated to determine the free energy profile for the peptide as a function of the distance between LFCinB and the membrane surface. To calculate the profile for this relatively large system, a variant of constrained MD and thermodynamic integration is used. A simplified method for relating the free energy profile to the LFCinB-POPG membrane binding constant is employed to predict a free energy of adsorption of -5.4±1.3kcal/mol and a corresponding maximum adsorption binding force of about 58 pN. We analyze the results using Poisson-Boltzmann theory. We find the peptide-membrane attraction to be dominated by the entropy increase due to the release of counterions and polarized water from the region between the charged membrane and peptide, as the two approach each other. We contrast these results with those found earlier for adsorption of LFCinB on the mammalianlike palmitoyl-oleoyl-phosphatidylcholine membrane.

  18. Method for detecting trace impurities in gases

    Science.gov (United States)

    Freund, S.M.; Maier, W.B. II; Holland, R.F.; Beattie, W.H.

    A technique for considerably improving the sensitivity and specificity of infrared spectrometry as applied to quantitative determination of trace impurities in various carrier or solvent gases is presented. A gas to be examined for impurities is liquefied and infrared absorption spectra of the liquid are obtained. Spectral simplification and number densities of impurities in the optical path are substantially higher than are obtainable in similar gas-phase analyses. Carbon dioxide impurity (approx. 2 ppM) present in commercial Xe and ppM levels of Freon 12 and vinyl chloride added to liquefied air are used to illustrate the method.

  19. Measuring and controlling method for organic impurities

    International Nuclear Information System (INIS)

    Aizawa, Motohiro; Igarashi, Hiroo

    1995-01-01

    The present invention concerns measurement and control for organic impurities contained in ultrapurified water for use in a nuclear power plant. A specimen containing organic impurities leached out of anionic exchange resins and cationic exchange resins is introduced to an organic material decomposing section to decompose organic impurities into organic carbon and other decomposed products. Sulfate ions, nitrate ions, nitrite ions and carbon dioxide are produced by the decomposition of the organic impurities. As a next step, carbon dioxide in the decomposed products is separated by deaerating with a nitrogen gas or an argon gas and then a TOC concentration is measured by a non-dispersion-type infrared spectrometer. Further, a specimen from which carbon dioxide was separated is introduced to a column filled with ion exchange resins and, after concentrating inorganic ion impurities, the inorganic ion impurities are identified by using a measuring theory of an ion chromatographic method of eluting and separating inorganic ion impurities and detecting them based on the change of electroconductivity depending on the kinds of the inorganic ion impurities. Organic impurities can be measured and controlled, to improve the reliability of water quality control. (N.H.)

  20. The role of charge symmetry breaking in binding energy difference of 17F-17O, 15O-15N mirror nuclei

    International Nuclear Information System (INIS)

    Asghari, M.

    2004-01-01

    Charge symmetry breaking potential due to the exchange of pseudoscalar(π-η),(π-η') and vector(ρ-ω) mesons in mirror nuclei are considered. With the computation of coulomb energy along with the present charge symmetry breaking effects provide a reasonably accurate description of the binding energy differences between mirror nuclei

  1. The Minimum Binding Energy and Size of Doubly Muonic D3 Molecule

    Science.gov (United States)

    Eskandari, M. R.; Faghihi, F.; Mahdavi, M.

    The minimum energy and size of doubly muonic D3 molecule, which two of the electrons are replaced by the much heavier muons, are calculated by the well-known variational method. The calculations show that the system possesses two minimum positions, one at typically muonic distance and the second at the atomic distance. It is shown that at the muonic distance, the effective charge, zeff is 2.9. We assumed a symmetric planar vibrational model between two minima and an oscillation potential energy is approximated in this region.

  2. Donor impurity-related optical absorption spectra in GaAs-Ga{sub 1-x}Al{sub x}As quantum wells: hydrostatic pressure and {gamma}-X conduction band mixing effects

    Energy Technology Data Exchange (ETDEWEB)

    Mora-Ramos, M.E. [Facultad de Ciencias, Universidad Autonoma del Estado de Morelos, Av. Universidad 1001, C.P. 62209, Cuernavaca, MOR (Mexico); Inst. de Ciencia de Materiales de Madrid, CSIC, Sor Juana Ines de la Cruz 3, 28049 Madrid (Spain); Lopez, S.Y. [Fac. de Educacion, Universidad de Antioquia, AA 1226, Medellin (Colombia); Duque, C.A. [Inst. de Fisica, Universidad de Antioquia, AA 1226, Medellin (Colombia); Velasco, V.R. [Inst. de Ciencia de Materiales de Madrid, CSIC, Sor Juana Ines de la Cruz 3, 28049 Madrid (Spain)

    2007-07-01

    Using a variational procedure within the effective mass approximation, the mixing between the {gamma} and X conduction band valleys in GaAs-Ga{sub 1-x}Al{sub x}As quantum wells is investigated by taking into account the effect of applied hydrostatic pressure. Some optical properties such as donor and/or acceptor binding energy and impurity-related transition energies are calculated and comparisons with available experimental data are presented. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  3. Impurity effects on the grain boundary cohesion in copper

    Science.gov (United States)

    Li, Yunguo; Korzhavyi, Pavel A.; Sandström, Rolf; Lilja, Christina

    2017-12-01

    Segregated impurities at grain boundaries can dramatically change the mechanical behavior of metals, while the mechanism is still obscure in some cases. Here, we suggest a unified approach to investigate segregation and its effects on the mechanical properties of polycrystalline alloys using the example of 3 s p impurities (Mg, Al, Si, P, or S) at a special type Σ 5 (310 )[001 ] tilt grain boundary in Cu. We show that for these impurities segregating to the grain boundary, the strain contribution to the work of grain boundary decohesion is small and that the chemical contribution correlates with the electronegativity difference between Cu and the impurity. The strain contribution to the work of dislocation emission is calculated to be negative, while the chemical contribution is calculated to be always positive. Both the strain and chemical contributions to the work of dislocation emission generally become weaker with the increasing electronegativity from Mg to S. By combining these contributions together, we find, in agreement with experimental observations, that a strong segregation of S can reduce the work of grain boundary separation below the work of dislocation emission, thus embrittling Cu, while such an embrittlement cannot be produced by a P segregation because it lowers the energy barrier for dislocation emission relatively more than for work separation.

  4. Size, Shape and Impurity Effects on Superconducting critical temperature.

    Science.gov (United States)

    Umeda, Masaki; Kato, Masaru; Sato, Osamu

    Bulk superconductors have their own critical temperatures Tc. However, for a nano-structured superconductor, Tc depends on size and shape of the superconductor. Nishizaki showed that the high pressure torsion on bulks of Nb makes Tc higher, because the torsion makes many nano-sized fine grains in the bulks. However the high pressure torsion on bulks of V makes Tc lower, and Nishizaki discussed that the decrease of Tc is caused by impurities in the bulks of V. We studied size, shape, and impurity effects on Tc, by solving the Gor'kov equations, using the finite element method. We found that smaller and narrower superconductors show higher Tc. We found how size and shape affects Tc by studying spacial order parameter distributions and quasi-particle eigen-energies. Also we studied the impurity effects on Tc, and found that Tc decreases with increase of scattering rate by impurities. This work was supported in part of KAKENHI Grant Number JP26400367 and JP16K05460, and program for leading graduate schools of ministry of education, culture, sports, science and technology-Japan.

  5. 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

  6. The impurity transport in HT-6B tokamak

    International Nuclear Information System (INIS)

    Huang Rong; Xie Jikang; Li Linzhong; He Yexi; Wang Shuya; Deng Chuanbao; Li Guoxiang; Qiu Lijian

    1992-06-01

    The quasi-stationary profiles of the impurity ionization stages in HT-6B tokamak were determined by monitoring the VUV (vacuum ultraviolet) and visible line emissions from impurities. An impurity transport code was set up. The impurity transport coefficients and other parameters of impurities in that device were simulated and determined. From the measurement of impurity emission profiles and simulation analysis, it is concluded that the impurity confinement is improved and the impurity recycling is reduced by the slow magnetic compression. Some characteristics of impurity transport in that device are also discussed

  7. Isotope effect of impurity diffusion of cadmium in silver

    International Nuclear Information System (INIS)

    Rockosch, H.J.; Herzig, C.

    1984-01-01

    The isotope effect of impurity diffusion of cadmium in silver single crystals was measured with the radioisotopes 115 Cd/ 109 Cd by gamma spectrometry. As a mean value E = 0.37 at T = 1060 K was obtained. The correlation factor f /SUB Cd/ = 0.41 is in disagreement with previous results of other investigators due to their unfavourable experimental approach. The present value of f /SUB Cd/ , however, is consistent with those of In and Sn in Ag. A comparison with the corresponding correlation factors in the copper solvent reveals a distinct influence of lattice perturbations because of the different atomic volumes of the solvents. Since the size effect is neglected in the electrostatic diffusion model, the agreement with this model is only qualitative. The frequency ratios for vacancy jumps were calculated. The free binding enthalpy of the vacancy-impurity complex was estimated to be Δg /SUB Cd/ = -0.064 eV. This value is smaller than those for In and Sn in Ag and complies with the relative diffusivities of these impurities in Ag

  8. Non-leftmost Unfolding in Partial Evaluation of Logic Programs with Impure Predicates

    DEFF Research Database (Denmark)

    Albert, Elvira; Puebla, German; Gallagher, John Patrick

    2006-01-01

    -leftmost unfolding steps can result in incorrect results since the independence of the computation rule no longer holds in the presence of impure predicates. Existing proposals allow non-leftmost unfolding steps, but at the cost of accuracy: bindings and failure are not propagated backwards to predicates which...

  9. Theoretical studies of Anderson impurity models

    International Nuclear Information System (INIS)

    Glossop, M.T.

    2000-01-01

    A Local Moment Approach (LMA) is developed for single-particle excitations of a symmetric single impurity Anderson model (SIAM) with a soft-gap hybridization vanishing at the Fermi level, Δ I ∝ vertical bar W vertical bar r with r > 0, and for the generic asymmetric case of the 'normal' (r = 0) SIAM. In all cases we work within a two-self-energy description with local moments introduced explicitly from the outset, and in which single-particle excitations are coupled dynamically to low-energy transverse spin fluctuations. For the soft-gap symmetric SIAM, the resultant theory is applicable on all energy scales, and captures both the spin-fluctuation regime of strong coupling (large-U), as well as the weak coupling regime where it is perturbatively exact for those r-domains in which perturbation theory in U is non-singular. While the primary emphasis is on single-particle dynamics, the quantum phase transition between strong coupling (SC) and local moment (LM) phases can also be addressed directly; for the spin-fluctuation regime in particular a number of asymptotically exact results are thereby obtained, notably for the behaviour of the critical U c (r) separating SC/LM states and the Kondo scale w m (r) characteristic of the SC phase. Results for both single-particle spectra and SG/LM phase boundaries are found to agree well with recent numerical renormalization group (NRG) studies; and a number of further testable predictions are made. Single-particle spectra are examined systematically for both SC and LM states; in particular, for all 0 ≤ r 0 SC phase which, in agreement with conclusions drawn from recent NRG work, may be viewed as a non-trivial but natural generalization of Fermi liquid physics. We also reinvestigate the problem via the NRG in light of the predictions arising from the LMA: all are borne out and excellent agreement is found. For the asymmetric single impurity Anderson model (ASIAM) we establish general conditions which must be satisfied

  10. Total binding energy of heavy positive ions including density treatment of Darwin and Breit corrections

    International Nuclear Information System (INIS)

    Hill, S.H.; Grout, P.J.; March, N.H.

    1987-01-01

    Previous work on the relativistic Thomas-Fermi treatment of total energies of neutral atoms is first generalised to heavy positive ions. To facilitate quantitative contact with the numerical predictions of Dirac-Fock theory, Darwin and Breit corrections are expressed in terms of electron density, and computed using input again from relativistic Thomas-Fermi theory. These corrections significantly improve the agreement between the two seemingly very different theories. (author)

  11. 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

  12. Fabrication of Gate-tunable Graphene Devices for Scanning Tunneling Microscopy Studies with Coulomb Impurities

    Science.gov (United States)

    Jung, Han Sae; Tsai, Hsin-Zon; Wong, Dillon; Germany, Chad; Kahn, Salman; Kim, Youngkyou; Aikawa, Andrew S.; Desai, Dhruv K.; Rodgers, Griffin F.; Bradley, Aaron J.; Velasco, Jairo; Watanabe, Kenji; Taniguchi, Takashi; Wang, Feng; Zettl, Alex; Crommie, Michael F.

    2015-01-01

    Owing to its relativistic low-energy charge carriers, the interaction between graphene and various impurities leads to a wealth of new physics and degrees of freedom to control electronic devices. In particular, the behavior of graphene’s charge carriers in response to potentials from charged Coulomb impurities is predicted to differ significantly from that of most materials. Scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) can provide detailed information on both the spatial and energy dependence of graphene's electronic structure in the presence of a charged impurity. The design of a hybrid impurity-graphene device, fabricated using controlled deposition of impurities onto a back-gated graphene surface, has enabled several novel methods for controllably tuning graphene’s electronic properties.1-8 Electrostatic gating enables control of the charge carrier density in graphene and the ability to reversibly tune the charge2 and/or molecular5 states of an impurity. This paper outlines the process of fabricating a gate-tunable graphene device decorated with individual Coulomb impurities for combined STM/STS studies.2-5 These studies provide valuable insights into the underlying physics, as well as signposts for designing hybrid graphene devices. PMID:26273961

  13. Binding energy of large icosahedral and cuboctahedral Lennard-Jones clusters

    International Nuclear Information System (INIS)

    Northby, J.A.; Xie, J.

    1989-01-01

    It is widely believed that the lowest energy configurations for small rare gas clusters have icosahedral symmetry. This contrasts with the bulk crystal structures which have cuboctahedral fcc symmetry. It is of interest to understand the transition between this finite and bulk behavior. To model this transition in rare gas clusters we have undertaken optimization studies within the Lennard-Jones pair potential model. Using a combination of Monte Carlo and Partan Search optimization methods, the lowest energy relaxed structures of Lennard-Jones clusters having icosahedral and cuboctahedral symmetry were found. Studies were performed for complete shell clusters ranging in size from one shell having 13 atoms to 14 shells having 10,179 atoms. It was found that the icosahedral structures are lower in energy than the cuboctahedral structures for cluster sizes having 13 shells or fewer. Additional studies were performed using the more accurate Aziz-Chen [HFD-C] pair potential parameterized for argon. The conclusions appear to be relatively insensitive to the form of the potential. (orig.)

  14. Orbital momentum distribution and binding energies for the complete valence shell of molecular chlorine by electron momentum spectroscopy

    International Nuclear Information System (INIS)

    Frost, L.; Grisogono, A.M.; McCarthy, I.E.

    1986-10-01

    The complete valence shell binding energy spectrum (10-50 eV) of Cl 2 has been determined using electron momentum (binary (e,2e)) spectroscopy. The inner valence region, corresponding to 4σ u and 4σ g ionization, has been measured for the first time and shows extensive splitting of the ionization strength due to electron correlation effects. These measurements are compared with the results of many-body calculations using Green's function and CI methods employing unpolarised as well as polarised wave functions. Momentum distributions, measured in both the outer and inner valence regions, are compared with calculations using a range of unpolarised and polarised wave functions. Computed orbital density maps in momentum and position space for oriented Cl 2 molecules are discussed in comparison with the measured and calculated spherically averaged momentum distributions

  15. On sulfur core level binding energies in thiol self-assembly and alternative adsorption sites: An experimental and theoretical study

    International Nuclear Information System (INIS)

    Jia, Juanjuan; Kara, Abdelkader; Pasquali, Luca; Bendounan, Azzedine; Sirotti, Fausto; Esaulov, Vladimir A.

    2015-01-01

    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

  16. 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.

  17. Efficiency calibration of x-ray HPGe detectors for photons with energies above the Ge K binding energy

    Energy Technology Data Exchange (ETDEWEB)

    Maidana, Nora L., E-mail: nmaidana@if.usp.br [Instituto de Física, Universidade de São Paulo, Travessa R 187, Cidade Universitária, CEP:05508-900 São Paulo, SP (Brazil); Vanin, Vito R.; Jahnke, Viktor [Instituto de Física, Universidade de São Paulo, Travessa R 187, Cidade Universitária, CEP:05508-900 São Paulo, SP (Brazil); Fernández-Varea, José M. [Facultat de Física (ECM and ICC), Universitat de Barcelona, Diagonal 645, E-08028 Barcelona (Spain); Martins, Marcos N. [Instituto de Física, Universidade de São Paulo, Travessa R 187, Cidade Universitária, CEP:05508-900 São Paulo, SP (Brazil); Brualla, Lorenzo [NCTeam, Strahlenklinik, Universitätsklinikum Essen, Hufelandstraße 55, D-45122 Essen (Germany)

    2013-11-21

    We report on the efficiency calibration of a HPGe x-ray detector using radioactive sources and an analytical expression taken from the literature, in two different arrangements, with and without a broad-angle collimator. The frontal surface of the Ge crystal was scanned with pencil beams of photons. The Ge dead layer was found to be nonuniform, with central and intermediate regions that have thin (μm range) and thick (mm range) dead layers, respectively, surrounded by an insensitive ring. We discuss how this fact explains the observed efficiency curves and generalize the adopted model. We show that changes in the thickness of the Ge-crystal dead layer affect the efficiency of x-ray detectors, but the use of an appropriate broad-beam external collimator limiting the photon flux to the thin dead layer in the central region leads to the expected efficiency dependence with energy and renders the calibration simpler.

  18. Quantum Impurity in a One-dimensional Trapped Bose Gas

    DEFF Research Database (Denmark)

    Salami Dehkharghani, Amin; Volosniev, A. G.; Zinner, N. T.

    2015-01-01

    We present a new theoretical framework for describing an impurity in a trapped Bose system in one spatial dimension. The theory handles any external confinement, arbitrary mass ratios, and a weak interaction may be included between the Bose particles. To demonstrate our technique, we calculate th...... the ground state energy and properties of a sample system with eight bosons and find an excellent agreement with numerically exact results. Our theory can thus provide definite predictions for experiments in cold atomic gases....

  19. Evaluation of B3LYP, X3LYP, and M06-Class Density Functionals for Predicting the Binding Energies of Neutral, Protonated, and Deprotonated Water Clusters.

    Science.gov (United States)

    Bryantsev, Vyacheslav S; Diallo, Mamadou S; van Duin, Adri C T; Goddard, William A

    2009-04-14

    In this paper we assess the accuracy of the B3LYP, X3LYP, and newly developed M06-L, M06-2X, and M06 functionals to predict the binding energies of neutral and charged water clusters including (H2O)n, n = 2-8, 20), H3O(+)(H2O)n, n = 1-6, and OH(-)(H2O)n, n = 1-6. We also compare the predicted energies of two ion hydration and neutralization reactions on the basis of the calculated binding energies. In all cases, we use as benchmarks calculated binding energies of water clusters extrapolated to the complete basis set limit of the second-order Møller-Plesset perturbation theory with the effects of higher order correlation estimated at the coupled-cluster theory with single, double, and perturbative triple excitations in the aug-cc-pVDZ basis set. We rank the accuracy of the functionals on the basis of the mean unsigned error (MUE) between calculated benchmark and density functional theory energies. The corresponding MUE (kcal/mol) for each functional is listed in parentheses. We find that M06-L (0.73) and M06 (0.84) give the most accurate binding energies using very extended basis sets such as aug-cc-pV5Z. For more affordable basis sets, the best methods for predicting the binding energies of water clusters are M06-L/aug-cc-pVTZ (1.24), B3LYP/6-311++G(2d,2p) (1.29), and M06/aug-cc-PVTZ (1.33). M06-L/aug-cc-pVTZ also gives more accurate energies for the neutralization reactions (1.38), whereas B3LYP/6-311++G(2d,2p) gives more accurate energies for the ion hydration reactions (1.69).

  20. Modification of the electronic transport in Au by prototypical impurities and interlayers

    KAUST Repository

    Fadlallah, Majida M.; Schuster, Cosima B.; Eckern, Ulrich; Schwingenschlö gl, Udo

    2010-01-01

    Electronic transport calculations for metallic interfaces based on density functional theory and a scattering theory on the Landauer-Büttiker level are presented. We study the modifications of the transport through Au due to prototypical impurities and interlayers. Our results show that the influence of S and Si impurities is well described in terms of simple vacancies. Metallic impurities and interlayers, on the other hand, have even more drastic effects, in particular when the Au s-d hybrid states at the Fermi energy are perturbed. The effects of a possible interface alloy formation are discussed in detail. © 2010 EPLA.

  1. Modification of the electronic transport in Au by prototypical impurities and interlayers

    KAUST Repository

    Fadlallah, Majida M.

    2010-02-01

    Electronic transport calculations for metallic interfaces based on density functional theory and a scattering theory on the Landauer-Büttiker level are presented. We study the modifications of the transport through Au due to prototypical impurities and interlayers. Our results show that the influence of S and Si impurities is well described in terms of simple vacancies. Metallic impurities and interlayers, on the other hand, have even more drastic effects, in particular when the Au s-d hybrid states at the Fermi energy are perturbed. The effects of a possible interface alloy formation are discussed in detail. © 2010 EPLA.

  2. Impurity effects in the electrothermal instability

    International Nuclear Information System (INIS)

    Tomimura, A.; Azevedo, M.T. de

    1982-01-01

    A 'impure' plasma model is proposed based on the homogeneous hydrogen plasma used in the theory formulated by Tomimura and Haines to explain the electrothermal instable mode growth with the wave vector perpendicular to the applied magnetic field. The impurities are introduced implicitly in the transport coefficients of the two-fluid model through a effective charge number Z sub(eff). (Author) [pt

  3. Depolarization of diffusing spins by paramagnetic impurities

    International Nuclear Information System (INIS)

    Schillaci, M.E.; Hutson, R.L.; Heffner, R.H.; Leon, M.; Dodds, S.A.; Estle, T.L.

    1981-01-01

    We study the depolarization of diffusing spins (muons) interacting with dilute paramagnetic impurities in a solid using a simple computational model which properly treats the muon motion and preserves correct muon-impurity distances. Long-range (dipolar) and nearest-neighbor (contact) interactions are treated together. Diffusion parameters are deduced and model comparisons made for AuGd (300 ppm). (orig.)

  4. Elimination device for metal impurities

    International Nuclear Information System (INIS)

    Yanagisawa, Ko.

    1982-01-01

    Purpose: To enable reuse of adsorbing materials by eliminating Fe 3 O 4 films reduced with adsorbing performance by way of electrolytic polishing and then forming fresh membranes using high temperature steams. Constitution: An elimination device is provided to a coolant clean-up system of a reactor for eliminating impurities such as cobalt. The elimination device comprises adsorbing materials made of stainless steel tips or the likes having Fe 3 O 4 films. The adsorbing materials are regenerated by applying an electric current between grid-like cathode plates and anode plates to leach out the Fe 3 O 4 films, washing out the electrolytic solution by cleaning water and then applying steams at high temperature onto the adsorbing materials to thereby form fresh Fe 3 O 4 films again thereon. The regeneration of the adsorbing materials enables to eliminate Co 60 and the like in the primary coolant efficiently. (Moriyama, K.)

  5. Hartree-Fock calculation of nuclear binding energy of sodium isotopes

    International Nuclear Information System (INIS)

    Campi, X.; Flocard, H.

    1975-01-01

    Mass spectrometer measurements of the neutron rich sodium isotopes show a sudden increase at 31 Na in the values of the two neutron separation energies. The spherical shell model naturally predicts a sudden decrease at 32 Na after the N=20 shell closure. It is proposed that the explanation for this disagreement lies in the fact that sodium isotopes in this mass region are strongly deformed due to the filling of negative parity orbitals from the 1f(7/2) shell. Hartree-Fock calculations are presented in support of this conjecture [fr

  6. Competitive cation binding computations of proton balance for reactions of the phosphagen and glycolytic energy systems within skeletal muscle

    Science.gov (United States)

    2017-01-01

    Limited research and data has been published for the H+ coefficients for the metabolites and reactions involved in non-mitochondrial energy metabolism. The purpose of this investigation was to compute the fractional binding of H+, K+, Na+ and Mg2+ to 21 metabolites of skeletal muscle non-mitochondrial energy metabolism, resulting in 104 different metabolite-cation complexes. Fractional binding of H+ to these metabolite-cation complexes were applied to 17 reactions of skeletal muscle non-mitochondrial energy metabolism, and 8 conditions of the glycolytic pathway based on the source of substrate (glycogen vs. glucose), completeness of glycolytic flux, and the end-point of pyruvate vs. lactate. For pH conditions of 6.0 and 7.0, respectively, H+ coefficients (-‘ve values = H+ release) for the creatine kinase, adenylate kinase, AMP deaminase and ATPase reactions were 0.8 and 0.97, -0.13 and -0.02, 1.2 and 1.09, and -0.01 and -0.66, respectively. The glycolytic pathway is net H+ releasing, regardless of lactate production, which consumes 1 H+. For glycolysis fueled by glycogen and ending in either pyruvate or lactate, H+ coefficients for pH 6.0 and 7.0 were -3.97 and -2.01 (pyruvate), and -1.96 and -0.01 (lactate), respectively. When starting with glucose, the same conditions result in H+ coefficients of -3.98 and -2.67, and -1.97 and –0.67, respectively. The most H+ releasing reaction of glycolysis is the glyceraldehyde-3-phosphate dehydrogenase reaction, with H+ coefficients for pH 6.0 and 7.0 of -1.58 and -0.76, respectively. Incomplete flux of substrate through glycolysis would increase net H+ release due to the absence of the pyruvate kinase and lactate dehydrogenase reactions, which collectively result in H+ coefficients for pH 6.0 and 7.0 of 1.35 and 1.88, respectively. The data presented provide an extensive reference source for academics and researchers to accurately profile the balance of protons for all metabolites and reactions of non-mitochondrial energy

  7. Competitive cation binding computations of proton balance for reactions of the phosphagen and glycolytic energy systems within skeletal muscle.

    Science.gov (United States)

    Robergs, Robert Andrew

    2017-01-01

    Limited research and data has been published for the H+ coefficients for the metabolites and reactions involved in non-mitochondrial energy metabolism. The purpose of this investigation was to compute the fractional binding of H+, K+, Na+ and Mg2+ to 21 metabolites of skeletal muscle non-mitochondrial energy metabolism, resulting in 104 different metabolite-cation complexes. Fractional binding of H+ to these metabolite-cation complexes were applied to 17 reactions of skeletal muscle non-mitochondrial energy metabolism, and 8 conditions of the glycolytic pathway based on the source of substrate (glycogen vs. glucose), completeness of glycolytic flux, and the end-point of pyruvate vs. lactate. For pH conditions of 6.0 and 7.0, respectively, H+ coefficients (-'ve values = H+ release) for the creatine kinase, adenylate kinase, AMP deaminase and ATPase reactions were 0.8 and 0.97, -0.13 and -0.02, 1.2 and 1.09, and -0.01 and -0.66, respectively. The glycolytic pathway is net H+ releasing, regardless of lactate production, which consumes 1 H+. For glycolysis fueled by glycogen and ending in either pyruvate or lactate, H+ coefficients for pH 6.0 and 7.0 were -3.97 and -2.01 (pyruvate), and -1.96 and -0.01 (lactate), respectively. When starting with glucose, the same conditions result in H+ coefficients of -3.98 and -2.67, and -1.97 and -0.67, respectively. The most H+ releasing reaction of glycolysis is the glyceraldehyde-3-phosphate dehydrogenase reaction, with H+ coefficients for pH 6.0 and 7.0 of -1.58 and -0.76, respectively. Incomplete flux of substrate through glycolysis would increase net H+ release due to the absence of the pyruvate kinase and lactate dehydrogenase reactions, which collectively result in H+ coefficients for pH 6.0 and 7.0 of 1.35 and 1.88, respectively. The data presented provide an extensive reference source for academics and researchers to accurately profile the balance of protons for all metabolites and reactions of non-mitochondrial energy

  8. Competitive cation binding computations of proton balance for reactions of the phosphagen and glycolytic energy systems within skeletal muscle.

    Directory of Open Access Journals (Sweden)

    Robert Andrew Robergs

    Full Text Available Limited research and data has been published for the H+ coefficients for the metabolites and reactions involved in non-mitochondrial energy metabolism. The purpose of this investigation was to compute the fractional binding of H+, K+, Na+ and Mg2+ to 21 metabolites of skeletal muscle non-mitochondrial energy metabolism, resulting in 104 different metabolite-cation complexes. Fractional binding of H+ to these metabolite-cation complexes were applied to 17 reactions of skeletal muscle non-mitochondrial energy metabolism, and 8 conditions of the glycolytic pathway based on the source of substrate (glycogen vs. glucose, completeness of glycolytic flux, and the end-point of pyruvate vs. lactate. For pH conditions of 6.0 and 7.0, respectively, H+ coefficients (-'ve values = H+ release for the creatine kinase, adenylate kinase, AMP deaminase and ATPase reactions were 0.8 and 0.97, -0.13 and -0.02, 1.2 and 1.09, and -0.01 and -0.66, respectively. The glycolytic pathway is net H+ releasing, regardless of lactate production, which consumes 1 H+. For glycolysis fueled by glycogen and ending in either pyruvate or lactate, H+ coefficients for pH 6.0 and 7.0 were -3.97 and -2.01 (pyruvate, and -1.96 and -0.01 (lactate, respectively. When starting with glucose, the same conditions result in H+ coefficients of -3.98 and -2.67, and -1.97 and -0.67, respectively. The most H+ releasing reaction of glycolysis is the glyceraldehyde-3-phosphate dehydrogenase reaction, with H+ coefficients for pH 6.0 and 7.0 of -1.58 and -0.76, respectively. Incomplete flux of substrate through glycolysis would increase net H+ release due to the absence of the pyruvate kinase and lactate dehydrogenase reactions, which collectively result in H+ coefficients for pH 6.0 and 7.0 of 1.35 and 1.88, respectively. The data presented provide an extensive reference source for academics and researchers to accurately profile the balance of protons for all metabolites and reactions of non

  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. A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1.

    Science.gov (United States)

    Stewart, James J P

    2016-11-01

    A new method for predicting the energy contributions to substrate binding and to specificity has been developed. Conventional global optimization methods do not permit the subtle effects responsible for these properties to be modeled with sufficient precision to allow confidence to be placed in the results, but by making simple alterations to the model, the precisions of the various energies involved can be improved from about ±2 kcal mol -1 to ±0.1 kcal mol -1 . This technique was applied to the oxidized nucleotide pyrophosphohydrolase enzyme MTH1. MTH1 is unusual in that the binding and reaction sites are well separated-an advantage from a computational chemistry perspective, as it allows the energetics involved in docking to be modeled without the need to consider any issues relating to reaction mechanisms. In this study, two types of energy terms were investigated: the noncovalent interactions between the binding site and the substrate, and those responsible for discriminating between the oxidized nucleotide 8-oxo-dGTP and the normal dGTP. Both of these were investigated using the semiempirical method PM7 in the program MOPAC. The contributions of the individual residues to both the binding energy and the specificity of MTH1 were calculated by simulating the effect of mutations. Where comparisons were possible, all calculated results were in agreement with experimental observations. This technique provides fresh insight into the binding mechanism that enzymes use for discriminating between possible substrates.

  11. Derivation of binding energies on the basis of fundamental nuclear theory

    International Nuclear Information System (INIS)

    Kouki, Tuomo.

    1975-10-01

    An attempt to assess the degree of consistency between the underlying ideas of two different approaches to nuclear energy relations is described. The fundamental approach in the form of density dependent Hartree-Fock theory, as well as the method of renormalizing shell model energies have both met with fair success. Whereas the former method is based on nuclear matter theory, the latter's central idea is to combine shell structure with an average liquid drop behaviour. The shell smoothing procedure employed there has been subject to intense theoretical study. Only little attention has been paid to the liquid drop aspect of the method. It is purposed to derive the liquid drop mass formula by means of a model force fitted to results of some nuclear matter calculations. Moreover, the force is tested by applying it to finite nuclei. Because of this, the present work could also be regarded as an attempt to find a very direct way of relating nuclear matter properties to those of finite nuclei. As the results in this respect are worse than expected, we conclude with a discussion of possible directions of improvement. (author)

  12. EUV impurity study of the Alcator tokamak

    International Nuclear Information System (INIS)

    Terry, J.L.; Chen, K.I.; Moos, H.W.; Marmar, E.S.

    1978-01-01

    The intensity of resonance line radiation from oxygen, nitrogen, carbon and molybdenum impurities has been measured in the high-field (80kG), high-density (6x10 14 cm -3 ) discharges of the Alcator Tokamak, using a 0.4-m normal-incidence monochromator (300-1300A) with its line of sight fixed along a major radius. Total light-impurity concentrations of a few tenths of a percent have been estimated by using both a simple model and a computer code which included Pfirsch-Schlueter impurity diffusion. The resulting values of Zsub(eff), including the contributions due to both the light impurities and molybdenum, were close to one. The power lost through the impurity line radiation from the lower ionization states accounted for approximately 10% of the total Ohmic input power at high densities. (author)

  13. Device for removing impurities from liquid metals

    International Nuclear Information System (INIS)

    Naito, Kesahiro; Yokota, Norikatsu; Shimoyashiki, Shigehiro; Takahashi, Kazuo; Ishida, Tomio.

    1984-01-01

    Purpose: To attain highly reliable and efficient impurity removal by forming temperature distribution the impurity removing device thereby providing the function of corrosion product trap, nuclear fission product trap and cold trap under the conditions suitable to the impurity removing materials. Constitution: The impurity removing device comprises a container containing impurity removing fillers. The fillers comprise material for removing corrosion products, material for removing nuclear fission products and material for removing depositions from liquid sodium. The positions for the respective materials are determined such that the materials are placed under the temperature conditions easy to attain their function depending on the temperature distribution formed in the removing device, whereby appropriate temperature condition is set to each of the materials. (Yoshino, Y.)

  14. Plasma Interactions with Mixed Materials and Impurity Transport

    Energy Technology Data Exchange (ETDEWEB)

    Rognlien, T. D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Beiersdorfer, Peter [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Chernov, A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Frolov, T. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Magee, E. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Rudd, R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Umansky, M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-10-28

    The project brings together three discipline areas at LLNL to develop advanced capability to predict the impact of plasma/material interactions (PMI) on metallic surfaces in magnetic fusion energy (MFE) devices. These areas are (1) modeling transport of wall impurity ions through the edge plasma to the core plasma, (2) construction of a laser blow-off (LBO) system for injecting precise amounts of metallic atoms into a tokamak plasma, and (3) material science analysis of fundamental processes that modify metallic surfaces during plasma bombardment. The focus is on tungsten (W), which is being used for the ITER divertor and in designs of future MFE devices. In area (1), we have worked with the University of California, San Diego (UCSD) on applications of the UEDGE/DUSTT coupled codes to predict the influx of impurity ions from W dust through the edge plasma, including periodic edge-plasma oscillations, and revived a parallel version of UEDGE to speed up these simulations. In addition, the impurity transport model in the 2D UEDGE code has been implemented into the 3D BOUT++ turbulence/transport code to allow fundamental analysis of the impact of strong plasma turbulence on the impurity transport. In area (2), construction and testing of the LBO injection system has been completed. The original plan to install the LBO on the National Spherical Torus Experiment Upgrade (NSTX-U) at Princeton and its use to validate the impurity transport simulations is delayed owing to NSTX-U being offline for substantial magnetic coil repair period. In area (3), an analytic model has been developed to explain the growth of W tendrils (or fuzz) observed for helium-containing plasmas. Molecular dynamics calculations of W sputtering by W and deuterium (D) ions shows that a spatial blending of interatomic potentials is needed to describe the near-surface and deeper regions of the material.

  15. Plasma Interactions with Mixed Materials and Impurity Transport

    International Nuclear Information System (INIS)

    Rognlien, T. D.; Beiersdorfer, Peter; Chernov, A.; Frolov, T.; Magee, E.; Rudd, R.; Umansky, M.

    2016-01-01

    The project brings together three discipline areas at LLNL to develop advanced capability to predict the impact of plasma/material interactions (PMI) on metallic surfaces in magnetic fusion energy (MFE) devices. These areas are (1) modeling transport of wall impurity ions through the edge plasma to the core plasma, (2) construction of a laser blow-off (LBO) system for injecting precise amounts of metallic atoms into a tokamak plasma, and (3) material science analysis of fundamental processes that modify metallic surfaces during plasma bombardment. The focus is on tungsten (W), which is being used for the ITER divertor and in designs of future MFE devices. In area (1), we have worked with the University of California, San Diego (UCSD) on applications of the UEDGE/DUSTT coupled codes to predict the influx of impurity ions from W dust through the edge plasma, including periodic edge-plasma oscillations, and revived a parallel version of UEDGE to speed up these simulations. In addition, the impurity transport model in the 2D UEDGE code has been implemented into the 3D BOUT++ turbulence/transport code to allow fundamental analysis of the impact of strong plasma turbulence on the impurity transport. In area (2), construction and testing of the LBO injection system has been completed. The original plan to install the LBO on the National Spherical Torus Experiment Upgrade (NSTX-U) at Princeton and its use to validate the impurity transport simulations is delayed owing to NSTX-U being offline for substantial magnetic coil repair period. In area (3), an analytic model has been developed to explain the growth of W tendrils (or fuzz) observed for helium-containing plasmas. Molecular dynamics calculations of W sputtering by W and deuterium (D) ions shows that a spatial blending of interatomic potentials is needed to describe the near-surface and deeper regions of the material.

  16. 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

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

    Science.gov (United States)

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

    2008-01-01

    We revisit the reactivity of trapped pure gold (Au(n)+, n cations (Ag(m)Au(n)+, m + n carbon monoxide as studied in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The experimental results are discussed in terms of ab initio computations which provide a comprehensive picture of the chemical binding behaviour (like binding energy, 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 < m + n < 7) as a function of composition. Here, binding energy drops with increasing silver content, while CO still binds always in a head-on fashion to a gold atom. Finally we show how the CO stretch frequency of Ag(m)Au(n)CO+ may be used to identify possible adsorption sites and pre-screen favorable isomers.

  18. Non-Fermi-liquid behavior: Exact results for ensembles of magnetic impurities

    CERN Document Server

    Zvyagin, A A

    2002-01-01

    In this work we consider several exactly solvable models of magnetic impurities in critical quantum antiferromagnetic spin chains and multichannel Kondo impurities. Their ground state properties are studied and the finite set of nonlinear integral equations, which exactly describe the thermodynamics of the models, is constructed. We obtain several analytic low-energy expressions for the temperature, magnetic field, and frequency dependences of important characteristics of exactly solvable disordered quantum spin models and disordered multichannel Kondo impurities with essential many-body interactions. We show that the only low-energy parameter that gets renormalized is the velocity of the low-lying excitations (or the effective crossover scale connected with each impurity); the others appear to be universal. In our study several kinds of strong disorder important for experiments were used. Some of them produce low divergences in certain characteristics of our strongly disordered critical systems (compared wit...

  19. Elimination of impurity phase formation in FePt magnetic thin films prepared by pulsed laser deposition

    International Nuclear Information System (INIS)

    Wang, Ying; Medwal, Rohit; Sehdev, Neeru; Yadian, Boluo; Tan, T.L.; Lee, P.; Talebitaher, A.; Ilyas, Usman; Ramanujan, R.V.; Huang, Yizhong; Rawat, R.S.

    2014-01-01

    The formation of impurity phases in FePt thin films severely degrades its magnetic properties. The X-ray diffraction patterns of FePt thin films, synthesized using pulsed laser deposition (PLD), showed peaks corresponding to impurity phases, resulting in softer magnetic properties. A systematic investigation was carried to determine the factors that might have led to impurity phase formation. The factors include (i) PLD target composition, (ii) substrate material, (iii) annealing parameters such as temperature, duration and ambience and (iv) PLD deposition parameters such as chamber ambience, laser energy fluence and target–substrate distance. Depositions on the different substrates revealed impurity phase formation only on Si substrates. It was found that the target composition, PLD chamber ambience, and annealing ambience were not the factors that caused the impurity phase formation. The annealing temperature and duration influenced the impurity phases, but are not the cause of their formation. A decrease in the laser energy fluence and increase of the target–substrate distance resulted in elimination of the impurity phases and enhancement in the magnetic and structural properties of FePt thin films. The energy of the ablated plasma species, controlled by the laser energy fluence and the target–substrate distance, is found to be the main factor responsible for the formation of the impurity phases.

  20. Uranium analysis. Impurities determination by spark mass spectrometry

    International Nuclear Information System (INIS)

    Anon.

    Determination of impurities in uranium, suitable for atomic content greater than 10 -8 , particularly adapted for a low content. The method is quantitative for metallic impurities and qualitative for non metallic impurities [fr

  1. 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.

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

    Science.gov (United States)

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

    2018-01-01

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

  3. 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

  4. Impurity trapped excitons under high hydrostatic pressure

    Science.gov (United States)

    Grinberg, Marek

    2013-09-01

    Paper summarizes the results on pressure effect on energies of the 4fn → 4fn and 4fn-15d1 → 4fn transitions as well as influence of pressure on anomalous luminescence in Lnα+ doped oxides and fluorides. A model of impurity trapped exciton (ITE) was developed. Two types of ITE were considered. The first where a hole is localized at the Lnα+ ion (creation of Ln(α+1)+) and an electron is attracted by Coulomb potential at Rydberg-like states and the second where an electron captured at the Lnα+ ion (creation of Ln(α-1)+) and a hole is attracted by Coulomb potential at Rydberg-like states. Paper presents detailed analysis of nonlinear changes of energy of anomalous luminescence of BaxSr1-xF2:Eu2+ (x > 0.3) and LiBaF3:Eu2+, and relate them to ITE-4f65d1 states mixing.

  5. The Bi{sup 3+} 6s and 6p electron binding energies in relation to the chemical environment of inorganic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Awater, Roy H.P., E-mail: R.H.P.Awater@tudelft.nl; Dorenbos, Pieter

    2017-04-15

    This paper provides an overview and interpretation of the spectroscopic data of the Bi{sup 3+} activator ion in 117 different inorganic compounds. The energies of the metal-to-metal charge transfer and the interconfigurational transitions of Bi{sup 3+} were collected from the archival literature. Using these energies, in combination with the electron binding energies in the host conduction and valence band, the binding energies in the 6s ground state and 6p excited state were determined relative to the vacuum level. The locations of the Bi{sup 3+} energy levels within the forbidden gap of the host compound provides valuable insight in the physical properties of the Bi{sup 3+} activator ion in different compounds.

  6. Spatial effects of Fano resonance in local tunneling conductivity in vicinity of impurity on semiconductor surface

    OpenAIRE

    Mantsevich, V. N.; Maslova, N. S.

    2009-01-01

    We present the results of local tunneling conductivity spatial distribution detailed theoretical investigations in vicinity of impurity atom for a wide range of applied bias voltage. We observed Fano resonance in tunneling conductivity resulting from interference between resonant tunneling channel through impurity energy level and direct tunneling channel between the tunneling contact leads. We have found that interference between tunneling channels strongly modifies form of tunneling conduct...

  7. Impurity coupled to an artificial magnetic field in a Fermi gas in a ring trap

    Science.gov (United States)

    Ünal, F. Nur; Hetényi, B.; Oktel, M. Ã.-.

    2015-05-01

    The dynamics of a single impurity interacting with a many-particle background is one of the central problems of condensed-matter physics. Recent progress in ultracold-atom experiments makes it possible to control this dynamics by coupling an artificial gauge field specifically to the impurity. In this paper, we consider a narrow toroidal trap in which a Fermi gas is interacting with a single atom. We show that an external magnetic field coupled to the impurity is a versatile tool to probe the impurity dynamics. Using a Bethe ansatz, we calculate the eigenstates and corresponding energies exactly as a function of the flux through the trap. Adiabatic change of flux connects the ground state to excited states due to flux quantization. For repulsive interactions, the impurity disturbs the Fermi sea by dragging the fermions whose momentum matches the flux. This drag transfers momentum from the impurity to the background and increases the effective mass. The effective mass saturates to the total mass of the system for infinitely repulsive interactions. For attractive interactions, the drag again increases the effective mass which quickly saturates to twice the mass of a single particle as a dimer of the impurity and one fermion is formed. For excited states with momentum comparable to number of particles, effective mass shows a resonant behavior. We argue that standard tools in cold-atom experiments can be used to test these predictions.

  8. Dynamic conductivity modified by impurity resonant states in doping three-dimensional Dirac semimetals

    Science.gov (United States)

    Li, Shuai; Wang, Chen; Zheng, Shi-Han; Wang, Rui-Qiang; Li, Jun; Yang, Mou

    2018-04-01

    The impurity effect is studied in three-dimensional Dirac semimetals in the framework of a T-matrix method to consider the multiple scattering events of Dirac electrons off impurities. It has been found that a strong impurity potential can significantly restructure the energy dispersion and the density of states of Dirac electrons. An impurity-induced resonant state emerges and significantly modifies the pristine optical response. It is shown that the impurity state disturbs the common longitudinal optical conductivity by creating either an optical conductivity peak or double absorption jumps, depending on the relative position of the impurity band and the Fermi level. More importantly, these conductivity features appear in the forbidden region between the Drude and interband transition, completely or partially filling the Pauli block region of optical response. The underlying physics is that the appearance of resonance states as well as the broadening of the bands leads to a more complicated selection rule for the optical transitions, making it possible to excite new electron-hole pairs in the forbidden region. These features in optical conductivity provide valuable information to understand the impurity behaviors in 3D Dirac materials.

  9. Influence of iron impurities on defected graphene

    Energy Technology Data Exchange (ETDEWEB)

    Faccio, Ricardo; Pardo, Helena [Centro NanoMat, Cryssmat-Lab, DETEMA, Polo Tecnológico de Pando, Facultad de Química, Universidad de la República, Cno. Saravia s/n, CP 91000 Pando (Uruguay); Centro Interdisciplinario en Nanotecnología, Química y Física de Materiales, Espacio Interdisciplinario, Universidad de la República, Montevideo (Uruguay); Araújo-Moreira, Fernando M. [Materials and Devices Group, Department of Physics, Universidade Federal de São Carlos, SP 13565-905 (Brazil); Mombrú, Alvaro W., E-mail: amombru@fq.edu.uy [Centro NanoMat, Cryssmat-Lab, DETEMA, Polo Tecnológico de Pando, Facultad de Química, Universidad de la República, Cno. Saravia s/n, CP 91000 Pando (Uruguay); Centro Interdisciplinario en Nanotecnología, Química y Física de Materiales, Espacio Interdisciplinario, Universidad de la República, Montevideo (Uruguay)

    2015-03-01

    Highlights: • The interaction among a multivacancy graphene system and iron impurities is studied. • The studied iron impurities were single atom and tetrahedral and octahedral clusters. • DFT calculations using the VASP code were performed. • The embedding of Fe affects the structure and electronic behavior in the graphene. • Half metal or semimetal behavior can be obtained, depending on the Fe impurities. - Abstract: The aim of this work is to study the interaction of selected iron cluster impurities and a multivacancy graphene system, in terms of the structural distortion that the impurities cause as well as their magnetic response. While originally, the interaction has been limited to vacancies and isolated metallic atoms, in this case, we consider small iron clusters. This study was undertaken using Density Functional Theory (DFT) calculations. The influence of the iron impurities in the electronic structure of the vacant graphene system is discussed. The main conclusion of this work is that the presence of iron impurities acts lowering the magnetic signal due to the occurrence of spin pairing between carbon and iron, instead of enhancing the possible intrinsic carbon magnetism.

  10. Influence of iron impurities on defected graphene

    International Nuclear Information System (INIS)

    Faccio, Ricardo; Pardo, Helena; Araújo-Moreira, Fernando M.; Mombrú, Alvaro W.

    2015-01-01

    Highlights: • The interaction among a multivacancy graphene system and iron impurities is studied. • The studied iron impurities were single atom and tetrahedral and octahedral clusters. • DFT calculations using the VASP code were performed. • The embedding of Fe affects the structure and electronic behavior in the graphene. • Half metal or semimetal behavior can be obtained, depending on the Fe impurities. - Abstract: The aim of this work is to study the interaction of selected iron cluster impurities and a multivacancy graphene system, in terms of the structural distortion that the impurities cause as well as their magnetic response. While originally, the interaction has been limited to vacancies and isolated metallic atoms, in this case, we consider small iron clusters. This study was undertaken using Density Functional Theory (DFT) calculations. The influence of the iron impurities in the electronic structure of the vacant graphene system is discussed. The main conclusion of this work is that the presence of iron impurities acts lowering the magnetic signal due to the occurrence of spin pairing between carbon and iron, instead of enhancing the possible intrinsic carbon magnetism

  11. Continuous-time quantum Monte Carlo impurity solvers

    Science.gov (United States)

    Gull, Emanuel; Werner, Philipp; Fuchs, Sebastian; Surer, Brigitte; Pruschke, Thomas; Troyer, Matthias

    2011-04-01

    representations of quantum dots and molecular conductors and play an increasingly important role in the theory of "correlated electron" materials as auxiliary problems whose solution gives the "dynamical mean field" approximation to the self-energy and local correlation functions. Solution method: Quantum impurity models require a method of solution which provides access to both high and low energy scales and is effective for wide classes of physically realistic models. The continuous-time quantum Monte Carlo algorithms for which we present implementations here meet this challenge. Continuous-time quantum impurity methods are based on partition function expansions of quantum impurity models that are stochastically sampled to all orders using diagrammatic quantum Monte Carlo techniques. For a review of quantum impurity models and their applications and of continuous-time quantum Monte Carlo methods for impurity models we refer the reader to [2]. Additional comments: Use of dmft requires citation of this paper. Use of any ALPS program requires citation of the ALPS [1] paper. Running time: 60 s-8 h per iteration.

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

    KAUST Repository

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

    2018-01-01

    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.

  13. 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.

  14. 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.

  15. Behaviour of impurities during the H-mode in JET

    International Nuclear Information System (INIS)

    Gianella, R.; Behringer, K.; Denne, B.; Gottardi, N.; Hellermann, M. von; Morgan, P.D.; Pasini, D.; Stamp, M.F.

    1989-01-01

    In additionally-heated tokamak discharges, the H-mode phases are reported to display, together with a better energy confinement, a longer global containment time for particles. In particular, steep gradients of electron density and temperature are sustained in the outer region of the plasma column. This enhanced performance is observed especially in discharges in which the activity of edge localized modes (ELMs) is low or absent. High confinement and accumulation of metallic impurities, which quickly give raise to terminal disruptions have been described under similar conditions. In JET H-modes very long impurity confinement times are also observed. However the experimental condition is somewhat more favourable since quiescent H-modes are obtained lasting much longer than the energy confinement times and the radiation from metals is generally negligible. The dominant impurities are normally carbon and oxygen, the latter generally accounting for half or more of the power radiated from the bulk plasma. During the X-point operation the effective influx of carbon into the discharge, which is normally in close correlation with that of deuterium, is substantially reduced while the influx of oxygen, whose production mechanisms is believed to be of a chemical nature, does not show significant variations. (author) 5 refs., 4 figs

  16. 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.

  17. Calculation technique of free and impurity ion electronic structures

    International Nuclear Information System (INIS)

    Kulagin, N.A.; Sviridov, D.T.

    1986-01-01

    The monograph deals with calculation technique of free and impurity ion spectra with completed nl N -shell. The principles of the theory of irreducible tensor operators, genealogical coefficients, calculation technique of angular and radial parts of matrix elements operators are stated. The correlation accounting methods in free ions are considered in detail. The principles of the theory of crystal field and ligand field, the method of self-consistent field for impurity ions are reported. The technique efficiency based on example of lanthanum and actinium group ions is shown. Experimental data by nf N -ion spectra are given. The tables of angular coefficients, energy values of X-ray lines of rare earth ions and genealogical coefficients are given in the appendix

  18. Plasma response on impurity injection in W7-AS

    International Nuclear Information System (INIS)

    Hildebrandt, D.; Brakel, R.; Elsner, A.; Grigull, P.; Hacker, H.; Burhenn, R.; Fiedler, S.; Giannone, L.; Goerner, C.; Hartfuss, H.J.; Herre, G.; Herrmann, A.; Hofmann, J.V.; Kuehner, G.; Naujoks, D.; Sardei, F.; Weller, A.; Wolf, R.

    1997-01-01

    In order to study impurity transport and radiation behavior nitrogen has been injected into the scrape-off plasma of limiter-dominated discharges by gas puffing or into natural magnetic islands at the plasma edge of separatrix-dominated discharges by a reciprocating erosion probe. Strong radiative plasma edge cooling with a reduction of the power flux to the limiter could be obtained. The accompanied degradation of the energy confinement and the observed decrease of the central electron temperature can partly be explained by the reduction of the effective heating power. At high plasma densities and sufficiently strong impurity injection phenomena well known from tokamaks, like plasma shrinking, plasma detachment from the limiters and MARFE's were transiently observed. (orig.)

  19. Plasma response on impurity injection in W7-AS

    Energy Technology Data Exchange (ETDEWEB)

    Hildebrandt, D [Euratom Assoc., Berlin (Germany). Max-Planck-Inst. of Plasma Phys.; Brakel, R; Elsner, A; Grigull, P; Hacker, H; Burhenn, R; Fiedler, S; Giannone, L.; Goerner, C; Hartfuss, H J; Herre, G; Herrmann, A; Hofmann, J V; Kuehner, G; Naujoks, D; Sardei, F; Weller, A; Wolf, R

    1997-02-01

    In order to study impurity transport and radiation behavior nitrogen has been injected into the scrape-off plasma of limiter-dominated discharges by gas puffing or into natural magnetic islands at the plasma edge of separatrix-dominated discharges by a reciprocating erosion probe. Strong radiative plasma edge cooling with a reduction of the power flux to the limiter could be obtained. The accompanied degradation of the energy confinement and the observed decrease of the central electron temperature can partly be explained by the reduction of the effective heating power. At high plasma densities and sufficiently strong impurity injection phenomena well known from tokamaks, like plasma shrinking, plasma detachment from the limiters and MARFE`s were transiently observed. (orig.).

  20. Change in detector properties caused by electronegative impurities

    International Nuclear Information System (INIS)

    Deptuch, M.; Kowalski, T.Z.; Mindur, B.

    2006-01-01

    Detector properties (energy resolution, gas gain, drift-time measurements) depend quite critically on the concentration of impurities. The most frequent impurities in the working gas are water vapour and oxygen. Systematic measurements of the detector properties as a function of both H 2 O vapour and O 2 concentration have been made. Ar/CO 2 (80/20) and Ar/CO 2 /CF 4 (70/10/20) have been selected as the working gases. The first mixture is commonly used, the second one is very promising due to its fastness. The concentration of H 2 O vapour and O 2 was varied from 0% to 1.9% and 3%, respectively

  1. Chemical impurity production under boronized wall conditions in TEXTOR

    International Nuclear Information System (INIS)

    Philipps, V.; Vietzke, E.; Erdweg, M.

    1992-01-01

    The TEXTOR SNIFFER probe has been used to analyse the chemical impurity production under various plasma and boronized wall conditions. Methane formation has been observed to 0.6-1 x 10 -2 CH 4 /H at room temperature, increasing slightly with increasing density in the SOL. The hydrocarbon formation yields increase from R.T. to the maximum at about 500 o C by a factor of 1.5-2.5. Increasing the impact energy by biasing the graphite plate leads to a decrease of the hydrocarbon yield at room temperature but to an increase at 500 o C. Chemical CO formation due interaction of oxygen impurities with the graphite reaches ratios between 0.5 and 3 x 10 -2 CO/H,D increasing with increasing distance to the limiter edge. (author) 10 refs., 6 figs

  2. The effect of higher order different meson exchange nucleon-nucleon interactions on the three-nucleon binding energy coupling problem

    International Nuclear Information System (INIS)

    Osman, A.; Ramadan, S.

    1989-01-01

    Faddeev equations of bound three-nucleon system are presented as a set of integral equations. To solve them, a sutable form of the nucleon-nucleon interactions is used: with the exchange of a scalar meson, a pseudoscalar meson and a massless vector meson. Higher orders of these different meson exchanges in the nucleon-nucleon interactions have been taken into account. With these nuclear forces and nucleon-nucleon interactions, the three-nucleon binding energy is calculated by solving the Faddeev integral equations. The obtained value of the three-nucleon binding energy is 8.441 MeV. The inclusion of the higher order terms of the different meson exchange in the nuclear nucleon-nucleon interaction is found to affect the three-nucleon binding by about 3.92%. 3 figs., 16 refs

  3. Low-Z impurities in PLT

    International Nuclear Information System (INIS)

    Hinnov, E.; Suckewer, S.; Bol, K.; Hawryluk, R.; Hosea, J.; Meservey, E.

    1977-11-01

    Low-Z impurities concentrations (oxygen and carbon) have been measured in different discharges in PLT. The contribution to Z/sub eff/, influx rates and radiation losses by oxygen and carbon were obtained. An inverse correlation was found between the low-Z impurity density (and also the edge ion temperature) and the high-Z impurity (tungsten) density. A one-dimensional computer transport model has been used to calculate the spatial profiles of different oxygen and carbon ionization states. This model predicts that fully stripped oxygen and carbon ions should exist near the plasma periphery

  4. Impurities in radioactive solutions for gamma spectroscopy

    International Nuclear Information System (INIS)

    Delgado, J.U.

    1990-01-01

    The absolute and relative methods for radioactive sources calibration, like 4 Πβ-γ and 4Πγ ionization chamber respectively, allows to reach 0,1% of exactiness in activity measurement, but cannot distinguish radioactive impurities that interfere in the activity. Then, one of the problems associated to a quality control of calibrated sources furnished to users is the identification and quantification of the impurities. In this work, a routine technical procedure, using the facilities of gamma spectrometry method that allows to identify and to determine the impurities relative contribution to the source main radionuclide activity, is described. (author) [pt

  5. Simulated impurity transport in LHD from MIST

    Energy Technology Data Exchange (ETDEWEB)

    Rice, J.E. [National Inst. for Fusion Science, Toki, Gifu (Japan)

    1998-05-01

    The impurity transport code MIST and atomic physics package LINES are used to calculate the time evolution of charge state density profiles, individual line emissivity profiles and total radiated power profiles for impurities in LHD plasmas. Three model LHD plasmas are considered; a high density, low temperature case, a low density, high temperature case and the initial LHD start-up plasma (500 kW ECH), using impurity transport coefficient profiles from Heliotron E. The elements oxygen, neon, scandium, iron, nickel and molybdenum are considered, both injected and in steady state. (author)

  6. Impurities of oxygen in silicon

    International Nuclear Information System (INIS)

    Gomes, V.M.S.

    1985-01-01

    The electronic structure of oxygen complex defects in silicon, using molecular cluster model with saturation by watson sphere into the formalism of Xα multiple scattering method is studied. A systematic study of the simulation of perfect silicon crystal and an analysis of the increasing of atom number in the clusters are done to choose the suitable cluster for the calculations. The divacancy in three charge states (Si:V 2 + , Si:V 2 0 , Si:V 2 - ), of the oxygen pair (Si:O 2 ) and the oxygen-vacancy pair (Si:O.V) neighbours in the silicon lattice, is studied. Distortions for the symmetry were included in the Si:V 2 + and Si:O 2 systems. The behavior of defect levels related to the cluster size of Si:V 2 0 and Si:O 2 systems, the insulated oxygen impurity of silicon in interstitial position (Si:O i ), and the complexes involving four oxygen atoms are analysed. (M.C.K.) [pt

  7. 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.

  8. Modification of energy band alignment and electric properties of Pt/Ba{sub 0.6}Sr{sub 0.4}TiO{sub 3}/Pt thin-film ferroelectric varactors by Ag impurities at interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Hirsch, S.; Komissinskiy, P., E-mail: komissinskiy@oxide.tu-darmstadt.de; Flege, S.; Li, S.; Rachut, K.; Klein, A.; Alff, L. [Institute of Materials Science, Technische Universität Darmstadt, 64287 Darmstadt (Germany)

    2014-06-28

    We report on the effects of Ag impurities at interfaces of parallel-plate Pt/Ba{sub 0.6}Sr{sub 0.4}TiO{sub 3}/Pt thin film ferroelectric varactors. Ag impurities occur at the interfaces due to diffusion of Ag from colloidal silver paint used to attach the varactor samples with their back side to the plate heated at 600–750 °C during deposition of Ba{sub 0.6}Sr{sub 0.4}TiO{sub 3}. X-ray photoelectron spectroscopy and secondary ion mass spectrometry suggest that amount and distribution of Ag adsorbed at the interfaces depend strongly on the adsorbent surface layer. In particular, Ag preferentially accumulates on top of the Pt bottom electrode. The presence of Ag significantly reduces the barrier height between Pt and Ba{sub 0.6}Sr{sub 0.4}TiO{sub 3} leading to an increased leakage current density and, thus, to a severe degradation of the varactor performance.

  9. Trends on 3d transition metal impurities in diamond

    International Nuclear Information System (INIS)

    Assali, L.V.C.; Machado, W.V.M.; Justo, J.F.

    2009-01-01

    We carried out a first principles investigation on the electronic properties and chemical trends of 3d transition metal related impurities in diamond. In terms of formation energy, the interstitial site is considerably more unfavorable than the substitutional or divacancy ones. Going from Ti to Ni, the 3d-related energy levels in the gap become deeper toward the valence band in all three sites. However, in the divacancy one, those levels cross with the divacancy-related ones, such that the electronic property of the center depends on the character of the highest occupied level.

  10. Discrete impurity band from surface danging bonds in nitrogen and phosphorus doped SiC nanowires

    Science.gov (United States)

    Li, Yan-Jing; Li, Shu-Long; Gong, Pei; Li, Ya-Lin; Cao, Mao-Sheng; Fang, Xiao-Yong

    2018-04-01

    The electronic structure and optical properties of the nitrogen and phosphorus doped silicon carbide nanowires (SiCNWs) are investigated using first-principle calculations based on density functional theory. The results show doping can change the type of the band gap and improve the conductivity. However, the doped SiCNWs form a discrete impurity levels at the Fermi energy, and the dispersion degree decreases with the diameter increasing. In order to reveal the root of this phenomenon, we hydrogenated the doped SiCNWs, found that the surface dangling bonds were saturated, and the discrete impurity levels are degeneracy, which indicates that the discrete impurity band of the doped SiCNWs is derived from the dangling bonds. The surface passivation can degenerate the impurity levels. Therefore, both doping and surface passivation can better improve the photoelectric properties of the SiCNWs. The result can provide additional candidates in producing nano-optoelectronic devices.

  11. Impurity photovoltaic effect in silicon solar cell doped with sulphur: A numerical simulation

    International Nuclear Information System (INIS)

    Azzouzi, Ghania; Chegaar, Mohamed

    2011-01-01

    The impurity photovoltaic effect (IPV) has mostly been studied in various semiconductors such as silicon, silicon carbide and GaAs in order to increase infrared absorption and hence cell efficiency. In this work, sulphur is used as the IPV effect impurity incorporated in silicon solar cells. For our simulation we use the numerical device simulator (SCAPS). We calculate the solar cell performances (short circuit current density J sc , open circuit voltage V oc , conversion efficiency η and quantum efficiency QE). We study the influence of light trapping and certain impurity parameters like impurity concentration and position in the gap on the solar cell performances. Simulation results for IPV effect on silicon doped with sulphur show an improvement of the short circuit current and the efficiency for sulphur energy levels located far from the middle of the band gap especially at E c -E t =0.18 eV.

  12. Non-Fermi-liquid theory of a compactified Anderson single-impurity model

    International Nuclear Information System (INIS)

    Zhang, G.; Hewson, A.C.

    1996-01-01

    We consider a version of the symmetric Anderson impurity model (compactified) which has a non-Fermi-liquid weak-coupling regime. We find that in the Majorana fermion representation the perturbation theory can be conveniently developed in terms of Pfaffian determinants and we use this formalism to calculate the impurity free energy, self-energies, and vertex functions. We derive expressions for the impurity and the local conduction-electron charge and spin-dynamical susceptibilities in terms of the impurity self-energies and vertex functions. In the second-order perturbation theory, a linear temperature dependence of the electrical resistivity is obtained, and the leading corrections to the impurity specific heat are found to behave as TlnT. The impurity static susceptibilities have terms in lnT to zero, first, and second order, and corrections of ln 2 T to second order as well. The conduction-electron static susceptibilities, and the singlet superconducting paired static susceptibility at the impurity site, have second-order corrections lnT, which indicate that a singlet conduction-electron pairing resonance forms at the Fermi level (the chemical potential). When the perturbation theory is extended to third order logarithmic divergences are found in the only vertex function Γ 0,1,2,3 (0,0,0,0), which is nonvanishing in the zero-frequency limit. We use the multiplicative renormalization-group (RG) method to sum all the leading-order logarithmic contributions. This gives a weak-coupling low-temperature energy scale T c =Δexp[-(1/9)(πΔ/U) 2 ], which is the combination of the two independent coupling parameters. The RG scaling equation is derived and shows that the dimensionless coupling constant bar U=U/πΔ is increased as the high-energy scale Δ is reduced, so our perturbational results can be justified in the regime T approx-gt T c

  13. Numerical studies of impurities in fusion plasmas

    International Nuclear Information System (INIS)

    Hulse, R.A.

    1982-09-01

    The coupled partial differential equations used to describe the behavior of impurity ions in magnetically confined controlled fusion plasmas require numerical solution for cases of practical interest. Computer codes developed for impurity modeling at the Princeton Plasma Physics Laboratory are used as examples of the types of codes employed for this purpose. These codes solve for the impurity ionization state densities and associated radiation rates using atomic physics appropriate for these low-density, high-temperature plasmas. The simpler codes solve local equations in zero spatial dimensions while more complex cases require codes which explicitly include transport of the impurity ions simultaneously with the atomic processes of ionization and recombination. Typical applications are discussed and computational results are presented for selected cases of interest

  14. The origin of metal impurities in DIVA

    International Nuclear Information System (INIS)

    Ohasa, Kazumi; Sengoku, Seio; Maeda, Hikosuke; Ohtsuka, Hideo; Yamamoto, Shin

    1978-10-01

    The origin of metal impurities in DIVA (JFT-2a Tokamak) has been studied experimentally. Three processes of metal impurity release from the first wall were identified; i.e. ion sputtering, evaporation, and arcing. Among of these, ion sputtering is the predominant process in the quiet phase of the discharge, which is characterized by no spikes in the loop voltage and no localized heat flux concentrations on the first wall. ''Cones'' formation due to the sputtering is observed on the gold protection plate (guard limiter) exposed to about 10,000 discharges by scanning electron micrograph. In the SEM photographs, the spacial distribution of cones on the shell surface due to the ion sputtering coincides with the spacial distribution of intensity of Au-I line radiation. Gold is the dominant metal impurity in DIVA. The honeycomb structure can decrease release of the metal impurity. (author)

  15. Models for impurity effects in tokamaks

    International Nuclear Information System (INIS)

    Hogan, J.T.

    1980-03-01

    Models for impurity effects in tokamaks are described with an emphasis on the relationship between attainment of high β and impurity problems. We briefly describe the status of attempts to employ neutral beam heating to achieve high β in tokamaks and propose a qualitative model for the mechanism by which heavy metal impurities may be produced in the startup phase of the discharge. We then describe paradoxes in impurity diffusion theory and discuss possible resolutions in terms of the effects of large-scale islands and sawtooth oscillations. Finally, we examine the prospects for the Zakharov-Shafranov catastrophe (long time scale disintegration of FCT equilibria) in the context of present and near-term experimental capability

  16. Glycolic acid physical properties and impurities assessment

    Energy Technology Data Exchange (ETDEWEB)

    Lambert, D. P. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Pickenheim, B. R. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Hay, M. S. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); BIBLER, N. E. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2017-08-09

    This document has been revised to add analytical data for fresh, 1 year old, and 4 year old glycolic acid as recommended in Revision 2 of this document. This was needed to understand the concentration of formaldehyde and methoxyacetic acid, impurities present in the glycolic acid used in Savannah River National Laboratory (SRNL) experiments. Based on this information, the concentration of these impurities did not change during storage. These impurities were in the glycolic acid used in the testing included in this report and in subsequent testing using DuPont (now called Chemours) supplied Technical Grade 70 wt% glycolic acid. However, these impurities were not reported in the first two versions of this report. The Defense Waste Processing Facility (DWPF) is planning to implement a nitric-glycolic acid flowsheets to increase attainment to meet closure commitment dates during Sludge Batch 9. In fiscal year 2009, SRNL was requested to determine the physical properties of formic and glycolic acid blends.

  17. Impurity induced resistivity upturns in underdoped cuprates

    Energy Technology Data Exchange (ETDEWEB)

    Das, Nabyendu, E-mail: nabyendudas@gmail.com; Singh, Navinder

    2016-01-28

    Impurity induced low temperature upturns in both the ab-plane and the c-axis dc-resistivities of cuprates in the pseudogap state have been observed in experiments. We provide an explanation of this phenomenon by incorporating impurity scattering of the charge carriers within a phenomenological model proposed by Yang, Rice and Zhang. The scattering between charge carriers and the impurity atom is considered within the lowest order Born approximation. Resistivity is calculated within Kubo formula using the impurity renormalized spectral functions. Using physical parameters for cuprates, we describe qualitative features of the upturn phenomena and its doping evolution that coincides with the experimental findings. We stress that this effect is largely due to the strong electronic correlations.

  18. Impurity induced resistivity upturns in underdoped cuprates

    International Nuclear Information System (INIS)

    Das, Nabyendu; Singh, Navinder

    2016-01-01

    Impurity induced low temperature upturns in both the ab-plane and the c-axis dc-resistivities of cuprates in the pseudogap state have been observed in experiments. We provide an explanation of this phenomenon by incorporating impurity scattering of the charge carriers within a phenomenological model proposed by Yang, Rice and Zhang. The scattering between charge carriers and the impurity atom is considered within the lowest order Born approximation. Resistivity is calculated within Kubo formula using the impurity renormalized spectral functions. Using physical parameters for cuprates, we describe qualitative features of the upturn phenomena and its doping evolution that coincides with the experimental findings. We stress that this effect is largely due to the strong electronic correlations.

  19. 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.

  20. An experimental and theoretical investigation of the valence orbital momentum distributions and binding energy spectra of nitrogen

    International Nuclear Information System (INIS)

    Cook, J.P.D.; Pascual, R.; Weigold, E.

    1989-05-01

    A detailed electron momentum spectrosocpy (EMS) and a manybody theoretical study of the complete valence region of N 2 was carried out. The 1500eV EMS momentum distributions show that they provide a sensitive test for orbital wavefunctions of SCF calculations, and of correlation effects. The outermost 3σ g orbital is more sharply peaked at the origin than predicted by the orbital wavefunction. The inner valence 2σ g orbital is severely split, with spectroscopic strength ranging from 34eV to over 60eV in binding energy. The results of the present extended basis 1p Green's function calculations, as well as those of several previous manybody calculations, are only in semiquantitative agreement with this. There is a 2σ u pole at 25eV with a pole strength of approximately 0.067 in agreement with the results of manybody calculations. There is significant 2σ u and or 1π u strength and little 2σ g strength in the region 26-34eV. Poles observed at 29 and 32eV, previously attributed to the 2σ g orbital, are shown to be largely 2σ u in character. The manybody calculations predict too much 2σ g strength in the region 26-34eV. 29 refs., 1 tab., 16 figs