WorldWideScience

Sample records for polaron binding energy

  1. Variational energy band theory for polarons: Mapping polaron structure with the global-local method

    International Nuclear Information System (INIS)

    Brown, D.W.; Lindenberg, K.; Zhao, Y.

    1997-01-01

    In this paper we revisit from a contemporary perspective a classic problem of polaron theory in one dimension using a new variational approach generalizing that of Toyozawa, based on delocalized trial states including mixed gobal and local exciton-phonon correlations. Polaron structure is represented by variational surfaces giving the optimal values of the complete set of exciton and phonon amplitudes for every value of the joint exciton-phonon crystal momentum κ. Characteristic small polaron, large polaron, and nearly free phonon structures are identified, and the manner in which these compete and/or coexist is examined in detail. Through such examination, the parameter space of the problem is mapped, with particular attention given to problematic areas such as the highly quantum mechanical weak-coupling regime, the highly nonlinear intermediate-coupling regime, and to the self-trapping transition that may be said to mark the onset of the strong-coupling regime. Complete energy bands are presented in illustrative cases, and the principal trends in the ground-state energy, polaron bandwidth, and effective mass are identified. The internal structure of our variational Bloch states is examined for qualities that might reflect the typical characteristics of solitons, finding some intriguing qualitative comparisons, but little that bears close scrutiny. copyright 1997 American Institute of Physics

  2. Importance of polaron effects for charge carrier mobility above and ...

    Indian Academy of Sciences (India)

    Orifjon Ganiev

    2017-05-30

    May 30, 2017 ... It is shown that the scattering of polaronic charge carriers and bosonic Cooper pairs at acoustic and optical phonons are responsible for the charge carrier mobility above and below the PG temperature. We show that the energy scales of the binding energies of large polarons and polaronic Cooper pairs.

  3. Importance of polaron effects for charge carrier mobility above and ...

    Indian Academy of Sciences (India)

    It is shown that the scattering of polaronic charge carriers and bosonic Cooper pairs at acoustic and optical phonons are responsible for the charge carrier mobility above and below the PG temperature. We show that the energy scales of the binding energies of large polarons and polaronic Cooper pairs can be identified by ...

  4. Asymptotic dependence of Gross–Tulub polaron ground-state energy in the strong coupling region

    Directory of Open Access Journals (Sweden)

    N.I. Kashirina

    2017-12-01

    Full Text Available The properties of translationally invariant polaron functional have been investigated in the region of strong and extremely strong coupling. It has been shown that the Gross–Tulub polaron functional obtained earlier using the methods of field theory was derived only for the region , where is the Fröhlich constant of the electron-phonon coupling. Various representations of exact and approximate polaron functionals have been considered. Asymptotic dependences of the polaron energy have been obtained using a functional extending the Gross–Tulub functional to the region of extremely strong coupling. The asymptotic dependence of polaron energies for an extremely strong coupling are (for the one-parameter variational function fk, and (for a two-parameter function . It has been shown that the virial theorem 1:3:4 holds for the two-parameter function . Minimization of the approximate functional obtained by expanding the exact Gross–Tulub functional in a series on leads to a quadratic dependence of the polaron energy. This approximation is justified for . For a two-parameter function , the corresponding dependence has the form . However, the use of approximate functionals, in contrast to the strict variational procedure, when the exact polaron functional varies, does not guarantee obtaining the upper limit for the polaron energy.

  5. Properties of a Bound Polaron under a Perpendicular Magnetic Field

    International Nuclear Information System (INIS)

    Liu Jia; Chen Ziyu; Xiao Jinglin; Huo Shufen

    2007-01-01

    We investigate the influence of a perpendicular magnetic field on a bound polaron near the interface of a polar-polar semiconductor with Rashba effect. The external magnetic field strongly changes the ground state binding energy of the polaron and the Rashba spin-orbit (SO) interaction originating from the inversion asymmetry in the heterostructure splits the ground state binding energy of the bound polaron. In this paper, we have shown how the ground state binding energy will be with the change of the external magnetic field, the location of a single impurity, the wave vector of the electron and the electron areal density, taking into account the SO coupling. Due to the presence of the phonons, whose energy gives negative contribution to the polaron's, the spin-splitting states of the bound polaron are more stable, and we find that in the condition of week magnetic field, the Zeeaman effect can be neglected.

  6. Energy versus wave vector for the conduction band of La-doped SrTiO{sub 3} interpreted by mixed-polaron theory

    Energy Technology Data Exchange (ETDEWEB)

    Eagles, D.M., E-mail: d.eagles@ic.ac.uk

    2015-01-15

    An unusual published energy versus wave vector curve extending to the zone edge determined by ARPES in 5% La-doped SrTiO{sub 3} is interpreted using mixed-polaron theory. After modification of the theory to permit tight-binding bare energy bands and anisotropy, a fit is made to the 24 points nearest to the Fermi energy, adding the constraints (a) that the Fermi volume is approximately equal to that determined from the carrier concentration and (b) that the transport mass from experiments is approximately twice the bare mass. In order to fit the remaining five of 29 observed points we empirically add the effect of a kink. The fit to all points is good. From the parameters of the fit to the 24 points it appears that (a) The energy overlap integral for the narrow band in the heavy direction has the opposite sign to that for the wide band, implying that it is energetically favorable for the nearly-small polaron to be centred in between two sites; and (b) The narrower energy band in the theory may be nearly-small-polaron-like in the heavy direction but large-polaron-like in the other two directions. A simpler energy versus wave vector curve for a 1% La-doped crystal is discussed more briefly.

  7. The elusive role of NbLi bound polaron energy in hopping charge transport in Fe: LiNbO3

    Science.gov (United States)

    Guilbert, Laurent; Vittadello, Laura; Bazzan, Marco; Mhaouech, Imed; Messerschmidt, Simon; Imlau, Mirco

    2018-03-01

    Charge transport due to small polarons hopping among defective (bound polarons) and regular (free polarons) sites is shown to depend in a non-trivial way on the value of the stabilization energy provided by the lattice distortion surrounding the charge carriers. This energy, normally not directly accessible for bound polarons using spectroscopic techniques, is determined here by a combination of experimental and numerical methods for the important case of small electron polarons bound to NbLi defects in the prototype ferroelectric oxide lithium niobate. Our findings provide an estimation of the NbLi polaron stabilization energy E_GP=(0.75+/-0.05)~eV and demonstrate that in lithium niobate both free and bound polarons contribute to charge transport at room temperature, explaining the fast decay of the light-induced bound polaron population observed by transient absorption spectroscopy.

  8. Diagrams in the polaron model

    International Nuclear Information System (INIS)

    Smondyrev, M.A.

    1985-01-01

    The perturbation theory for the polaron energy is systematically treated on the diagrammatic basis. Feynman diagrams being constructed allow to calculate the polaron energy up to the third order in powers of the coupling constant. Similar calculations are performed for the average number of virtual phonons

  9. Fractal dimension study of polaron effects in cylindrical GaAs/Al x Ga1- x As core-shell nanowires

    Science.gov (United States)

    Sun, Hui; Li, Hua; Tian, Qiang

    2018-04-01

    Polaron effects in cylindrical GaAs/Al x Ga1- x As core-shell nanowires are studied by applying the fractal dimension method. In this paper, the polaron properties of GaAs/Al x Ga1- x As core-shell nanowires with different core radii and aluminum concentrations are discussed. The polaron binding energy, polaron mass shift, and fractal dimension parameter are numerically determined as functions of shell width. The calculation results reveal that the binding energy and mass shift of the polaron first increase and then decrease as the shell width increases. A maximum value appears at a certain shell width for different aluminum concentrations and a given core radius. By using the fractal dimension method, polaron problems in cylindrical GaAs/Al x Ga1- x As core-shell nanowires are solved in a simple manner that avoids complex and lengthy calculations.

  10. Energy levels of an anisotropic three-dimensional polaron in a magnetic field

    International Nuclear Information System (INIS)

    Brancus, D. E. N.; Stan, G.

    2001-01-01

    In the context of the improved Wigner-Brillouin theory, the energy levels are found of a Frohlich polaron in a uniaxial anisotropic polar semiconductor with complex structure, placed in a magnetic field directed either along the optical axis or orthogonal to it. All sources of anisotropy that are contained in the shape of constant-energy surfaces of the bare electron, the electron - optical-phonon interaction, and the frequency spectrum of the extraordinary phonon modes are considered. Analytical results for the electron-phonon interaction correction to the Landau levels below the optical-phonon continuum are given and, numerical results for the magnetic-field dependence of the cyclotron resonance frequency at low temperature are presented for the particular case of the layered semiconductors InSe and GaSe. Although the interaction between the bare electron and quasitransverse optical-phonon modes is weak, these modes play an important role in the pinning of Landau levels. The results given by Das Sarma for a two-dimensional isotropic magnetopolaron are generalized to the anisotropic uniaxial case by taking formally m # parallel→infinity# in the expression of the perturbed Landau levels found when the magnetic field is directed along the optical axis, m # parallel# being the component of the bare-electron effective-mass tensor along the optical axis

  11. Quarkeosynthesis Binding Energy

    Science.gov (United States)

    Webb, Bill

    2009-05-01

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

  12. Neutral impurities in a Bose-Einstein condensate for simulation of the Froehlich-polaron

    Energy Technology Data Exchange (ETDEWEB)

    Hohmann, Michael; Kindermann, Farina; Gaenger, Benjamin; Lausch, Tobias [University of Kaiserslautern, Department of Physics and Research Center OPTIMAS, Kaiserslautern (Germany); Mayer, Daniel; Schmidt, Felix; Widera, Artur [University of Kaiserslautern, Department of Physics and Research Center OPTIMAS, Kaiserslautern (Germany); Graduate School Materials Science in Mainz, Kaiserslautern (Germany)

    2015-12-15

    We present an experimental system to study the Bose polaron by immersion of single, well-controllable neutral Cs impurities into a Rb Bose-Einstein condensate (BEC). We show that, by proper optical traps, independent control over impurity and BEC allows for precision relative positioning of the two sub-systems as well as for dynamical studies and independent read-out. We furthermore estimate that measuring the polaron binding energy of Froehlich-type Bose polarons in the low and intermediate coupling regime is feasible with our experimental constraints and limitations discussed, and we outline how a parameter regime can be reached to characterize differences between Froehlich and Bose-polaron in the strong coupling regime. (orig.)

  13. Excitonic and Polaronic Properties of 2D Hybrid Organic–Inorganic Perovskites

    KAUST Repository

    Yin, Jun

    2017-01-20

    We theoretically characterize the unusual white-light emission properties of two-dimensional (2D) hybrid organic inorganic perovskites with an APbX(4) structure (where A is a bidentate organic cation and X = Cl, Br). In addition to band structure calculations including corrections due to spin orbit couplings and electron hole interactions, a computationally intensive molecular cluster approach is exploited to describe the excitonic and polaronic properties of these 2D perovskites at the atomistic level. Upon adding or removing an electron from the neutral systems, we find that strongly localized small polarons form in the 2D clusters. The polaron charge density is distributed over just lattice sites, which is consistent with the calculated large polaron binding energies, on the order of similar to 0.4-1.2 eV.

  14. The Bogolubov Representation of the Polaron Model and Its Completely Integrable RPA-Approximation

    International Nuclear Information System (INIS)

    Bogolubov, Nikolai N. Jr.; Prykarpatsky, Yarema A.; Ghazaryan, Anna A.

    2009-12-01

    The polaron model in ionic crystal is studied in the N. Bogolubov representation using a special RPA-approximation. A new exactly solvable approximated polaron model is derived and described in detail. Its free energy at finite temperature is calculated analytically. The polaron free energy in the constant magnetic field at finite temperature is also discussed. Based on the structure of the N. Bogolubov unitary transformed polaron Hamiltonian a very important new result is stated: the full polaron model is exactly solvable. (author)

  15. Polarons in advanced materials

    CERN Document Server

    Alexandrov, Alexandre Sergeevich

    2008-01-01

    Polarons in Advanced Materials will lead the reader from single-polaron problems to multi-polaron systems and finally to a description of many interesting phenomena in high-temperature superconductors, ferromagnetic oxides, conducting polymers and molecular nanowires. The book divides naturally into four parts. Part I introduces a single polaron and describes recent achievements in analytical and numerical studies of polaron properties in different electron-phonon models. Part II and Part III describe multi-polaron physics, and Part IV describes many key physical properties of high-temperature superconductors, colossal magnetoresistance oxides, conducting polymers and molecular nanowires, which were understood with polarons and bipolarons. The book is written in the form of self-consistent reviews authored by well-established researchers actively working in the field and will benefit scientists and postgraduate students with a background in condensed matter physics and materials sciences.

  16. Spin-polaron theory of high-Tc superconductivity: I, spin polarons and high-Tc pairing

    International Nuclear Information System (INIS)

    Wood, R.F.

    1993-06-01

    The concept of a spin polaron is introduced and contrasted with the more familiar ionic polaron picture. A brief review of aspects of ionic bipolaronic superconductivity is given with particular emphasis on the real-space pairing and true Bose condensation characteristics. The formation energy of spin polarons is then calculated in analogy with ionic polarons. The spin-flip energy of a Cu spin in an antiferromagnetically aligned CuO 2 plane is discussed. It is shown that the introduction of holes into the CuO 2 planes will always lead to the destruction of long-range AF ordering due to the formation of spin polarons. The pairing of two spin polarons can be expected because of the reestablishment of local (short-range) AF ordering; the magnitude of the pairing energy is estimated using a simplified model. The paper closes with a brief discussion of the formal theory of spin polarons

  17. The role of hydrostatic pressure and temperature on bound polaron in semiconductor quantum dot

    International Nuclear Information System (INIS)

    El Moussaouy, A.; Ouchani, N.

    2014-01-01

    We studied theoretically the effects of hydrostatic pressure and temperature on the binding energy of shallow hydrogenic impurity in a cylindrical quantum dot (QD) using a variational approach within the effective mass approximation. The hydrostatic stress was applied along the QD growth axis. The interactions between the charge carriers and confined longitudinal optical (LO) phonon modes are taken into account. The numerical computation for GaAs/Ga 1−x Al x As QD has shown that the binding energy with and without the polaronic correction depends on the location of the impurity and the pressure effect and it is more pronounced for impurities in the QD center. Both the binding energy and the polaronic contribution increase linearly with increasing stress. For each pressure value, these energies are also found to decrease as the temperature increases. The results obtained show that in experimental studies of optical and electronic properties of QDs, the effects of pressure, temperature and polaronic correction on donor impurity binding energy should be taken into consideration

  18. Thermoelectric power of small polarons in magnetic semiconductors

    International Nuclear Information System (INIS)

    Liu, N.H.; Emin, D.

    1984-01-01

    The thermoelectric power (Seebeck coefficient) α of a small polaron in both ferromagnetic and antiferromagnetic semiconductors and insulators is calculated for the first time. In particular, we obtain the contribution to the Seebeck coefficient arising from exchange interactions between the severely localized carrier (i.e., small polaron) of charge q and the spins of the host lattice. In essence, we study the heat transported along with a carrier. This heat, the Peltier heat, Pi, is related to the Seebeck coefficient by the Kelvin relation: Pi = qTα, where T is the temperature. The heat per carrier is simply the product of the temperature and the change of the entropy of the system when a small polaron is added to it. The magnetic contribution to the Seebeck coefficient is therefore directly related to the change of the magnetic entropy of the system upon introduction of a charge carrier. We explicitly treat the intrasite and intersite exchange interactions between a small polaron and the spins of a spin-1/2 system. These magnetic interactions produce two competing contributions to the Seebeck coefficient. First, adding the carrier tends to provide extra spin freedom (e.g., spin up or spin down of the carrier). This effect augments the entropy of the system, thereby producing a positive contribution to the Peltier heat. Second, however, the additional exchange between the carrier and the sites about it enhances the exchange binding among these sites. This generally reduces the energetically allowable spin configurations. The concomitant reduction of the system's entropy provides a negative contribution to the Peltier heat. At the highest of temperatures, when kT exceeds the intrasite exchange energy, the first effect dominates. Then, the Peltier heat is simply augmented by kT ln2

  19. Mobile Polaronic States in α-MoO3: An ab Initio Investigation of the Role of Oxygen Vacancies and Alkali Ions.

    Science.gov (United States)

    Tahini, Hassan A; Tan, Xin; Lou, Shi Nee; Scott, Jason; Amal, Rose; Ng, Yun Hau; Smith, Sean C

    2016-05-04

    Some oxides have the ability to trap excess electrons in the form of small polarons. Here, using first-principles techniques, we investigate the interaction of excess electrons with α-MoO3. Polarons are found to be about 0.6 eV more stable than delocalized electrons. They can propagate with a high degree of anisotropicity along different crystallographic directions with the lowest barrier found to be about 0.08 eV. In addition to the band gap photoexcited charge carriers that can populate such polaron states, we investigate the role of oxygen vacancies as an intrinsic source of electrons. We also investigate intercalated alkali ions that can form complexes with the created polarons in the lattice. The alkali-polaron complex (AxMoO6, A = alkali ion) binding energies are relatively low, making it easy for the complex to dissociate. This, coupled with the low polaron migration energies, can generate a non-negligible contribution to electronic conductivity even in the absence of illumination, which is experimentally verified. Combined, this light-induced intercalation of alkali ion in MoO3 and its subsequent deintercalation (complex dissociation) processes lead to a novel self-photocharghing phenomenon.

  20. Binding energy of protonium ions

    Science.gov (United States)

    Assad Abdel-Raouf, Mohamed

    2009-11-01

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

  1. Visualizing the Efimov Correlation in Bose Polarons

    Science.gov (United States)

    Sun, Mingyuan; Zhai, Hui; Cui, Xiaoling

    2017-07-01

    The Bose polaron is a quasiparticle of an impurity dressed by surrounding bosons. In few-body physics, it is known that two identical bosons and a third distinguishable particle can form a sequence of Efimov bound states in the vicinity of interspecies scattering resonance. On the other hand, in the Bose polaron system with an impurity atom embedded in many bosons, no signature of Efimov physics has been reported in the existing spectroscopy measurements to date. In this Letter, we propose that a large mass imbalance between a light impurity and heavy bosons can help produce visible signatures of Efimov physics in such a spectroscopy measurement. Using the diagrammatic approach in the virial expansion to include three-body effects from pair-wise interactions, we determine the impurity self-energy and its spectral function. Taking the 6Li - 133Cs system as a concrete example, we find two visible Efimov branches in the polaron spectrum, as well as their hybridizations with the attractive polaron branch. We also discuss the general scenarios for observing the signature of Efimov physics in polaron systems. This work paves the way for experimentally exploring intriguing few-body correlations in a many-body system in the near future.

  2. Polaronic exciton behavior in gas-phase water

    Science.gov (United States)

    Udal'tsov, Alexander V.

    2018-03-01

    Features of the absorption spectrum of gas-phase water in the energy range 7-10 eV have been considered applying polaronic exciton theory. The interaction of the incident photon generating polaronic exciton in water is described taking into account angular momentum of the electron so that polaronic exciton radii have been estimated in dependence on spin-orbit coupling under proton sharing. The suggested approach admits an estimate of kinetic and rotation energies of the polaronic exciton. As a result sixteen steps of half Compton wavelength, λC/2 = h/(2mec) changing polaronic exciton radius were found consistent with local maxima and shoulders in the spectrum. Thus, the absorption of gas-phase water in the energy range 8.5-10 eV has been interpreted in terms of polaronic exciton rotation mainly coupled with the proton sharing. The incident photon interaction with water is also considered in terms of Compton interaction, when the rotation energy plays a role like the energy loss of the incident photon under Compton scattering. The found symmetry and the other evidence allowed to conclude about polaronic exciton migration under the interaction angle 90°.

  3. Multiphonon generation during photodissociation of slow Landau-Pekar polarons

    International Nuclear Information System (INIS)

    Myasnikov, E. N.; Myasnikova, A. E.; Mastropas, Z. P.

    2006-01-01

    The spectra of the low-temperature photodissociation (photoionization) of Landau-Pekar polarons are calculated using the theory of quantum-coherent states and a new method of variation with respect to the parameters of phonon vacuum deformation. It is shown that the final polaron states upon photodissociation may have different numbers of phonons produced in a single dissociation event and different momenta of charge carriers. The spectrum of optical absorption related to the photodissociation of polarons exhibits a superposition of bands corresponding to various numbers of phonons formed as a result of dissociation of a single polaron. Due to a large width of the energy region corresponding to the final states of charge carriers, the halfwidth of each band is on the order of the energy of polaron coupling and is much greater than the phonon energy. For this reason, the individual phonon bands exhibit strong overlap. The very broad and, probably, structureless band formed as a result of the superposition of all these components begins at an energy equal to the sum of the polaron coupling energy (E p ) and the phonon energy. This band has a maximum at a frequency of about 5.6E p /ℎ and a halfwidth on the order of 5.6E p /ℎ at a unit effective mass (m* = m e ) of band electrons. For an effective charge carrier mass within m* = (1-3)m e , the energy of the polaron band maximum can be estimated as 5E p with an error of about 10%, and the halfwidth falls within 3.4E p 1/2 p . The multiphonon character of this band is related to a decay of the phonon condensate after the escape of charge carrier from a polaron. Such polarons are likely to be observed in the spectra of complex metal oxides, including high-temperature superconductors. Examples of such polaron bands in the reported absorption and photoconductivity spectra of nonstoichiometric cuprates, manganites, nickelates, and titanates are presented. A theory of the formation of Landau-Pekar polarons with the

  4. Polaronic transport in polysilanes

    Czech Academy of Sciences Publication Activity Database

    Nešpůrek, Stanislav; Nožár, Juraj; Kadashchuk, A.; Fishchuk, I. I.

    2009-01-01

    Roč. 193, č. 1 (2009), s. 1-4 ISSN 1742-6588. [International Conference on Electron Dynamics in Semiconductors, Optoelectronics and Nanostructures /16./. Montpellier, 24.08.2009-28.08.2009] R&D Projects: GA AV ČR IAA100100622; GA AV ČR KAN400720701 Institutional research plan: CEZ:AV0Z40500505 Keywords : polaronic transport * polysilanes * charge carrier mobility Subject RIV: CD - Macromolecular Chemistry

  5. Stability of the two-dimensional Fermi polaron

    Science.gov (United States)

    Griesemer, Marcel; Linden, Ulrich

    2018-02-01

    A system composed of an ideal gas of N fermions interacting with an impurity particle in two space dimensions is considered. The interaction between impurity and fermions is given in terms of two-body point interactions whose strength is determined by the two-body binding energy, which is a free parameter of the model. If the mass of the impurity is 1.225 times larger than the mass of a fermion, it is shown that the energy is bounded below uniformly in the number N of fermions. This result improves previous, N-dependent lower bounds, and it complements a recent, similar bound for the Fermi polaron in three space dimensions.

  6. Peltier heat of a small polaron in a magnetic semiconductor

    International Nuclear Information System (INIS)

    Liu, N.H.; Emin, D.

    1985-01-01

    For the first time the heat transported with a small polaron in both antiferromagnetic and ferromagnetic semiconductors is calculated. This heat, the Peltier heat, π, is obtained from the change of the entropy of the total system upon introduction of a charge carrier. We explicitly consider both the intrasite and intersite exchange interactions between a small polaron and the interacting spins of a spin-1/2 magnet. There are two competing magnetic contributions to the Peltier heat. First, adding the carrier increases the spin entropy of the system. This provides a positive contribution to π. Second, the exchange between the carrier and the sites about it enhances the exchange binding between these sites. This reduces the energetically allowable spin configurations and provides a negative contribution to π. At extremely high temperatures when kT exceeds the intrasite exchange energy, the first effect dominates. Then π is simply augmented by kT ln 2. However, well below the magnetic transition temperature the second effect dominates. In the experimentally accessible range between these limits both effects are comparable and sizable. The net magnetic contribution to the Peltier heat rises with temperature. Thus, a carrier's interactions with its magnetic environment produces a significant and distinctive contribution to its Peltier heat

  7. Peltier heat of a small polaron in a magnetic semiconductor

    International Nuclear Information System (INIS)

    Liu, N.L.H.; Emin, D.

    1984-01-01

    The heat transported with a small polaron in both antiferromagnetic and ferromagnetic semiconductors is calculated. This heat, the Peltier heat, π, is obtained from the change of the entropy of the total system upon introduction of a charge carrier. We explicitly consider both the intrasite and intersite exchange interactions between a small polaron and the interacting spins of a spin-1/2 magnet. There are two competing magnetic contributions to the Peltier heat. First, adding the carrier increases the spin entropy of the system. This provides a positive contribution to π. Second, the exchange between the carrier and the sites about it enhances the exchange binding between these sites. This reduces the energetically allowable spin configurations and provides a negative contribution to π. At extremely high temperature when kT exceeds the intrasite exchange energy, the first effect dominates. Then π is simply augmented by kTln2. However, well below the magnetic transition temperature the second effect dominates. In the experimentally accessible range between these limits both effects are comparable and sizable. The net magnetic contribution to the Peltier heat rises with temperature. Thus, a carrier's interactions with its magnetic environment produces a significant and distinctive contribution to its Peltier heat

  8. Binding energy of the barbell exciton

    Science.gov (United States)

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

    1991-02-01

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

  9. Spin-polarons and high-Tc superconductivity

    International Nuclear Information System (INIS)

    Wood, R.F.

    1994-03-01

    The spin-polaron concept is introduced in analogy to ionic and electronic polarons and the assumptions underlying the author's approach to spin-polaron mediated high-T c superconductivity are discussed. Elementary considerations about the spin-polaron formation energy are reviewed and the possible origin of the pairing mechanism illustrated schematically. The electronic structure of the CuO 2 planes is treated from the standpoint of antiferromagnetic band calculations that lead directly to the picture of holes predominantly on the oxygen sublattice in a Mott-Hubbard/charge transfer insulator. Assuming the holes to be described in a Bloch representation but with the effective mass renormalized by spin-polaron formation, equations for the superconducting gap, Δ, and transition temperature, T c , are developed and the symmetry of Δ discussed. After further simplifications, T c is calculated as a function of the carrier concentration, x. It is shown that the calculated behavior of T c (x) follows the experimental results closely and leads to a natural explanation of the effects of under- and over-doping. The paper concludes with a few remarks about the evidence for the carriers being fermions (polarons) or bosons (bipolarons)

  10. 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.

  11. O{sup -} bound small polarons in oxide materials

    Energy Technology Data Exchange (ETDEWEB)

    Schirmer, O F [Department of Physics, University of Osnabrueck, D-49076 Osnabrueck (Germany)

    2006-11-01

    Holes bound to acceptor defects in oxide crystals are often localized by lattice distortion at just one of the equivalent oxygen ligands of the defect. Such holes thus form small polarons in symmetric clusters of a few oxygen ions. An overview on mainly the optical manifestations of those clusters is given. The article is essentially divided into two parts: the first one covers the basic features of the phenomena and their explanations, exemplified by several paradigmatic defects; in the second part numerous oxide materials are presented which exhibit bound small polaron optical properties. The first part starts with summaries on the production of bound hole polarons and the identification of their structure. It is demonstrated why they show strong, wide absorption bands, usually visible, based on polaron stabilization energies of typically 1 eV. The basic absorption process is detailed with a fictitious two-well system. Clusters with four, six and twelve equivalent ions are realized in various oxide compounds. In these cases several degenerate optically excited polaron states occur, leading to characteristic final state resonance splittings. The peak energies of the absorption bands as well as the sign of the transfer energy depend on the topology of the clusters. A special section is devoted to the distinction between interpolaron and intrapolaron optical transitions. The latter are usually comparatively weak. The oxide compounds exhibiting bound hole small polaron absorptions include the alkaline earth oxides (e.g. MgO), BeO and ZnO, the perovskites BaTiO{sub 3} and KTaO{sub 3}, quartz, the sillenites (e.g. Bi{sub 12}TiO{sub 20}), Al{sub 2}O{sub 3}, LiNbO{sub 3}, topaz and various other materials. There are indications that the magnetic crystals NiO, doped with Li, and LaMnO{sub 3}, doped with Sr, also show optical features caused by bound hole polarons. Beyond being elementary paradigms for the properties of small polarons in general, the defect species treated

  12. Repulsive polarons and itinerant ferromagnetism in strongly polarized Fermi gases

    DEFF Research Database (Denmark)

    Massignan, Pietro; Bruun, Georg

    2011-01-01

    We analyze the properties of a single impurity immersed in a Fermi sea. At positive energy and scattering lengths, we show that the system possesses a well-defined but metastable excitation, the repulsive polaron, and we calculate its energy, quasiparticle residue and effective mass. From a therm...

  13. 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....

  14. 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.

  15. 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

  16. Method of intermediate problems in the Fröhlich polaron model

    Directory of Open Access Journals (Sweden)

    A.V. Soldatov

    2009-01-01

    Full Text Available Method of intermediate problems in the theory of linear semi-bounded self-adjoint operators on rigged Hilbert space was applied to the investigation of the ground state energy of the Fröhlich polaron model. It was shown that various infinite sequences of non-decreasing improvable lower bound estimates for the polaron ground state energy can be derived for arbitrary values of the electron-phonon interaction constant. The proposed approach allows for explicit numerical evaluation of the thus obtained lower bound estimates at all orders and can be straightforwardly generalized for investigation of the low-lying branch of the slow-moving polaron excitation energy spectral curve adjacent to the ground state energy of the polaron at rest. In conjunction with numerous, already derived by multitudinous methods, well-known upper bound estimates for the energy spectral curve of the Fröhlich polaron as a function of the electron-phonon interaction constant and the polaron total momentum, the aforesaid improvable lower bound estimates might provide one with virtually precise magnitude for the energy of the slow-moving polaron.

  17. A self-consistent theory of the magnetic polaron

    International Nuclear Information System (INIS)

    Marvakov, D.I.; Kuzemsky, A.L.; Vlahov, J.P.

    1984-10-01

    A finite temperature self-consistent theory of magnetic polaron in the s-f model of ferromagnetic semiconductors is developed. The calculations are based on the novel approach of the thermodynamic two-time Green function methods. This approach consists in the introduction of the ''irreducible'' Green functions (IGF) and derivation of the exact Dyson equation and exact self-energy operator. It is shown that IGF method gives a unified and natural approach for a calculation of the magnetic polaron states by taking explicitly into account the damping effects and finite lifetime. (author)

  18. Observation of Spin-Polarons in a strongly interacting Fermi liquid

    Science.gov (United States)

    Zwierlein, Martin

    2009-03-01

    We have observed spin-polarons in a highly imbalanced mixture of fermionic atoms using tomographic RF spectroscopy. Feshbach resonances allow to freely tune the interactions between the two spin states involved. A single spin down atom immersed in a Fermi sea of spin up atoms can do one of two things: For strong attraction, it can form a molecule with exactly one spin up partner, but for weaker interaction it will spread its attraction and surround itself with a collection of majority atoms. This spin down atom ``dressed'' with a spin up cloud constitutes the spin-polaron. We have observed a striking spectroscopic signature of this quasi-particle for various interaction strengths, a narrow peak in the spin down spectrum that emerges above a broad background. The narrow width signals a long lifetime of the spin-polaron, much longer than the collision rate with spin up atoms, as it must be for a proper quasi-particle. The peak position allows to directly measure the polaron energy. The broad pedestal at high energies reveals physics at short distances and is thus ``molecule-like'': It is exactly matched by the spin up spectra. The comparison with the area under the polaron peak allows to directly obtain the quasi-particle weight Z. We observe a smooth transition from polarons to molecules. At a critical interaction strength of 1/kFa = 0.7, the polaron peak vanishes and spin up and spin down spectra exactly match, signalling the formation of molecules. This is the same critical interaction strength found earlier to separate a normal Fermi mixture from a superfluid molecular Bose-Einstein condensate. The spin-polarons determine the low-temperature phase diagram of imbalanced Fermi mixtures. In principle, polarons can interact with each other and should, at low enough temperatures, form a superfluid of p-wave pairs. We will present a first indication for interactions between polarons.

  19. Dynamics of photogenerated polarons and polaron pairs in P3HT thin films

    Science.gov (United States)

    Menšík, M.; Pfleger, J.; Toman, P.

    2017-06-01

    On the basis of the analysis of the experimental data of the transient absorption spectroscopy of thin films of regioregular poly(3-hexyl thiophene) we suggest a mechanism of the polaron pairs decay based on the coherent up and down conversion cycling between hot polaron pairs and free polarons. Compared to previously adopted models, based on single molecular processes or bimolecular collisions, the suggested model reproduced well both the polaron pairs and polaron population kinetics at short time after photoexcitation. For longer times, when the polaron pairs are already thermalized, they decay via 1-D diffusion limited bi-molecular collision processes.

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

    Science.gov (United States)

    Bauschlicher, Charles W.

    2018-02-01

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

  1. 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.

  2. Large polarons in lead halide perovskites

    OpenAIRE

    Miyata, Kiyoshi; Meggiolaro, Daniele; Trinh, M. Tuan; Joshi, Prakriti P.; Mosconi, Edoardo; Jones, Skyler C.; De Angelis, Filippo; Zhu, X.-Y.

    2017-01-01

    Lead halide perovskites show marked defect tolerance responsible for their excellent optoelectronic properties. These properties might be explained by the formation of large polarons, but how they are formed and whether organic cations are essential remain open questions. We provide a direct time domain view of large polaron formation in single-crystal lead bromide perovskites CH3NH3PbBr3 and CsPbBr3. We found that large polaron forms predominantly from the deformation of the PbBr3 ? framewor...

  3. Binding-energy distribution and dephasing of localized biexcitons

    DEFF Research Database (Denmark)

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

    1997-01-01

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

  4. 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

  5. Small polaron hopping in magnetic semiconductors

    International Nuclear Information System (INIS)

    Emin, D.; Liu, N.L.H.

    1978-01-01

    In a number of magnetic insulators it has been hypothesized that the charge carriers form small polarons. The transfer of an electron between magnetic sites and how the magnetic nature of the material affects the rate which characterizes small-polaron hops between magnetic sites were studied. The basic transfer processes are addressed from a many-electron point in which the itinerant electron is treated as indistinguishable from those which contribute unpaired spins at the magnetic sites

  6. 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.

  7. Effect of base-pair inhomogeneities on charge transport along the DNA molecule, mediated by twist and radial polarons

    International Nuclear Information System (INIS)

    Palmero, F; Archilla, J F R; Hennig, D; Romero, F R

    2004-01-01

    Some recent results for a three-dimensional, semi-classical, tight-binding model for DNA show that there are two types of polarons, namely radial and twist polarons, which can transport charge along the DNA molecule. However, the existence of two types of base pairs in real DNA makes it crucial to find out if charge transport also exists in DNA chains with different base pairs. In this paper, we address this problem in its simple case, a homogeneous chain except for a single different base pair, which we call a base-pair inhomogeneity, and its effect on charge transport. Radial polarons experience either reflection or trapping. However, twist polarons are good candidates for charge transport along real DNA. This transport is also very robust with respect to weak parametric and diagonal disorder

  8. Effect of base-pair inhomogeneities on charge transport along the DNA molecule, mediated by twist and radial polarons

    Energy Technology Data Exchange (ETDEWEB)

    Palmero, F [ETS IngenierIa Informatica, Universidad de Sevilla, Avda Reina Mercedes s/n, 41012-Sevilla (Spain); Archilla, J F R [ETS IngenierIa Informatica, Universidad de Sevilla, Avda Reina Mercedes s/n, 41012-Sevilla (Spain); Hennig, D [Freie Universitaet Berlin, Fachbereich Physik, Arnimallee 14, 14195-Berlin (Germany); Romero, F R [Facultad de FIsica, Universidad de Sevilla, Avda Reina Mercedes s/n, 41012-Sevilla (Spain)

    2004-02-01

    Some recent results for a three-dimensional, semi-classical, tight-binding model for DNA show that there are two types of polarons, namely radial and twist polarons, which can transport charge along the DNA molecule. However, the existence of two types of base pairs in real DNA makes it crucial to find out if charge transport also exists in DNA chains with different base pairs. In this paper, we address this problem in its simple case, a homogeneous chain except for a single different base pair, which we call a base-pair inhomogeneity, and its effect on charge transport. Radial polarons experience either reflection or trapping. However, twist polarons are good candidates for charge transport along real DNA. This transport is also very robust with respect to weak parametric and diagonal disorder.

  9. Strong-coupling Bose polarons out of equilibrium: Dynamical renormalization-group approach

    Science.gov (United States)

    Grusdt, Fabian; Seetharam, Kushal; Shchadilova, Yulia; Demler, Eugene

    2018-03-01

    When a mobile impurity interacts with a surrounding bath of bosons, it forms a polaron. Numerous methods have been developed to calculate how the energy and the effective mass of the polaron are renormalized by the medium for equilibrium situations. Here, we address the much less studied nonequilibrium regime and investigate how polarons form dynamically in time. To this end, we develop a time-dependent renormalization-group approach which allows calculations of all dynamical properties of the system and takes into account the effects of quantum fluctuations in the polaron cloud. We apply this method to calculate trajectories of polarons following a sudden quench of the impurity-boson interaction strength, revealing how the polaronic cloud around the impurity forms in time. Such trajectories provide additional information about the polaron's properties which are challenging to extract directly from the spectral function measured experimentally using ultracold atoms. At strong couplings, our calculations predict the appearance of trajectories where the impurity wavers back at intermediate times as a result of quantum fluctuations. Our method is applicable to a broader class of nonequilibrium problems. As a check, we also apply it to calculate the spectral function and find good agreement with experimental results. At very strong couplings, we predict that quantum fluctuations lead to the appearance of a dark continuum with strongly suppressed spectral weight at low energies. While our calculations start from an effective Fröhlich Hamiltonian describing impurities in a three-dimensional Bose-Einstein condensate, we also calculate the effects of additional terms in the Hamiltonian beyond the Fröhlich paradigm. We demonstrate that the main effect of these additional terms on the attractive side of a Feshbach resonance is to renormalize the coupling strength of the effective Fröhlich model.

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

    Indian Academy of Sciences (India)

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

  11. Extrapolations of nuclear binding energies from new linear mass relations

    DEFF Research Database (Denmark)

    Hove, D.; Jensen, A. S.; Riisager, K.

    2013-01-01

    We present a method to extrapolate nuclear binding energies from known values for neighboring nuclei. We select four specific mass relations constructed to eliminate smooth variation of the binding energy as function nucleon numbers. The fast odd-even variations are avoided by comparing nuclei...

  12. 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 ...

  13. Dynamics of photogenerated polarons and polaron pairs in P3HT thin films

    Czech Academy of Sciences Publication Activity Database

    Menšík, Miroslav; Pfleger, Jiří; Toman, Petr

    2017-01-01

    Roč. 677, 1 June (2017), s. 87-91 ISSN 0009-2614 R&D Projects: GA MŠk(CZ) LO1507 Institutional support: RVO:61389013 Keywords : poly(3-hexyl thiophene) * transient absorption spectroscopy * polaron and polaron pairs Subject RIV: CD - Macromolecular Chemistry OBOR OECD: Polymer science Impact factor: 1.815, year: 2016

  14. Computation of pH-Dependent Binding Free Energies

    Science.gov (United States)

    Kim, M. Olivia; McCammon, J. Andrew

    2015-01-01

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

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

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume A `Nuclei with Z = 1 - 54' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms'. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Y-90 (Yttrium, atomic number Z = 39, mass number A = 90).

  16. 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.

  17. Large polarons in lead halide perovskites

    Science.gov (United States)

    Miyata, Kiyoshi; Meggiolaro, Daniele; Trinh, M. Tuan; Joshi, Prakriti P.; Mosconi, Edoardo; Jones, Skyler C.; De Angelis, Filippo; Zhu, X.-Y.

    2017-01-01

    Lead halide perovskites show marked defect tolerance responsible for their excellent optoelectronic properties. These properties might be explained by the formation of large polarons, but how they are formed and whether organic cations are essential remain open questions. We provide a direct time domain view of large polaron formation in single-crystal lead bromide perovskites CH3NH3PbBr3 and CsPbBr3. We found that large polaron forms predominantly from the deformation of the PbBr3− frameworks, irrespective of the cation type. The difference lies in the polaron formation time, which, in CH3NH3PbBr3 (0.3 ps), is less than half of that in CsPbBr3 (0.7 ps). First-principles calculations confirm large polaron formation, identify the Pb-Br-Pb deformation modes as responsible, and explain quantitatively the rate difference between CH3NH3PbBr3 and CsPbBr3. The findings reveal the general advantage of the soft [PbX3]− sublattice in charge carrier protection and suggest that there is likely no mechanistic limitations in using all-inorganic or mixed-cation lead halide perovskites to overcome instability problems and to tune the balance between charge carrier protection and mobility. PMID:28819647

  18. 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...

  19. 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.

  20. Al-bound hole polarons in TiO{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Stashans, Arvids, E-mail: arvids@utpl.edu.ec [Grupo de Fisicoquimica de Materiales, Instituto de Quimica Aplicada, Universidad Tecnica Particular de Loja, Apartado 11-01-608, Loja (Ecuador); Bermeo, Sthefano [Grupo de Fisicoquimica de Materiales, Instituto de Quimica Aplicada, Universidad Tecnica Particular de Loja, Apartado 11-01-608, Loja (Ecuador)] [Escuela de Electronica y Telecomunicaciones, Universidad Tecnica Particular de Loja, Apartado 11-01-608, Loja (Ecuador)

    2009-09-18

    Changes in the structural and electronic properties of TiO{sub 2} (anatase and rutile) due to the Al-doping are studied using a quantum-chemical approach based on the Hartree-Fock theory. The formation of hole polarons trapped at oxygen sites near the Al impurity has been discovered and their spatial configuration are discussed. The occurrence of well-localized one-center hole polarons in rutile may influence its photocatalytic activity. Optical absorption energy for this hole center is obtained, 0.4 eV, using the {Delta}SCF approach.

  1. Renormalization group approach to the Fröhlich polaron model: application to impurity-BEC problem.

    Science.gov (United States)

    Grusdt, F; Shchadilova, Y E; Rubtsov, A N; Demler, E

    2015-07-17

    When a mobile impurity interacts with a many-body system, such as a phonon bath, a polaron is formed. Despite the importance of the polaron problem for a wide range of physical systems, a unified theoretical description valid for arbitrary coupling strengths is still lacking. Here we develop a renormalization group approach for analyzing a paradigmatic model of polarons, the so-called Fröhlich model, and apply it to a problem of impurity atoms immersed in a Bose-Einstein condensate of ultra cold atoms. Polaron energies obtained by our method are in excellent agreement with recent diagrammatic Monte Carlo calculations for a wide range of interaction strengths. They are found to be logarithmically divergent with the ultra-violet cut-off, but physically meaningful regularized polaron energies are also presented. Moreover, we calculate the effective mass of polarons and find a smooth crossover from weak to strong coupling regimes. Possible experimental tests of our results in current experiments with ultra cold atoms are discussed.

  2. Breakdown of the lattice polaron picture in La0.7Ca0.3MnO3 single crystals

    International Nuclear Information System (INIS)

    Chun, S. H.; Salamon, M. B.; Tomioka, Y.; Tokura, Y.

    2000-01-01

    When heated through the magnetic transition at T C , La 0.7 Ca 0.3 MnO 3 changes from a band metal to a polaronic insulator. The Hall constant R H , through its activated behavior and sign anomaly, provides key evidence for polaronic behavior. We use R H and the Hall mobility to demonstrate the breakdown of the polaron phase. Above 1.4T C , the polaron picture holds in detail, while below, the activation energies of both R H and the mobility deviate strongly from their polaronic values. These changes reflect the presence of metallic, ferromagnetic fluctuations, in the volume of which the Hall effect develops additional contributions tied to quantal phases. (c) 2000 The American Physical Society

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

    Science.gov (United States)

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

    2017-03-01

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

  4. Small polarons in 2D perovskites

    KAUST Repository

    Cortecchia, Daniele

    2017-11-02

    We demonstrate that white light luminescence in two-dimensional (2D) perovskites stems from photoinduced formation of small polarons confined at specific sites of the inorganic framework in the form of self-trapped electrons and holes. We discuss their application in white light emitting devices and X-ray scintillators.

  5. Effect of doping Ca on polaron hopping in LaSr 2 Mn 2 O 7

    Indian Academy of Sciences (India)

    From the transport studies in the bilayer manganites LaSr2-CaMn2O7, we have found the variable-range hopping model proposed by Viret et al to be inadequate to describe the transport of charge in these materials. The polarons appear to hop to their nearest neighbors with an activation energy, which in part is ...

  6. Quantum Monte Carlo simulations of the Fermi-polaron problem and bosons with Gaussian interactions

    Energy Technology Data Exchange (ETDEWEB)

    Kroiss, Peter Michael

    2017-02-01

    This thesis deals with the application of current Quantum Monte Carlo algorithms to many-body systems of fermionic and bosonic species. The first part applies the diagrammatic Monte Carlo method to the Fermi polaron problem, a system of an impurity interacting resonantly with a homogeneous Fermi bath. It is numerically shown that the three particle-hole diagrams do not contribute significantly to the final answer in a quasi-two-dimensional setup, thus demonstrating a nearly perfect destructive interference of contributions in subspaces with higher-order particle-hole lines. Consequently, for strong-enough confinement in the third direction, the transition between the polaron and the molecule ground state is found to be in good agreement with the pure two-dimensional case and agrees very well with the one found by the wave-function approach in the two-particle-hole subspace. In three-dimensional Fermi-polaron systems with mass imbalance of impurity and bath atoms, polaron energy and quasiparticle residue can be accurately determined over a broad range of impurity masses. Furthermore, the spectral function of an imbalanced polaron demonstrates the stability of the quasiparticle and also allows us to locate the repulsive polaron as an excited state. The quantitative exactness of two-particle-hole wave functions is investigated, resulting in a relative lowering of polaronic energies in the mass-imbalance phase diagram. Tan's contact coefficient for the mass-balanced polaron system is found to be in good agreement with variational methods. Mass-imbalanced systems can be studied experimentally by ultracold atom mixtures such as {sup 6}Li-{sup 40}K. In the second part of the thesis, the ground state of a two-dimensional system of Bose particles of spin zero, interacting via a repulsive Gaussian-Core potential, is investigated by means of path integral Monte Carlo simulations. The quantum phase diagram is qualitatively identical to that of two-dimensional Yukawa

  7. 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

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

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Cf-252 (Californium, atomic number Z = 98, mass number A = 252).

  9. Energy, decay rate, and effective masses for a moving polaron in a Fermi sea: Explicit results in the weakly attractive limit

    Science.gov (United States)

    Christian, Trefzger; Yvan, Castin

    2014-03-01

    We study the properties of an impurity of mass M moving through a spatially homogeneous three-dimensional fully polarized Fermi gas of particles of mass m. In the weakly attractive limit, where the effective coupling constant g -->0- and perturbation theory can be used, both for a broad and a narrow Feshbach resonance, we obtain an explicit analytical expression for the complex energy ΔE(K) of the moving impurity up to order two included in g. This also gives access to its longitudinal and transverse effective masses m∥*(K) , m⊥*(K) , as functions of the impurity wave vector K. Depending on the modulus of K and on the impurity-to-fermion mass ratio M / m we identify four regions separated by singularities in derivatives with respect to K of the second-order term of ΔE(K) , and we discuss the physical origin of these regions. Remarkably, the second-order term of m∥*(K) presents points of non-differentiability, replaced by a logarithmic divergence for M = m , when K is on the Fermi surface of the fermions. We also discuss the third-order contribution and relevance for cold atom experiments. C. T. acknowledges support from a Marie Curie Intra European grant INTERPOL N.298449.

  10. Time Domain View of Liquid-like Screening and Large Polaron Formation in Lead Halide Perovskites

    Science.gov (United States)

    Joshi, Prakriti Pradhan; Miyata, Kiyoshi; Trinh, M. Tuan; Zhu, Xiaoyang

    The structural softness and dynamic disorder of lead halide perovskites contributes to their remarkable optoelectronic properties through efficient charge screening and large polaron formation. Here we provide a direct time-domain view of the liquid-like structural dynamics and polaron formation in single crystal CH3NH3PbBr3 and CsPbBr3 using femtosecond optical Kerr effect spectroscopy in conjunction with transient reflectance spectroscopy. We investigate structural dynamics as function of pump energy, which enables us to examine the dynamics in the absence and presence of charge carriers. In the absence of charge carriers, structural dynamics are dominated by over-damped picosecond motions of the inorganic PbBr3- sub-lattice and these motions are strongly coupled to band-gap electronic transitions. Carrier injection from across-gap optical excitation triggers additional 0.26 ps dynamics in CH3NH3PbBr3 that can be attributed to the formation of large polarons. In comparison, large polaron formation is slower in CsPbBr3 with a time constant of 0.6 ps. We discuss how such dynamic screening protects charge carriers in lead halide perovskites. US Department of Energy, Office of Science - Basic Energy Sciences.

  11. Diagrammatic Monte Carlo study of Fröhlich polaron dispersion in two and three dimensions

    Science.gov (United States)

    Hahn, Thomas; Klimin, Sergei; Tempere, Jacques; Devreese, Jozef T.; Franchini, Cesare

    2018-04-01

    We present results for the solution of the large polaron Fröhlich Hamiltonian in 3 dimensions (3D) and 2 dimensions (2D) obtained via the diagrammatic Monte Carlo (DMC) method. Our implementation is based on the approach by Mishchenko [A. S. Mishchenko et al., Phys. Rev. B 62, 6317 (2000), 10.1103/PhysRevB.62.6317]. Polaron ground state energies and effective polaron masses are successfully benchmarked with data obtained using Feynman's path integral formalism. By comparing 3D and 2D data, we verify the analytically exact scaling relations for energies and effective masses from 3 D →2 D , which provides a stringent test for the quality of DMC predictions. The accuracy of our results is further proven by providing values for the exactly known coefficients in weak- and strong-coupling expansions. Moreover, we compute polaron dispersion curves which are validated with analytically known lower and upper limits in the small-coupling regime and verify the first-order expansion results for larger couplings, thus disproving previous critiques on the apparent incompatibility of DMC with analytical results and furnishing useful reference for a wide range of coupling strengths.

  12. Evidence for polaron conduction in nanostructured manganese ferrite

    International Nuclear Information System (INIS)

    Gopalan, E Veena; Anantharaman, M R; Malini, K A; Saravanan, S; Kumar, D Sakthi; Yoshida, Yasuhiko

    2008-01-01

    Nanoparticles of manganese ferrite were prepared by the chemical co-precipitation technique. The dielectric parameters, namely, real and imaginary dielectric permittivity (ε' and ε-prime), ac conductivity (σ ac ) and dielectric loss tangent (tanδ), were measured in the frequency range of 100 kHz-8 MHz at different temperatures. The variations of dielectric dispersion (ε') and dielectric absorption (ε-prime) with frequency and temperature were also investigated. The variation of dielectric permittivity with frequency and temperature followed the Maxwell-Wagner model based on interfacial polarization in consonance with Koops phenomenological theory. The dielectric loss tangent and hence ε-prime exhibited a relaxation at certain frequencies and at relatively higher temperatures. The dispersion of dielectric permittivity and broadening of the dielectric absorption suggest the possibility of a distribution of relaxation time and the existence of multiple equilibrium states in manganese ferrite. The activation energy estimated from the dielectric relaxation is found to be high and is characteristic of polaron conduction in the nanosized manganese ferrite. The ac conductivity followed a power law dependence σ ac = Bω n typical of charge transport assisted by a hopping or tunnelling process. The observed minimum in the temperature dependence of the frequency exponent n strongly suggests that tunnelling of the large polarons is the dominant transport process

  13. 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.

  14. Magnon-polaron transport in magnetic insulators

    Science.gov (United States)

    Flebus, Benedetta; Shen, Ka; Kikkawa, Takashi; Uchida, Ken-ichi; Qiu, Zhiyong; Saitoh, Eiji; Duine, Rembert A.; Bauer, Gerrit E. W.

    2017-04-01

    We theoretically study the effects of strong magnetoelastic coupling on the transport properties of magnetic insulators. We develop a Boltzmann transport theory for the mixed magnon-phonon modes ("magnon polarons") and determine transport coefficients and the spin diffusion length. Magnon-polaron formation causes anomalous features in the magnetic field and temperature dependence of the spin Seebeck effect when the disorder scattering in the magnetic and elastic subsystems is sufficiently different. Experimental data by Kikkawa et al. [Phys. Rev. Lett. 117, 207203 (2016), 10.1103/PhysRevLett.117.207203] on yttrium iron garnet films can be explained by an acoustic quality that is much better than the magnetic quality of the material. We predict similar anomalous features in the spin and heat conductivity and nonlocal spin transport experiments.

  15. Magnetic polarons in a nonequilibrium polariton condensate

    Science.gov (United States)

    Mietki, Paweł; Matuszewski, Michał

    2017-09-01

    We consider a condensate of exciton polaritons in a diluted magnetic semiconductor microcavity. Such a system may exhibit magnetic self-trapping in the case of sufficiently strong coupling between polaritons and magnetic ions embedded in the semiconductor. We investigate the effect of the nonequilibrium nature of exciton polaritons on the physics of the resulting self-trapped magnetic polarons. We find that multiple polarons can exist at the same time, and we derive a critical condition for self-trapping that is different from the one predicted previously in the equilibrium case. Using the Bogoliubov-de Gennes approximation, we calculate the excitation spectrum and provide a physical explanation in terms of the effective magnetic attraction between polaritons, mediated by the ion subsystem.

  16. 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

  17. 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...

  18. 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…

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

    Science.gov (United States)

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

    2018-01-01

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

  20. Displacement of polarons by vibrational modes in doped conjugated polymers

    NARCIS (Netherlands)

    Anderson, M.; Ramanan, C.; Fontanesi, C.; Frick, A.; Surana, S.; Cheyns, D.; Furno, M.; Keller, T.; Allard, S.; Scherf, U.; Beljonne, D.; D'Avino, G.; von Hauff, E.; Da Como, E.

    2017-01-01

    Organic pi-conjugated polymers are deemed to be soft materials with strong electron-phonon coupling, which results in the formation of polarons, i.e., charge carriers dressed by self-localized distortion of the nuclei. Universal signatures for polarons are optical resonances below the band gap and

  1. Small-polaron formation and motion in magnetic semiconductors

    International Nuclear Information System (INIS)

    Emin, D.

    1979-01-01

    The fundamental physical processes associated with small-polaron formation are described with various magnetic semi-conductors being cited as examples. Attention is then directed toward the mechanisms of charge transfer and small-polaron hopping motion in magnetic semiconductors

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

    Science.gov (United States)

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

    2015-03-01

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

  3. 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

  4. Effect of valence nucleons on nuclear binding energy

    Energy Technology Data Exchange (ETDEWEB)

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

    1991-10-01

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

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

    Indian Academy of Sciences (India)

    Administrator

    Abstract. The binding energy of an impurity delta layer situated either in the centre or at the edge of a quantum well (QW) is theoretically considered for the example of n-type Si0∙8Ge0∙2/Si/Si0∙8Ge0∙2 QW doped with phosphorus. Calculations are made for the case of not so big impurity concentrations, when impurity.

  6. Creation of Rydberg Polarons in a Bose Gas

    Science.gov (United States)

    Schmidt, Richard

    2017-04-01

    In this talk we review the theory of various types of Bose polarons that can be realized in ultracold atomic systems. We then report the spectroscopic observation of Rydberg polarons in a Bose gas which is in excellent agreement with theoretical predictions. This novel type of polaron is created by excitation of Rydberg atoms in a strontium Bose-Einstein condensate and it is distinguished by the occupation of a large number bound molecular states. The cross-over from few-body bound molecular oligomers to many-body polaron features is described with a functional determinant theory that solves an extended Froehlich Hamiltonian for an impurity in a Bose gas. The detailed analysis of the red-detuned tail of the excitation spectrum describes the contribution from the region of highest density in the condensate and provides a clear signature of Rydberg polarons. This work has been performed in collaboration with groups at Rice University, Harvard University, and the TU Vienna.

  7. Weak coupling polaron and Landau-Zener scenario: Qubits modeling

    Science.gov (United States)

    Jipdi, M. N.; Tchoffo, M.; Fokou, I. F.; Fai, L. C.; Ateuafack, M. E.

    2017-06-01

    The paper presents a weak coupling polaron in a spherical dot with magnetic impurities and investigates conditions for which the system mimics a qubit. Particularly, the work focuses on the Landau-Zener (LZ) scenario undergone by the polaron and derives transition coefficients (transition probabilities) as well as selection rules for polaron's transitions. It is proven that, the magnetic impurities drive the polaron to a two-state superposition leading to a qubit structure. We also showed that the symmetry deficiency induced by the magnetic impurities (strong magnetic field) yields to the banishment of transition coefficients with non-stacking states. However, the transition coefficients revived for large confinement frequency (or weak magnetic field) with the orbital quantum numbers escorting transitions. The polaron is then shown to map a qubit independently of the number of relevant states with the transition coefficients lifted as LZ probabilities and given as a function of the electron-phonon coupling constant (Fröhlich constant).

  8. Soliton and polaron generation in polyacetylene

    International Nuclear Information System (INIS)

    Su, Zhao-bin; Yu, Lu.

    1984-07-01

    The nonradiative decay of an e-h pair into soliton pair and that of an electron (hole) into polaron as well as the photoproduction of soliton pairs are considered using the lattice relaxation theory of multiphonon processes generalized to include the self-consistency of the multi-electron states with the lattice symmetry breaking. The selection rule which forbids the direct process of photogeneration for neutral pair is derived from the symmetry arguments. The branching ratio of the photogenerated neutral to charged soliton pairs is estimated. The recent related experiments are discussed. (author)

  9. Effects of interaction and disorder on polarons in colossal resistance manganite Pr0.68Ca0.32MnO3 thin films

    Science.gov (United States)

    Hoffmann, J.; Moschkau, P.; Mildner, S.; Norpoth, J.; Jooss, Ch; Wu, L.; Zhu, Y.

    2014-12-01

    The colossal magnetoresistance effect (CMR), the drop of the electric resistance by orders of magnitude in a strong magnetic field, is a fascinating property of strongly correlated electrons in doped manganites. Here, we present a detailed analysis of the magnetotransport properties of small polarons in thin films of the low bandwidth manganite Pr0.68Ca0.32MnO3 with different degrees of preparation-induced octahedral disorder. The crystal and defect structure is investigated by means of high-resolution transmission electron microscopy. We apply the small polaron theory developed by Firsov and Lang in order to study the hopping mobility in the paramagnetic phase and its changes due to the formation of the antiferromagnetic charge ordered (CO) and the ferromagnetic metallic phases. Although it represents a single particle theory, reasonable estimates of small polaron properties such as formation energy, activation energy and transfer integral are possible, if the effects of interactions and disorder are taken into account. Beyond the well-known effect of the magnetic double exchange on the transfer integral, we show that the emergence of band transport of small polarons in the CMR transition sensibly depends on the degree of octahedral disorder, the polaron-polaron interactions and the resulting long range order leading to a structural phase transition in the CO phase.

  10. The effect of interface hopping on inelastic scattering of oppositely charged polarons in polymers

    International Nuclear Information System (INIS)

    Di Bing; Wang Ya-Dong; Zhang Ya-Lin; An Zhong

    2013-01-01

    The inelastic scattering of oppositely charge polarons in polymer heterojunctions is believed to be of fundamental importance for the light-emitting and transport properties of conjugated polymers. Based on the tight-binding SSH model, and by using a nonadiabatic molecular dynamic method, we investigate the effects of interface hopping on inelastic scattering of oppositely charged polarons in a polymer heterojunction. It is found that the scattering processes of the charge and lattice defect depend sensitively on the hopping integrals at the polymer/polymer interface when the interface potential barrier and applied electric field strength are constant. In particular, at an intermediate electric field, when the interface hopping integral of the polymer/polymer heterojunction material is increased beyond a critical value, two polarons can combine to become a lattice deformation in one of the two polymer chains, with the electron and the hole bound together, i.e., a self-trapped polaron—exciton. The yield of excitons then increases to a peak value. These results show that interface hopping is of fundamental importance and facilitates the formation of polaron—excitons

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. Polaronic localisation of an electron in a magnetic field

    International Nuclear Information System (INIS)

    Aubry, S.

    1994-01-01

    When a uniform magnetic field is applied to a single electron in 2D and 3D continuous and elastically deformable medium, a polaronic self localisation occurs at any small coupling although it does not without magnetic field. In 3D, there is also a first order transition as a function of the magnetic field corresponding to the collapse of the large polaron into a small polaron. The discrete lattice effect were numerically investigated in 2D for completing this picture. It is suggested that strong anisotropies in real systems could brought these phenomena in the physically observable range. (author). 6 refs., 5 figs

  17. Holstein polarons and triplet bipolarons with NNN hopping

    Science.gov (United States)

    Chakraborty, Monodeep; Taraphder, A.; Berciu, Mona

    2017-05-01

    We study the ground state of 1D Holstein single polaron with next nearest neighbour electron hopping (NNN), employing a variational approximation based on exact diagonalization. Our investigation reveals that, depending upon the sign and magnitude of the NNN hopping integral with respect to nearest neighbour hopping, the polaron band minima may occur at non-zero kGS. We compare the present scenario with the SSH polarons, where a similar feature is also observed, albeit, due to very different mechanism. Our initial investigation of triplet bipolarons, in presence of an attractive extended Hubbard interactions, further substantiates the differences between the present model and the SSH model.

  18. Understanding Birnessite MnO2: Effects of Small Polaron and Local Dipole

    Science.gov (United States)

    Peng, Haowei; Perdew, John P.

    Birnessite MnO2, usually with cations like K and Na intercalated between layers, is a class of potential cheap oxygen evolution reaction (OER) catalyst. Using hybrid density functional calculations, we investigate the electronic structures of the layered MnO2 with the intercalated cation modelled as a defect. We found that an electron small polaron will form when an extra electron is doped in the pure MnO2, turning a Mn(IV) to a Mn(III) with a singly occupied eg orbital located within the band gap, and the resulting small-polaron hopping conduction explains the observed low electric conductivity. The inter-layer doped K atom will donate one electron to one Mn ion as expected, and also contributes to a local dipole forming between K and the Mn(III), raising the electrostatic potential of the specific layer. With a certain spatial distribution of such local dipoles, the small-polaron eg states become comparable in energy with the global conduction band minimum, and charge transfer occurs. This further results in a singly or partially occupied eg orbital near the Fermi level, which has been regarded as a signal for an excellent OER catalyst. Our calculation helps understanding several experimental observations. This work was supported as part of the CCDM-EFRC funded by the U.S. DOE, Office of Science, Basic Energy Sciences.

  19. Effect of defects on the small polaron formation and transport properties of hematite from first-principles calculations.

    Science.gov (United States)

    Smart, Tyler J; Ping, Yuan

    2017-10-04

    Hematite (α-Fe 2 O 3 ) is a promising candidate as a photoanode material for solar-to-fuel conversion due to its favorable band gap for visible light absorption, its stability in an aqueous environment and its relatively low cost in comparison to other prospective materials. However, the small polaron transport nature in α-Fe 2 O 3 results in low carrier mobility and conductivity, significantly lowering its efficiency from the theoretical limit. Experimentally, it has been found that the incorporation of oxygen vacancies and other dopants, such as Sn, into the material appreciably enhances its photo-to-current efficiency. Yet no quantitative explanation has been provided to understand the role of oxygen vacancy or Sn-doping in hematite. We employed density functional theory to probe the small polaron formation in oxygen deficient hematite, N-doped as well as Sn-doped hematite. We computed the charged defect formation energies, the small polaron formation energy and hopping activation energies to understand the effect of defects on carrier concentration and mobility. This work provides us with a fundamental understanding regarding the role of defects on small polaron formation and transport properties in hematite, offering key insights into the design of new dopants to further improve the efficiency of transition metal oxides for solar-to-fuel conversion.

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

    CERN Document Server

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

    2001-01-01

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

  1. 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.

  2. Spin polaron in the J1-J2 Heisenberg model

    Science.gov (United States)

    Hamad, I. J.; Trumper, A. E.; Feiguin, A. E.; Manuel, L. O.

    2008-01-01

    We have studied the validity of the spin-polaron picture in the frustrated J1-J2 Heisenberg model. For this purpose, we have computed the hole spectral functions for the Néel, collinear, and disordered phases of this model by means of the self-consistent Born approximation and Lanczos exact diagonalization on finite-size clusters. We have found that the spin-polaron quasiparticle excitation is always well defined for the magnetically ordered Néel and collinear phases, even in the vicinity of the magnetic quantum critical points, where the local magnetization vanishes. As a general feature, the effect of frustration is to increase the amplitude of the multimagnon states that build up the spin-polaron wave function, leading to the reduction of the quasiparticle coherence. Based on Lanczos results, we discuss the validity of the spin-polaron picture in the disordered phase.

  3. Importance of polaron effects for charge carrier mobility above and ...

    Indian Academy of Sciences (India)

    HTSCs) have been investigated theoretically. The appropriate Boltzmann transport equations under relaxation time approximation were used to calculate the mobility of polaronic charge carriers and bosonic Cooper pairs above and below the ...

  4. Watching the coherent birth of polaron pairs in conjugated polymers

    OpenAIRE

    De Sio, Antonietta; Troiani, Filippo; Maiuri, Margherita; Réhault, Julien; Sommer, Ephraim; Lim, James; Huelga, Susana F.; Plenio, Martin B.; Rozzi, Carlo Andrea; Cerullo, Giulio; Molinari, Elisa; Lienau, Christoph

    2016-01-01

    Organic semiconductors have the remarkable property that their optical excitation not only generates charge-neutral electron-hole pairs (excitons) but also charge-separated polaron pairs with high yield. The microscopic mechanisms underlying this charge separation have been debated for many years. Here we use ultrafast two-dimensional electronic spectroscopy to study the dynamics of polaron pair formation in a prototypical polymer thin film on a sub-20-fs time scale. We observe multi-period p...

  5. Polarons, free charge localisation and effective dielectric permittivity in oxides

    OpenAIRE

    Maglione, Mario

    2010-01-01

    This review will deal with several types of free charge localisation in oxides and their consequences on the effective dielectric spectra of such materials. The first one is the polaronic localisation at the unit cell scale on residual impurities in ferroelectric networks. The second one is the collective localisation of free charge at macroscopic interfaces like surfaces, electrodes and grain boundaries in ceramics. Polarons have been observed in many oxide perovskites mostly when cations ha...

  6. Polaron self-localization in white-light emitting hybrid perovskites

    KAUST Repository

    Cortecchia, Daniele

    2017-02-03

    Two-dimensional (2D) perovskites with the general formula APbX are attracting increasing interest as solution processable, white-light emissive materials. Recent studies have shown that their broadband emission is related to the formation of intra-gap colour centres. Here, we provide an in-depth description of the charge localization sites underlying the generation of such radiative centres and their corresponding decay dynamics, highlighting the formation of small polarons trapped within their lattice distortion field. Using a combination of spectroscopic techniques and first-principles calculations to study the white-light emitting 2D perovskites (EDBE)PbCl and (EDBE)PbBr, we infer the formation of Pb , Pb, and X (where X = Cl or Br) species confined within the inorganic perovskite framework. Due to strong Coulombic interactions, these species retain their original excitonic character and form self-trapped polaron-excitons acting as radiative colour centres. These findings are expected to be relevant for a broad class of white-light emitting perovskites with large polaron relaxation energy.

  7. Thermodynamics of the polaron master equation at finite bias

    International Nuclear Information System (INIS)

    Krause, Thilo; Brandes, Tobias; Schaller, Gernot; Esposito, Massimiliano

    2015-01-01

    We study coherent transport through a double quantum dot. Its two electronic leads induce electronic matter and energy transport and a phonon reservoir contributes further energy exchanges. By treating the system-lead couplings perturbatively, whereas the coupling to vibrations is treated non-perturbatively in a polaron-transformed frame, we derive a thermodynamic consistent low-dimensional master equation. When the number of phonon modes is finite, a Markovian description is only possible when these couple symmetrically to both quantum dots. For a continuum of phonon modes however, also asymmetric couplings can be described with a Markovian master equation. We compute the electronic current and dephasing rate. The electronic current enables transport spectroscopy of the phonon frequency and displays signatures of Franck-Condon blockade. For infinite external bias but finite tunneling bandwidths, we find oscillations in the current as a function of the internal bias due to the electron-phonon coupling. Furthermore, we derive the full fluctuation theorem and show its identity to the entropy production in the system

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

    Science.gov (United States)

    Qi, Chong

    2012-10-01

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

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

    NARCIS (Netherlands)

    Harmsen, Robert; Eichhammer, Wolfgang; Wesselink, Bart

    2014-01-01

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

  10. Exploring Polaronic, Excitonic Structures and Luminescence in Cs4PbBr6/CsPbBr3.

    Science.gov (United States)

    Kang, Byungkyun; Biswas, Koushik

    2018-02-15

    Among the important family of halide perovskites, one particular case of all-inorganic, 0-D Cs 4 PbBr 6 and 3-D CsPbBr 3 -based nanostructures and thin films is witnessing intense activity due to ultrafast luminescence with high quantum yield. To understand their emissive behavior, we use hybrid density functional calculations to first compare the ground-state electronic structure of the two prospective compounds. The dispersive band edges of CsPbBr 3 do not support self-trapped carriers, which agrees with reports of weak exciton binding energy and high photocurrent. The larger gap 0-D material Cs 4 PbBr 6 , however, reveals polaronic and excitonic features. We show that those lattice-coupled carriers are likely responsible for observed ultraviolet emission around ∼375 nm, reported in bulk Cs 4 PbBr 6 and Cs 4 PbBr 6 /CsPbBr 3 composites. Ionization potential calculations and estimates of type-I band alignment support the notion of quantum confinement leading to fast, green emission from CsPbBr 3 nanostructures embedded in Cs 4 PbBr 6 .

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

    Science.gov (United States)

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

    2011-10-18

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

  13. 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.

  14. Superconducting pairing of spin polarons in the t - J model

    International Nuclear Information System (INIS)

    Plakida, N.M.; Horsch, P.; Liechtenstein, A.; Oudovenko, V.S.

    1995-07-01

    A spin polaron model derived from the t - J model on a two-sublattice antiferromagnet is considered. The self-consistent Born approximation for the matrix Green functions for doped holes (spin polarons) and magnons is used to study temperature and doping dependence of the quasi-particle hole spectrum and superconducting pairing of two holes on different sublattices. A numerical solution of the self-consistent system of equations by the fast Fourier transformation method shows a strong renormalization of the quasi-particle hole spectrum due to spin fluctuations, and a singlet superconducting pairing of d-wave symmetry with maximal T c ∼ 0.01t around the hole concentration 0.25. We argue that the superconducting pairing of spin polarons for the model with strong electron correlations represents the mechanism of high-temperature superconductivity. (author). 26 refs, 10 figs

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

    Science.gov (United States)

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

    2008-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-03-12

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

  17. Inelastic scattering in a local polaron model with quadratic coupling to bosons

    DEFF Research Database (Denmark)

    Olsen, Thomas

    2009-01-01

    We calculate the inelastic scattering probabilities in the wide band limit of a local polaron model with quadratic coupling to bosons. The central object is a two-particle Green's function which is calculated exactly using a purely algebraic approach. Compared with the usual linear interaction term...... a quadratic interaction term gives higher probabilities for inelastic scattering involving a large number of bosons. As an application we consider the problem hot-electron-mediated energy transfer at surfaces and use the delta self-consistent field extension of density-functional theory to calculate...

  18. Problems of linear electron (polaron) transport theory in semiconductors

    CERN Document Server

    Klinger, M I

    1979-01-01

    Problems of Linear Electron (Polaron) Transport Theory in Semiconductors summarizes and discusses the development of areas in electron transport theory in semiconductors, with emphasis on the fundamental aspects of the theory and the essential physical nature of the transport processes. The book is organized into three parts. Part I focuses on some general topics in the theory of transport phenomena: the general dynamical theory of linear transport in dissipative systems (Kubo formulae) and the phenomenological theory. Part II deals with the theory of polaron transport in a crystalline semicon

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

    DEFF Research Database (Denmark)

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

    2002-01-01

    The biexciton binding energy E-XX is investigated in ZnSe/ZnMgSe quantum wells and quantum wires as a function of the lateral confinement by transient four-wave mixing. In the quantum wells one observes for decreasing well width a significant increase in the relative binding energy, saturating fo...

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

    Directory of Open Access Journals (Sweden)

    Manuela Maurer

    2016-04-01

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

  1. Many-body interferometry of magnetic polaron dynamics

    Science.gov (United States)

    Ashida, Yuto; Schmidt, Richard; Tarruell, Leticia; Demler, Eugene

    2018-02-01

    The physics of quantum impurities coupled to a many-body environment is among the most important paradigms of condensed-matter physics. In particular, the formation of polarons, quasiparticles dressed by the polarization cloud, is key to the understanding of transport, optical response, and induced interactions in a variety of materials. Despite recent remarkable developments in ultracold atoms and solid-state materials, the direct measurement of their ultimate building block, the polaron cloud, has remained a fundamental challenge. We propose and analyze a platform to probe time-resolved dynamics of polaron-cloud formation with an interferometric protocol. We consider an impurity atom immersed in a two-component Bose-Einstein condensate where the impurity generates spin-wave excitations that can be directly measured by the Ramsey interference of surrounding atoms. The dressing by spin waves leads to the formation of magnetic polarons and reveals a unique interplay between few- and many-body physics that is signified by single- and multi-frequency oscillatory dynamics corresponding to the formation of many-body bound states. Finally, we discuss concrete experimental implementations in ultracold atoms.

  2. Transport through a vibrating quantum dot: Polaronic effects

    Czech Academy of Sciences Publication Activity Database

    Koch, T.; Loos, Jan; Alvermann, A.; Bishop, A. R.; Fehske, H.

    2010-01-01

    Roč. 220, č. 1 (2010), 012014/1-012014/9 ISSN 1742-6588 Institutional research plan: CEZ:AV0Z10100521 Keywords : quantum dot, * polaronic effects * low-temperature transport properties Subject RIV: BM - Solid Matter Physics ; Magnetism

  3. Numerical calculation of path integrals : The small-polaron model

    NARCIS (Netherlands)

    Raedt, Hans De; Lagendijk, Ad

    1983-01-01

    The thermodynamic properties of the small-polaron model are studied by means of a discrete version of the Feynman path-integral representation of the partition function. This lattice model describes a fermion interacting with a boson field. The bosons are treated analytically, the fermion

  4. Critical Quantum Fluctuations and Localization of the Small Polaron

    NARCIS (Netherlands)

    Raedt, Hans De; Lagendijk, Ad

    1982-01-01

    The first quantitative evidence of critical quantum fluctuations and superlocalization of the small polaron model in one, two, and three dimensions is presented. Starting from a discrete version of the Feynman path-integral representation of the partition function, the boson field is eliminated

  5. Polaron variable range hopping in TiO2-δ(-0.04=<δ=<0.2) thin films

    International Nuclear Information System (INIS)

    Heluani, S.P.; Comedi, D.; Villafuerte, M.; Juarez, G.

    2007-01-01

    The mechanisms of electrical conduction in TiO 2-δ (-0.04= 2 +Ar gas atmospheres where changes in δ and film structure had been achieved by varying the O 2 flow rate and the substrate temperature. The electrical transport properties of these samples were investigated by measuring the conductivity as a function of temperature between 17K and room temperature. At the temperature range between 200 and 290K the best fit to the experimental data was obtained assuming a dependence characteristic of adiabatic variable range hopping. At lower temperature the activation energy for the conductivity tends to zero. The results suggest that the conduction mechanism is adiabatic small polaron hopping, which switches to conduction in a polaron band at low temperatures

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-01-10

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

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

    NARCIS (Netherlands)

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

    2012-01-01

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

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

    Science.gov (United States)

    Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

    2018-03-14

    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.

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

    Science.gov (United States)

    Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

    2018-03-01

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

  10. 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 ...

  11. 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 ...

  12. Density functional theory + U modeling of polarons in organohalide lead perovskites

    Directory of Open Access Journals (Sweden)

    Eric Welch

    2016-12-01

    Full Text Available We investigate the possible formation of polarons in four organic perovskites (CH3NH3PbI3, CH3NH3PbBr3, CH3NH3PbCl3, and CH3NH3PbI2Cl1 using a density functional theory (DFT calculations with local potentials and hybrid functionals. We show that DFT+U method with U = 8 eV predicts a correct band-gap and matches the forces on ions from hybrid calculations. We then use the DFT + U approach to study the effect of polarons, i.e. to search the configuration space and locate the lowest energy localized band gap state self-trapped hole (STH. STH configurations were found for three pure halides and one mixed halide system. Spin orbit coupling (SOC was also taken into account and the results may be found in the supplementary material. This study focuses on the +U method; however, SOC corrections added to the DFT+U calculations also resulted in STH states in all four systems.

  13. Polaron effects on the dc- and ac-tunneling characteristics of molecular Josephson junctions

    Science.gov (United States)

    Wu, B. H.; Cao, J. C.; Timm, C.

    2012-07-01

    We study the interplay of polaronic effect and superconductivity in transport through molecular Josephson junctions. The tunneling rates of electrons are dominated by vibronic replicas of the superconducting gap, which show up as prominent features in the differential conductance for the dc and ac current. For relatively large molecule-lead coupling, a features that appears when the Josephson frequency matches the vibron frequency can be identified with an over-the-gap structure observed by Marchenkov [Nat. Nanotech. 1748-338710.1038/nnano.2007.2182, 481 (2007)]. However, we are more concerned with the weak-coupling limit, where resonant tunneling through the molecular level dominates. We find that certain features involving both Andreev reflection and vibron emission show an unusual shift of the bias voltage V at their maximum with the gate voltage Vg as V˜(2/3)Vg. Moreover, due to the polaronic effect, the ac Josephson current shows a phase shift of π when the bias eV is increased by one vibronic energy quantum ℏωv. This distinctive even-odd effect is explained in terms of the different sign of the coupling to vibrons of electrons and of Andreev-reflected holes.

  14. Appearance of small polaron hopping conduction in iron modified cobalt lithium bismuth borate glasses

    Energy Technology Data Exchange (ETDEWEB)

    Dahiya, M. S.; Khasa, S., E-mail: skhasa@yahoo.com; Yadav, Arti [Physics Department, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, India-131039 (India); Agarwal, A. [Applied Physics Department, Guru Jambheshwara University of Science and Technology, Hisar, India-125001 (India)

    2016-05-23

    Lithium bismuth borate glasses containing different amounts of cobalt and iron oxides having chemical composition xFe{sub 2}O{sub 3}•(20-x)CoO•30Li{sub 2}O•10Bi{sub 2}O{sub 3}•40B{sub 2}O{sub 3} (x = 0, 5, 10, 15 and 20 mol% abbreviated as CFLBB1-5 respectively) prepared via melt quench technique have been investigated for their dc electrical conductivity. The amorphous nature of prepared glasses has been confirmed through X-ray diffraction measurements. The dc electrical conductivity has been analyzed by applying Mott’s small polaron hopping model. Activation energies corresponding to lower and higher temperature region have been evaluated. The iron ion concentration (N), mean spacing between iron ions (R) and polaron radius (R{sub p}) has been evaluated using the values of phonon radius (R{sub ph}) and Debye temperature (θ{sub D}). The glass sample without iron (CFLBB1) shows ionic conductivity but the incorporation of iron in the glass matrix results in the appearance of electronic conductivity.

  15. Polarons and Mobile Impurities Near a Quantum Phase Transition

    Science.gov (United States)

    Shadkhoo, Shahriar

    This dissertation aims at improving the current understanding of the physics of mobile impurities in highly correlated liquid-like phases of matter. Impurity problems pose challenging and intricate questions in different realms of many-body physics. For instance, the problem of ''solvation'' of charged solutes in polar solvents, has been the subject of longstanding debates among chemical physicists. The significant role of quantum fluctuations of the solvent, as well as the break down of linear response theory, render the ordinary treatments intractable. Inspired by this complicated problem, we first attempt to understand the role of non-specific quantum fluctuations in the solvation process. To this end, we calculate the dynamic structure factor of a model polar liquid, using the classical Molecular Dynamics (MD) simulations. We verify the failure of linear response approximation in the vicinity of a hydrated electron, by comparing the outcomes of MD simulations with the predictions of linear response theory. This nonlinear behavior is associated with the pronounced peaks of the structure factor, which reflect the strong fluctuations of the local modes. A cavity picture is constructed based on heuristic arguments, which suggests that the electron, along with the surrounding polarization cloud, behave like a frozen sphere, for which the linear response theory is broken inside and valid outside. The inverse radius of the spherical region serves as a UV momentum cutoff for the linear response approximation to be applicable. The problem of mobile impurities in polar liquids can be also addressed in the framework of the ''polaron'' problem. Polaron is a quasiparticle that typically acquires an extended state at weak couplings, and crossovers to a self-trapped state at strong couplings. Using the analytical fits to the numerically obtained charge-charge structure factor, a phenomenological approach is proposed within the Leggett's influence functional formalism, which

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

    Science.gov (United States)

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

    2008-12-01

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

  17. 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/.

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

    Indian Academy of Sciences (India)

    Nilanjan Sil

    2017-12-18

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

  19. Charged Polaron Polaritons in an Organic Semiconductor Microcavity

    Science.gov (United States)

    Cheng, Chiao-Yu; Dhanker, Rijul; Gray, Christopher L.; Mukhopadhyay, Sukrit; Kennehan, Eric R.; Asbury, John B.; Sokolov, Anatoliy; Giebink, Noel C.

    2018-01-01

    We report strong coupling between light and polaron optical excitations in a doped organic semiconductor microcavity at room temperature. Codepositing MoO3 and the hole transport material 4, 4' -cyclohexylidenebis[N , N -bis(4-methylphenyl)benzenamine] introduces a large hole density with a narrow linewidth optical transition centered at 1.8 eV and an absorption coefficient exceeding 104 cm-1 . Coupling this transition to a Fabry-Pérot cavity mode yields upper and lower polaron polariton branches that are clearly resolved in angle-dependent reflectivity with a vacuum Rabi splitting ℏ ΩR>0.3 eV . This result establishes a path to electrically control polaritons in organic semiconductors and may lead to increased polariton-polariton Coulombic interactions that lower the threshold for nonlinear phenomena such as polariton condensation and lasing.

  20. Optical Detection of Polarons in High - Tc Cuprate

    International Nuclear Information System (INIS)

    Calvani, P.; Capizzi, M.; Lupi, S.; Maselli, P.; Paolone, A.; Roy LURE, P.; Berger, H.

    1995-01-01

    The optical conductivity σ (ω) of slightly e-doped single-crystals of (Nd,Gd) 2 CuO 4-y shows local modes in the far-infrared as well as a broad infrared absorption centered at ∼ 0.1 eV (d-band). This latter shows a fine structure, in agreement with recent calculations of Alexandrov et al., which is made up by intense overtones of the local modes observed in the far-infrared. Similar polaronic structures are shown to exist in the normal metallic phase of Nd 2-x Ce x CuO 4-y and even in the σ (ω ) of YBCO crystals, measured by different authors. The present observations provide evidence for the existence of small polarons in all materials with a Cu-O plane

  1. Absolute instability of polaron mode in semiconductor magnetoplasma

    Science.gov (United States)

    Paliwal, Ayushi; Dubey, Swati; Ghosh, S.

    2018-01-01

    Using coupled mode theory under hydrodynamic regime, a compact dispersion relation is derived for polaron mode in semiconductor magnetoplasma. The propagation and amplification characteristics of the wave are explored in detail. The analysis deals with the behaviour of anomalous threshold and amplification derived from dispersion relation, as function of external parameters like doping concentration and applied magnetic field. The results of this investigation are hoped to be useful in understanding electron-longitudinal optical phonon interplay in polar n-type semiconductor plasmas under the influence of coupled collective cyclotron excitations. The best results in terms of smaller threshold and higher gain of polaron mode could be achieved by choosing moderate doping concentration in the medium at higher magnetic field. For numerical appreciation of the results, relevant data of III-V n-GaAs compound semiconductor at 77 K is used. Present study provides a qualitative picture of polaron mode in magnetized n-type polar semiconductor medium duly shined by a CO2 laser.

  2. Electron localization, polarons and clustered states in manganites

    International Nuclear Information System (INIS)

    Mannella, N.

    2004-01-01

    Full text: A recent multi-spectroscopic study of prototypical colossal magnetoresistance (CMR) compounds La 1-x Sr x MnO 3 (LSMO, x = 0.3, 0.4) using photoemission (PE), x-ray absorption (XAS), x-ray emission (XES) and extended x-ray absorption e structure (EXAFS) has exposed a dramatic change in the electronic structure on crossing the ferromagnetic-to-paramagnetic transition temperature (T C ). In particular, this investigation revealed an increase of the Mn magnetic moment by ca. 1 Bohr magneton and charge transfer to the Mn atom on crossing T C concomitant with the presence of Jahn-Teller distortions, thus providing direct evidence of lattice polaron formation. These results thus challenge the belief of some authors that the LSMO compounds are canonical double-exchange (DE) systems in which polaron formation is unimportant, and thus help to unify the theoretical description of the CMR oxides. The relationship of these data to other recent work suggesting electron localization, polarons and phase separation, along with additional measurements of magnetic susceptibility indicating the formation of ferromagnetic clusters in the metallic paramagnetic state above T C will be discussed

  3. Non-linear polaronic conduction in magnetite nanowires

    International Nuclear Information System (INIS)

    Singh, Pooja; Rout, P.K.; Husale, Sudhir; Gupta, Anurag; Singh, Manju; Rakshit, R.K.; Dogra, Anjana

    2016-01-01

    We report the temperature dependent current (I) – voltage (V) characteristics of Fe 3 O 4 nanowires with varying width (w) of 132, 358, and 709 nm. While the widest nanowire (w=709 nm) shows ohmic I (V) curves for all temperatures, those for w=132 and 358 nm show nonlinearity, which can be expressed by a combination of linear (V) and cubic (V 3 ) terms. The behaviour of conductance (linear bias component of current) and non-linearity in these nanowires is related to small polaron hopping related conduction. Moreover, we observed an anomalously large hopping lengths, which may be related to the size of percolation cluster and/or antiphase domain. Our study presents first experimental evidence for such non-linear polaronic conduction in magnetite nanowires. - Highlights: • Temperature dependent I–V measurements of FIB fabricated magnetite nanowires. • Small polaron based conduction in non-linear I–V curves. • Anomalously large hopping lengths due to percolation effect and/or antiphase domains.

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

    Science.gov (United States)

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

    2017-07-01

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

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

    Indian Academy of Sciences (India)

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

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

    African Journals Online (AJOL)

    KEN

    2007-02-05

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

  7. 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

  8. Hypernuclear interactions and the binding energies of and hypernuclei

    Energy Technology Data Exchange (ETDEWEB)

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

    1988-01-01

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

  9. 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

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

    Science.gov (United States)

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

    2008-11-01

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

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

    Science.gov (United States)

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

    2016-01-01

    We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations. © 2015 The Protein Society.

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

    Science.gov (United States)

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

    2017-03-01

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

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

    DEFF Research Database (Denmark)

    Greeley, Jeffrey Philip; Nørskov, Jens Kehlet

    2005-01-01

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

  14. 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.

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

    Science.gov (United States)

    Myerson, Allan S.; Jang, Shyh M.

    1995-12-01

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

  16. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1985-01-01

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

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

    Science.gov (United States)

    Fahr, Hans-Jörg; Sokaliwska, Michael

    2012-06-01

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

  19. Polaron dynamics in molecular polysilane wires

    Czech Academy of Sciences Publication Activity Database

    Nešpůrek, Stanislav; Nožár, Juraj; Šebera, Jakub

    2011-01-01

    Roč. 15, Suppl. 2 (2011), s. 232-235 ISSN 1432-8917. [International Conference on Functional Materials and Devices /3./. Terengganu, 13.06.2010-17.06.2010] R&D Projects: GA AV ČR KAN400720701 Institutional research plan: CEZ:AV0Z40500505 Keywords : Marcus theory * electron-phonon coupling * reorganisation energy Subject RIV: CA - Inorganic Chemistry Impact factor: 0.409, year: 2011

  20. 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

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

    Science.gov (United States)

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

    1987-01-01

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

  2. 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.

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

    OpenAIRE

    Castellano, Brian M.; Eggers, Daryl K.

    2013-01-01

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

  4. Effect of interchain coupling on the excited polaron in conjugated polymers

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xiao-xue, E-mail: sps_lixx@ujn.edu.cn; Chen, Gang, E-mail: ss_cheng@ujn.edu.cn

    2017-02-05

    Based on the one-dimensional extended Su–Schrieffer–Heeger model, we theoretically investigate the effect of interchain coupling on the formation and polarization of the single-excited state of polaron in conjugated polymers. It is found that there exists a turnover value of the coupling strength, over which the excited polaron could not be formed in either of the two coupled chains. Instead, a polaron-like particle is localized at the center of each chain. In addition, we also find that the reverse polarization of the excited polaron could be enhanced for some cases in polymer when the interchain coupling becomes strong until it exceeds the critical value. - Highlights: • Effect of interchain coupling on the single-excited state of polaron is studied. • When coupling strength exceeds critical value, the excited polaron is dissociated. • Soliton pair could be dissociated into polaron-like particle with strong coupling. • Reverse polarization of excited polaron is enhanced by weak interchain coupling. • Reverse polarization is obtained more easily in solid film of polymer molecules.

  5. Parton Theory of Magnetic Polarons: Mesonic Resonances and Signatures in Dynamics

    Science.gov (United States)

    Grusdt, F.; Kánasz-Nagy, M.; Bohrdt, A.; Chiu, C. S.; Ji, G.; Greiner, M.; Greif, D.; Demler, E.

    2018-01-01

    When a mobile hole is moving in an antiferromagnet it distorts the surrounding Néel order and forms a magnetic polaron. Such interplay between hole motion and antiferromagnetism is believed to be at the heart of high-temperature superconductivity in cuprates. In this article, we study a single hole described by the t -Jz model with Ising interactions between the spins in two dimensions. This situation can be experimentally realized in quantum gas microscopes with Mott insulators of Rydberg-dressed bosons or fermions, or using polar molecules. We work at strong couplings, where hole hopping is much larger than couplings between the spins. In this regime we find strong theoretical evidence that magnetic polarons can be understood as bound states of two partons, a spinon and a holon carrying spin and charge quantum numbers, respectively. Starting from first principles, we introduce a microscopic parton description which is benchmarked by comparison with results from advanced numerical simulations. Using this parton theory, we predict a series of excited states that are invisible in the spectral function and correspond to rotational excitations of the spinon-holon pair. This is reminiscent of mesonic resonances observed in high-energy physics, which can be understood as rotating quark-antiquark pairs carrying orbital angular momentum. Moreover, we apply the strong-coupling parton theory to study far-from-equilibrium dynamics of magnetic polarons observable in current experiments with ultracold atoms. Our work supports earlier ideas that partons in a confining phase of matter represent a useful paradigm in condensed-matter physics and in the context of high-temperature superconductivity in particular. While direct observations of spinons and holons in real space are impossible in traditional solid-state experiments, quantum gas microscopes provide a new experimental toolbox. We show that, using this platform, direct observations of partons in and out of equilibrium are

  6. Conformation changes of polysilanes during the polaron formation

    Czech Academy of Sciences Publication Activity Database

    Toman, Petr; Nešpůrek, Stanislav; Jang, J. W.; Lee, C. E.

    2002-01-01

    Roč. 2, č. 4 (2002), s. 327-330 ISSN 1567-1739. [Multilateral Symposium between the Korean Academy of Science and Technology and the Foreign Academies. Seoul, 08.05.2002-10.05.2002] R&D Projects: GA ČR GA203/99/P009; GA AV ČR IAA1050901 Grant - others:GA-(PL) 4T09A 13222 Institutional research plan: CEZ:AV0Z4050913 Keywords : polaron * polysilane * quantum chemical calculation Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.117, year: 2002

  7. Diagrammatic Monte Carlo method as applied to the polaron problem

    International Nuclear Information System (INIS)

    Mishchenko, A.S.

    2005-01-01

    Exact numerical solution methods for the problem of a few particles interacting with one another and with several bosonic excitation modes are presented. The diagrammatic Monte Carlo method allows the exact calculation of the Green function, and the stochastic optimization technique provides an analytic continuation. Results unobtainable by conventional methods are discussed, including the properties of excited states in the self-trapping phenomenon, the optical spectra of polarons in all coupling regimes, the validity analysis of the exciton models, and the photoemission spectra of a phonon-coupled hole [ru

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

    Science.gov (United States)

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

    2017-05-01

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

  9. Electric field control of the small-polaron hopping conduction in spatial confined Pr0.7(Ca0.6Sr0.40.3MnO3/PMN-PT heterostructure

    Directory of Open Access Journals (Sweden)

    Hao Kuang

    2017-05-01

    Full Text Available The electric field dependent high-temperature small-polaron hopping conduction was investigated in patterned Pr0.7(Ca0.6Sr0.40.3MnO3 strips. The small-polaronic activation energy EA and the carrier localization were found to decrease with the reduction of the strip size. Meanwhile, a similar dependence on the strip size was also obtained for the calculated small-polaron coupling constants, which could be related to the strain relaxation in strips. These results indicate that the spatial confinement prefers to delocalize the carrier and reduce the electron-phonon interaction. Furthermore, opposite variation trends of EA under negative and positive electric field were found in the strips with small size, which could be attributed to the enhancement of polarization effect induced by the reduction of strip size.

  10. 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

  11. 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 ...

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

    Science.gov (United States)

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

    2015-09-28

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

  13. 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.

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

    Science.gov (United States)

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

    2012-04-05

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

  15. Spin polaron in two-dimensional antiferromagnetics - from local singlet to compound quasi-particle

    CERN Document Server

    Barabanov, A F; Belemuk, A M

    2002-01-01

    The basic theoretical concepts, related to the spin polaron scenario for the charge excitations in the two-dimensional antiferromagnetics, are presented. The distinctive peculiarity of the developed approach consists in consideration of the local polaron as the zero approximation for the quasi-particles. On the following stage this excitation is coated into the antiferromagnetic spin waves and the radius intermediate polaron is formed. The method makes it possible to continuously describe the transition from the zero temperatures to the finite ones and to consider the wide doping range. The above approach explains basic results of the ARPES-experiments in the CuO sub 2 plane

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

    Science.gov (United States)

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

    2018-03-26

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

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

    Science.gov (United States)

    Castellano, Brian M; Eggers, Daryl K

    2013-07-11

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

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

    Science.gov (United States)

    Castellano, Brian M.; Eggers, Daryl K.

    2013-01-01

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

  19. 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.

  20. 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.

  1. 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

  2. Diagrammatic Monte Carlo method as applied to the polaron problems

    International Nuclear Information System (INIS)

    Mishchenko, Andrei S

    2005-01-01

    Numerical methods whereby exact solutions to the problem of a few particles interacting with one another and with several bosonic excitation branches are presented. The diagrammatic Monte Carlo method allows the exact calculation of the Matsubara Green function, and the stochastic optimization technique provides an approximation-free analytic continuation. In this review, results unobtainable by conventional methods are discussed, including the properties of excited states in the self-trapping phenomenon, the optical spectra of polarons in all coupling regimes, the validity range analysis of the Frenkel and Wannier approximations relevant to the exciton, and the peculiarities of photoemission spectra of a lattice-coupled hole in a Mott insulator. (reviews of topical problems)

  3. Study of spin-polaron formation in 1D systems

    Energy Technology Data Exchange (ETDEWEB)

    Arredondo, Y.; Navarro, O. [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Apartado Postal 70-360, 04510 México D.F. (Mexico); Vallejo, E. [Facultad de Ingeniería Mecánica y Eléctrica, Universidad Autónoma de Coahuila, Carretera Torreón-Matamoros Km. 7.5 Ciudad Universitaria, 27276 Torreón, Coahuila (Mexico)

    2014-05-15

    We study numerically the formation of spin-polarons in low-dimensional systems. We consider a ferromagnetic Kondo lattice model with Hund coupling J{sub H} and localized spins interacting antiferromagnetically with coupling constant J. We investigate the ground state phase diagram as a function of the exchange couplings J{sub H} and J and as a function of the band filling, since it has been observed that doping either on the ferromagnetic or antiferromagnetic regime lead to formation of magnetic domains [1]. We explore the quasi-particle formation and phase separation using the density-matrix renormalization group method, which is a highly efficient method to investigate quasi-one-dimensional strongly correlated systems.

  4. 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.

  5. Polarons and excitons in insulators: insight from computer simulations

    Science.gov (United States)

    Shluger, Alexander

    2010-03-01

    Localization of electrons and holes as well as excitons in insulators is a ubiquitous phenomenon which controls carrier mobility, luminescence and radiation damage of many materials. When such localization takes place in a perfect lattice it is called self-trapping, however in many cases it is facilitated by perturbation induced by intrinsic defects and impurities. Whatever the mechanism, it is hard to prove experimentally and especially theoretically. I will first review briefly the established models of self-trapped polarons and excitons (STE) in alkali halides and cubic oxides and will demonstrate how they are linked to the mechanisms of photo-induced desorption of these materials [1]. I will then discuss the results of our modeling, which extend these models further to more complex oxides forming so called electrides -- materials where electrons serve as anions [2], and to a qualitatively new type of electron trapping at grain boundaries in polycrystalline materials with negative electron affinity [3]. Combining periodic and embedded cluster methods we can explain and sometimes predict the properties of polarons and excitons in a range of insulators, such as amorphous SiO2 [4], and polycrystalline HfO2 [5] and HfSiO4. I will discuss the applicability of different techniques to studying localization problems in insulators and will compare the predictions of periodic plane wave and embedded cluster DFT calculations. [4pt] [1] W. P. Hess, et al. J. Phys. Chem. B, 109, 19563 (2005) [0pt] [2] P. V. Sushko et al. J. Amer. Chem. Soc., 129, 942 (2007) [0pt] [3] K. P. McKenna and A. L. Shluger, Nature Materials, 7, 859 (2008) [0pt] [4] A. V. Kimmel, et al. J. Non-Cryst. Sol., 353, 599 (2007) [0pt] [5] D. Munoz Ramo, et al. Phys. Rev. Lett. 99, 155504 (2007)

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

    International Nuclear Information System (INIS)

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

    1996-01-01

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

  7. 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.

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

    Science.gov (United States)

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

    2017-11-01

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

  9. 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.

  10. Experimental neutron scattering evidence for proton polaron in hydrated metal oxide proton conductors

    Science.gov (United States)

    Braun, Artur; Chen, Qianli

    2017-06-01

    Hydration of oxygen-deficient metal oxides causes filling of oxygen vacancies and formation of hydroxyl groups with interstitial structural protons, rotating around the oxygen in localized motion. Thermal activation from 500 to 800 K triggers delocalization of the protons by jumping to adjacent oxygen ions, constituting proton conductivity. We report quantitative analyses of proton and lattice dynamics by neutron-scattering data, which reveal the interaction of protons with the crystal lattice and proton-phonon coupling. The motion for the proton trapped in the elastic crystal field yields Eigen frequencies and coupling constants, which satisfy Holstein's polaron model for electrons and thus constitutes first experimental evidence for a proton polaron at high temperature. Proton jump rates follow a polaron model for cerium-oxygen and hydroxyl stretching modes, which are thus vehicles for proton conductivity. This confirms that the polaron mechanism is not restricted to electrons, but a universal charge carrier transport process.

  11. Polaron theory of mid-infrared conductivity a numerical cluster solution

    Science.gov (United States)

    Alexandrov, A. S.; Kabanov, V. V.; Ray, D. K.

    1994-05-01

    Mid-infrared spectra are obtained with numerical calculations of the optical conductivity σ(ω) of a finite-size Holstein model. The results show that the analytic formula of Reik for the optical conductivity is valid only in a strong electron-phonon coupling regime. σ(ω) shows a number of peaks corresponding to the bound states of polarons with a different number of phonons. Calculation of σ(ω) has also been done in the adiabatic limit in the one-dimensional case. It is found that for intermediate coupling the peak in σ(ω) is strongly asymmetric. The optical conductivity of the two-site model in the presence of two electrons is studied. Numerical results show a shift of the peak in σ(ω) to the low-energy region with an increasing Hubbard U for the strong electron-phonon interaction (E p>U) whereas the peak moves to the high-energy region for U>E p high-energy region starts to develop in the large U limit in the presence of phonons. The significance of these calculations for the experimental observations of the mid-infrared spectra of high- Tc cuprates is discussed.

  12. 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.

  13. Comparative analysis of magnetic resonance in the polaron pair recombination and the triplet exciton-polaron quenching models

    Science.gov (United States)

    Mkhitaryan, V. V.; Danilović, D.; Hippola, C.; Raikh, M. E.; Shinar, J.

    2018-01-01

    We present a comparative theoretical study of magnetic resonance within the polaron pair recombination (PPR) and the triplet exciton-polaron quenching (TPQ) models. Both models have been invoked to interpret the photoluminescence detected magnetic resonance (PLDMR) results in π -conjugated materials and devices. We show that resonance line shapes calculated within the two models differ dramatically in several regards. First, in the PPR model, the line shape exhibits unusual behavior upon increasing the microwave power: it evolves from fully positive at weak power to fully negative at strong power. In contrast, in the TPQ model, the PLDMR is completely positive, showing a monotonic saturation. Second, the two models predict different dependencies of the resonance signal on the photoexcitation power, PL. At low PL, the resonance amplitude Δ I /I is ∝PL within the PPR model, while it is ∝PL2 crossing over to PL3 within the TPQ model. On the physical level, the differences stem from different underlying spin dynamics. Most prominently, a negative resonance within the PPR model has its origin in the microwave-induced spin-Dicke effect, leading to the resonant quenching of photoluminescence. The spin-Dicke effect results from the spin-selective recombination, leading to a highly correlated precession of the on-resonance pair partners under the strong microwave power. This effect is not relevant for TPQ mechanism, where the strong zero-field splitting renders the majority of triplets off resonance. On the technical level, the analytical evaluation of the line shapes for the two models is enabled by the fact that these shapes can be expressed via the eigenvalues of a complex Hamiltonian. This bypasses the necessity of solving the much larger complex linear system of the stochastic Liouville equations. Our findings pave the way towards a reliable discrimination between the two mechanisms via cw PLDMR.

  14. Polarons induced electronic transport, dielectric relaxation and magnetodielectric coupling in spin frustrated Ba{sub 2}FeWO{sub 6}

    Energy Technology Data Exchange (ETDEWEB)

    Pezhumkattil Palakkal, Jasnamol [Academy of Scientific and Innovative Research (AcSIR), CSIR—National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Campus, Trivandrum 695 019 (India); Materials Science and Technology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019 (India); Lekshmi, P. Neenu; Thomas, Senoy [Materials Science and Technology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019 (India); Valant, Matjaz [Materials Research Laboratory, University of Nova Gorica, Nova Gorica 5000 (Slovenia); Suresh, K.G. [Department of Physics, Indian Institute of Technology Bombay, Mumbai 400 076 (India); Varma, Manoj Raama, E-mail: manoj@niist.res.in [Academy of Scientific and Innovative Research (AcSIR), CSIR—National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Campus, Trivandrum 695 019 (India); Materials Science and Technology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019 (India)

    2016-04-15

    Highlights: • Ordered double perovskite Ba{sub 2}FeWO{sub 6} synthesized in reducing atmosphere possess a tetragonal I4/m crystal structure with mixed valent Fe/W cations. • Ba{sub 2}FeWO{sub 6} has an antiferromagnetic structure with T{sub N} at 19 K. • Insulating Ba{sub 2}FeWO{sub 6} shows different conducting mechanisms at different temperature regions and dielectric relaxation. • The polarons invoked by the mixed valence state of cations and their disordered arrangements are solely responsible for the various physical phenomena observed in Ba{sub 2}FeWO{sub 6}. - Abstract: Mixed valent double perovskite Ba{sub 2}FeWO{sub 6}, with tetragonal crystal structure, synthesized in a highly controlled reducing atmosphere, shows antiferromagnetic transition at T{sub N} = 19 K. A cluster glass-like transition is observed around 30 K arising from the competing interactions between inhomogeneous magnetic states. The structural distortion leads to the formation of polarons that are not contributing to DC conduction below charge ordering temperature, T{sub CO} = 279 K. Above T{sub CO}, small polarons will start to hop by exploiting thermal energy and participate in the conduction mechanism. The polarons are also responsible for the dielectric relaxor behavior, in which the dielectric relaxation time follows non-linearity in temperature as proposed by Fulcher. The material also exhibits a small room temperature magnetoresistance of 1.7% at 90 kOe. An intrinsic magnetodielectric coupling of ∼4% near room temperature and at lower temperatures, as well as an extrinsic magnetodielectric coupling change from +4% to −6% at around 210 K are reported.

  15. f-f Magnetic polaron Wigner glass and anomalous superconductivity in U sub 1 sub - sub x Th sub x Be sub 1 sub 3

    CERN Document Server

    Kasuya, T

    2000-01-01

    Mechanisms of the anomalous properties in the heavy fermion superconductor UBe sub 1 sub 3 and its alloys, in particular for the Th dopings, are studied in detail based on the fundamental electronic states to be consistent with all the crucial experimental results. As the reference systems for the magnetic polaron formation, Ce monopnictides, as well as USb and UTe, are mentioned. From detailed systematic studies of the dilute alloy systems, it is postulated that the 5f states in UBe sub 1 sub 3 split into the well-localized core 5f GAMMA sup 2 sub 7 singlet state and other delocalized 5f states situated around the Fermi energy forming the f-f magnetic polarons through the strong intra-atomic ferromagnetic f-f exchange interaction. The accompanied lattice polarons are also shown to play important roles. In the p-d band states, the f-f exchange interaction and the intersite p-f mixing interactions for the p-f Kondo state are of nearly equal strengths causing a rich variety of delicately balanced states. For th...

  16. Enhancing the Efimov correlation in Bose polarons with large mass imbalance

    Science.gov (United States)

    Sun, Mingyuan; Cui, Xiaoling

    2017-08-01

    We study the effect of Efimov physics (in the few-body sector) on the spectral response of the Bose polaron, a many-body system consisting of an impurity immersed in a bath of bosonic atoms. We find that the Efimov correlation can be greatly enhanced by increasing the mass ratio between the bosons and the impurity, which results in visible signatures in the rf spectrum of the polaron. Using a diagrammatic approach up to the third-order virial expansion, we show how the mass imbalance and the enhanced three-body effect modify the line shape and linewidth of the polaron spectrum. Moreover, we study the effect of a finite boson-boson interaction on the spectrum. Taking the realistic system of Li impurities immersed in Cs bosons with a positive Cs-Cs scattering length, we find a visible Efimov branch, which is associated with the second lowest Efimov trimer, in the polaron spectrum. In particular, by adjusting the boson density the Efimov branch can greatly hybridize with the attractive polaron branch, leading to spectrum broadening near their avoided level crossing. Our results can be directly probed in the cold atoms experiments on Li-Cs and Li-Rb Bose polarons.

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Arsen V Grigoryan

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

  19. 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.

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

    KAUST Repository

    Zhang, Qianfan

    2011-05-19

    Silicon nanowires (SiNWs) have recently been shown to be promising as high capacity lithium battery anodes. SiNWs can be grown with their long axis along several different crystallographic directions. Due to distinct atomic configuration and electronic structure of SiNWs with different axial orientations, their lithium insertion behavior could be different. This paper focuses on the characteristics of single Li defects, including binding energy, diffusion barriers, and dependence on uniaxial strain in [110], [100], [111], and [112] SiNWs. Our systematic ab initio study suggests that the Si-Li interaction is weaker when the Si-Li bond direction is aligned close to the SiNW long axis. This results in the [110] and [111] SiNWs having the highest and lowest Li binding energy, respectively, and it makes the diffusion barrier along the SiNW axis lower than other pathways. Under external strain, it was found that [110] and [001] SiNWs are the most and least sensitive, respectively. For diffusion along the axial direction, the barrier increases (decreases) under tension (compression). This feature results in a considerable difference in the magnitude of the energy barrier along different diffusion pathways. © 2011 American Chemical Society.

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

    CERN Document Server

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

    2000-01-01

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

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

    Science.gov (United States)

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

    2013-10-28

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

  3. Electron transport in pure and substituted iron oxyhydroxides by small-polaron migration

    Energy Technology Data Exchange (ETDEWEB)

    Alexandrov, Vitaly, E-mail: vitali.alexandrov@pnnl.gov; Rosso, Kevin M. [Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354 (United States)

    2014-06-21

    Iron oxyhydroxides (FeOOH) are common crystalline forms of iron that play a critical role in technology and the natural environment via a variety of important reduction-oxidation reactions, including electrical semiconduction as an aspect. However, a basic understanding of the electron transport properties of these systems is still lacking. We examine the electron mobility in goethite (α-FeOOH), akaganéite (β-FeOOH), and lepidocrocite (γ-FeOOH) polymorphs by means of density functional theory based (DFT+U) calculations. We show that room temperature charge transport should be dominated by the small-polaron hopping type, and that the attendant mobility should be highest for pure goethite and akaganéite. Hopping pathways through the various lattices are discussed in terms of individual electron exchange steps and rates for each. Given the usual occurrence of compositional impurities in natural iron oxyhydroxides, we also investigate the effect of common stoichiometric defects on the electron hopping activation energies such as Al and Cr substitutional cations in goethite, and Cl anions in the channels of akaganéite.

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

    Science.gov (United States)

    Wang, Linwang

    2014-03-01

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

  6. 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.

  7. 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

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

    Science.gov (United States)

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

    2008-12-02

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

  9. Efficacy of the DFT + U formalism for modeling hole polarons in perovskite oxides

    Science.gov (United States)

    Erhart, Paul; Klein, Andreas; Åberg, Daniel; Sadigh, Babak

    2014-07-01

    We investigate the formation of self-trapped holes (STH) in three prototypical perovskites (SrTiO3, BaTiO3, PbTiO3) using a combination of density functional theory (DFT) calculations with local potentials and hybrid functionals. First we construct a local correction potential for polaronic configurations in SrTiO3 that is applied via the DFT + U method and matches the forces from hybrid calculations. We then use the DFT + U potential to search the configuration space and locate the lowest energy STH configuration. It is demonstrated that both the DFT + U potential and the hybrid functional yield a piecewise linear dependence of the total energy on the occupation of the STH level, suggesting that self-interaction effects have been properly removed. The DFT + U model is found to be transferable to BaTiO3 and PbTiO3, and STH formation energies from DFT + U and hybrid calculations are in close agreement for all three materials. STH formation is found to be energetically favorable in SrTiO3 and BaTiO3 but not in PbTiO3, which can be rationalized by considering the alignment of the valence band edges on an absolute energy scale. In the case of PbTiO3 the strong coupling between Pb 6s and O 2p states lifts the valence band minimum (VBM) compared to SrTiO3 and BaTiO3. This reduces the separation between VBM and STH level and renders the STH configuration metastable with respect to delocalization (band hole state). We expect that the present approach can be adapted to study STH formation also in oxides with different crystal structures and chemical compositions.

  10. 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

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

    International Nuclear Information System (INIS)

    Kumar, K.P.; Chatterji, D.

    1990-01-01

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

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

    Science.gov (United States)

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

    2016-09-01

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

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

    Science.gov (United States)

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

    2015-01-08

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

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

    Directory of Open Access Journals (Sweden)

    Santanu Bera

    2012-01-01

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

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

    Science.gov (United States)

    Borodin, Oleg

    2009-09-10

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

  16. Signatures of mesoscopic Jahn-Teller polaron inhomogeneities in high-temperature superconductors

    CERN Document Server

    Bishop, A R; Leon, J M D

    2003-01-01

    We analyse complementary experimental results in high-temperature superconducting cuprates from x-ray absorption fine structure (XAFS), inelastic neutron scattering (INS) and inelastic x-ray scattering (IXS), Raman spectroscopy (RS), infrared absorption spectroscopy and femtosecond optical spectroscopy in terms of the predictions of a specific fully quantum mechanical calculation of small polaron formation and internal dynamics (phonon-assisted local charge oscillations). These analyses support the scenario in which the pseudogap-associated temperature, T*, marks the onset of an inhomogeneous ground state with polarons, in agreement with several theoretical models which attempt to explain the origin of high-temperature superconductivity in doped cuprates. The change in dynamics, which is observed across the superconducting transition temperature, T sub c in XAFS, INS and RS, indicates an intimate link of the dynamics of these polarons with the mechanism of high-temperature superconductivity. (letter to the ed...

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

    Directory of Open Access Journals (Sweden)

    Nicolas Panel

    2017-09-01

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

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Science.gov (United States)

    CHINNAYELKA, SWETHA; McSHANE, and MICHAEL J.

    2015-01-01

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

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

    International Nuclear Information System (INIS)

    Kasapoglu, E.; Soekmen, I.

    2007-01-01

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

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

    Science.gov (United States)

    Bertsch, G. F.; Bingham, Derek

    2017-12-01

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

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

    KAUST Repository

    Beke-Somfai, Tamás

    2010-01-26

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

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

    Science.gov (United States)

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

    2017-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-02-01

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

  5. 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.

  6. 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

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

    Science.gov (United States)

    Foroutan-Nejad, Cina; Marek, Radek

    2014-02-14

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

  8. Highly-efficient charge separation and polaron delocalization in polymer-fullerene bulk-heterojunctions: a comparative multi-frequency EPR and DFT study.

    Science.gov (United States)

    Niklas, Jens; Mardis, Kristy L; Banks, Brian P; Grooms, Gregory M; Sperlich, Andreas; Dyakonov, Vladimir; Beaupré, Serge; Leclerc, Mario; Xu, Tao; Yu, Luping; Poluektov, Oleg G

    2013-06-28

    The ongoing depletion of fossil fuels has led to an intensive search for additional renewable energy sources. Solar-based technologies could provide sufficient energy to satisfy the global economic demands in the near future. Photovoltaic (PV) cells are the most promising man-made devices for direct solar energy utilization. Understanding the charge separation and charge transport in PV materials at a molecular level is crucial for improving the efficiency of the solar cells. Here, we use light-induced EPR spectroscopy combined with DFT calculations to study the electronic structure of charge separated states in blends of polymers (P3HT, PCDTBT, and PTB7) and fullerene derivatives (C60-PCBM and C70-PCBM). Solar cells made with the same composites as active layers show power conversion efficiencies of 3.3% (P3HT), 6.1% (PCDTBT), and 7.3% (PTB7), respectively. Upon illumination of these composites, two paramagnetic species are formed due to photo-induced electron transfer between the conjugated polymer and the fullerene. They are the positive, P(+), and negative, P(-), polarons on the polymer backbone and fullerene cage, respectively, and correspond to radical cations and radical anions. Using the high spectral resolution of high-frequency EPR (130 GHz), the EPR spectra of these species were resolved and principal components of the g-tensors were assigned. Light-induced pulsed ENDOR spectroscopy allowed the determination of (1)H hyperfine coupling constants of photogenerated positive and negative polarons. The experimental results obtained for the different polymer-fullerene composites have been compared with DFT calculations, revealing that in all three systems the positive polaron is distributed over distances of 40-60 Å on the polymer chain. This corresponds to about 15 thiophene units for P3HT, approximately three units for PCDTBT, and about three to four units for PTB7. No spin density delocalization between neighboring fullerene molecules was detected by EPR

  9. Highly-Efficient Charge Separation and Polaron Delocalization in Polymer-Fullerene Bulk-Heterojunctions: A Comparative Multi-Frequency EPR & DFT Study

    Science.gov (United States)

    Niklas, Jens; Mardis, Kristy L.; Banks, Brian P.; Grooms, Gregory M.; Sperlich, Andreas; Dyakonov, Vladimir; Beaupré, Serge; Leclerc, Mario; Xu, Tao; Yu, Luping; Poluektov, Oleg G.

    2016-01-01

    The ongoing depletion of fossil fuels has led to an intensive search for additional renewable energy sources. Solar-based technologies could provide sufficient energy to satisfy the global economic demands in the near future. Photovoltaic (PV) cells are the most promising man-made devices for direct solar energy utilization. Understanding the charge separation and charge transport in PV materials at a molecular level is crucial for improving the efficiency of the solar cells. Here, we use light-induced EPR spectroscopy combined with DFT calculations to study the electronic structure of charge separated states in blends of polymers (P3HT, PCDTBT, and PTB7) and fullerene derivatives (C60-PCBM and C70-PCBM). Solar cells made with the same composites as active layers show power conversion efficiencies of 3.3% (P3HT), 6.1% (PCDTBT), and 7.3% (PTB7), respectively. Under illumination of these composites, two paramagnetic species are formed due to photo-induced electron transfer between the conjugated polymer and the fullerene. They are the positive, P+, and negative, P-, polarons on the polymer backbone and fullerene cage, respectively, and correspond to radical cations and radical anions. Using the high spectral resolution of high-frequency EPR (130 GHz), the EPR spectra of these species were resolved and principal components of the g-tensors were assigned. Light-induced pulsed ENDOR spectroscopy allowed the determination of 1H hyperfine coupling constants of photogenerated positive and negative polarons. The experimental results obtained for the different polymer-fullerene composites have been compared with DFT calculations, revealing that in all three systems the positive polaron is distributed over distances of 40 - 60 Å on the polymer chain. This corresponds to about 15 thiophene units for P3HT, approximately three units PCDTBT, and about three to four units for PTB7. No spin density delocalization between neighboring fullerene molecules was detected by EPR. Strong

  10. 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...

  11. DFT+U study of self-trapping, trapping, and mobility of oxygen-type hole polarons in barium stannate

    Science.gov (United States)

    Geneste, Grégory; Amadon, Bernard; Torrent, Marc; Dezanneau, Guilhem

    2017-10-01

    The charge-transfer insulating perovskite oxides currently used as fuel cell electrolytes undergo, at high temperature, an oxidation reaction 1/2 O2(g ) +VO••→OOX+2 h• , that produces oxygen-type holes. Understanding the nature and mobility of these oxygen-type holes is an important step to improve the performance of devices, but presents a theoretical challenge since, in their localized form, they cannot be captured by standard density functional theory. Here, we employ the DFT+U formalism with a Hubbard correction on the p orbitals of oxygen to investigate several properties of these holes, in the particular case of BaSnO3. We describe the small oxygen-type hole polarons, the self-trapping at their origin, and their trapping by trivalent dopants (Ga, Sc, In, Lu, Y, Gd, La). Strong similarities with protonic defects are observed concerning the evolution of the trapping energy with ionic radius of the dopant. Moreover, we show that long-range diffusion of holes is a complex phenomenon, that proceeds by a succession of several mechanisms. However, the standard implementation of DFT+U within the projector augmented-wave (PAW) formalism leads to use very large, unphysical values of U for the O-p orbital. We propose here a slightly modified DFT+U scheme, that takes into account the fact that the O-p is truncated in usual DFT+U implementation in PAW. This scheme yields more physical values of U than the ones traditionally used in the literature, and describes well the properties of the hole polaron.

  12. 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

  13. 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

  14. Fingerprints of spin-orbital polarons and of their disorder in the photoemission spectra of doped Mott insulators with orbital degeneracy

    Science.gov (United States)

    Avella, Adolfo; Oleś, Andrzej M.; Horsch, Peter

    2018-04-01

    We explore the effects of disordered charged defects on the electronic excitations observed in the photoemission spectra of doped transition metal oxides in the Mott insulating regime by the example of the R1 -xCaxVO3 perovskites, where R = La, ⋯, Lu. A fundamental characteristic of these vanadium d2 compounds with partly filled t2 g valence orbitals is the persistence of spin and orbital order up to high doping, in contrast to the loss of magnetic order in high-Tc cuprates at low defect concentration. We study the disordered electronic structure of such doped Mott-Hubbard insulators within the unrestricted Hartree-Fock approximation and, as a result, manage to explain the spectral features that occur in photoemission and inverse photoemission. In particular, (i) the atomic multiplet excitations in the inverse photoemission spectra and the various defect-related states and satellites are qualitatively well reproduced, (ii) a robust Mott gap survives up to large doping, and (iii) we show that the defect states inside the Mott gap develop a soft gap at the Fermi energy. The soft defect-states gap, which separates the highest occupied from the lowest unoccupied states, can be characterized by a shape and a scale parameter extracted from a Weibull statistical sampling of the density of states near the chemical potential. These parameters provide a criterion and a comprehensive schematization for the insulator-metal transition in disordered systems. Our results provide clear indications that doped holes are bound to charged defects and form small spin-orbital polarons whose internal kinetic energy is responsible for the opening of the soft defect-states gap. We show that this kinetic gap survives disorder fluctuations of defects and is amplified by the long-range electron-electron interactions, whereas we observe a Coulomb singularity in the atomic limit. The small size of spin-orbital polarons is inferred by an analysis of the inverse participation ratio and by

  15. 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

  16. Formation time of a small electron polaron in LiNbO3: measurements and interpretation

    International Nuclear Information System (INIS)

    Qiu, Yong; Ucer, K.B.; Williams, R.T.

    2005-01-01

    Infrared optical absorption attributed to the electron polaron on a non-defective site in LiNbO 3 and KNbO 3 has previously been observed using pulsed electron and laser techniques. With subpicosecond laser excitation and spectroscopy, it is possible to measure a rise time of the infrared absorption, which may be interpreted as the time for a band-state conduction electron to cool by phonon scattering, collapse its wavefunction around a site made attractive by thermal disorder, and relax vibrationally to a small polaron. This is a process which is of fundamental interest, involving dynamics of self-localization from band states and vibrational relaxation of a localized electron in an otherwise non-defective lattice. For example, Gavartin and Shluger have recently performed calculations on the role of thermal fluctuations in self-trapping of holes in MgO. We report initial measurements on the rise time of infrared absorption at 0.95 eV (Mg-perturbed polaron) in LiNbO 3 :Mg to be τ R ∼230 fs at T=20 K and τ R ∼110 fs at T=296 K. We discuss 2 stages that together may account for the delay and its temperature dependence: free-electron cooling and vibrational relaxation of a ''defect'' (small polaron) in a host. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  17. Stability and Polaronic Motion of Self-Trapped Holes in Silver Halides

    DEFF Research Database (Denmark)

    Loftager, Simon; Garcia-Fernandez, P.; Aramburu, J. A.

    2016-01-01

    Polarons and their associated transport properties are a field of great current interest both in chemistry and physics. To further our understanding of these quasi-particles, we have carried out first-principles calculations of self-trapped holes (STHs) in the model compounds AgCl and AgBr, for w...

  18. Effect of doping Ca on polaron hopping in LaSr 2 Mn 2 O 7

    Indian Academy of Sciences (India)

    ... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Pramana – Journal of Physics; Volume 58; Issue 5-6. Effect of doping Ca on polaron hopping in LaSr2Mn2O7. S N Bhatia Osama A Yassin. Colossal Magnetoresistance & Other Materials Volume 58 Issue 5-6 May-June 2002 pp 1061- ...

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

    Science.gov (United States)

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

    2012-03-01

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

  20. 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.

  1. 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.

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

    Science.gov (United States)

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

    2017-01-01

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

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

    NARCIS (Netherlands)

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

    2004-01-01

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

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

    International Nuclear Information System (INIS)

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

    1993-01-01

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

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

    International Nuclear Information System (INIS)

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

    1986-01-01

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

  6. The effect of correlations on the non-ohmic behavior of the small-polaron hopping conductivity in 1D and 3D disordered systems

    International Nuclear Information System (INIS)

    Dimakogianni, M; Triberis, G P

    2010-01-01

    According to percolation theory the investigation of charge transport in disordered systems is equivalent to the study of the possibility of the passage of the carriers through a random network of impedances which interconnect the different lattice sites. When the site energies are not the same, the energy of a site affects the incoming as well as the outgoing impedances connected to the given site and this gives rise to correlations between neighboring impedances. This new condition characterizes the transport process and imposes the evaluation of the average number of sites accessible by a bond from a given site for all possible configurations of sites that satisfy the percolation condition. The generalized molecular crystal model, appropriate for the study of small-polaron hopping transport in disordered systems, and the Kubo formula permit the evaluation of these impedances. Taking correlations into account, theoretical percolation considerations applicable to one-dimensional and three-dimensional disordered systems, lead to analytical expressions for the temperature and electric field dependence of the DC conductivity at high (multi-phonon-assisted hopping) and low (few-phonon-assisted hopping) temperatures. The theoretical analysis reveals the effect of correlations on the non-ohmic behavior of the small-polaron hopping conductivity and permits the evaluation of the maximum hopping distance. Quantitative estimates of this effect are presented comparing the theoretical results, including correlations with those ignoring them, previously reported, applying them to recent experimental data for a wide temperature range and from low up to moderate electric fields.

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

    Science.gov (United States)

    Nikiforov, Theo T; Beechem, Joseph M

    2006-10-01

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

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

    Science.gov (United States)

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

    2018-03-01

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

  9. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-04-04

    Graphical abstract: In-plane minimum geometries for benzene-H{sup -} non-covalent adducts: linear adduct (left) with the hydride ion hydrogen bonded to one aromatic hydrogen; bifurcated adduct (right), with the hydride ion hydrogen bonded to two adjacent aromatic hydrogens. Highlights: Black-Right-Pointing-Pointer Theoretical study on covalent and non-covalent binding in benzene-hydride. Black-Right-Pointing-Pointer Two non-covalent stable adducts were characterized in the in-plane geometry. Black-Right-Pointing-Pointer Significant sections of the potential energy surface were determined. Black-Right-Pointing-Pointer Formation of a very stable C{sub 6}H{sub 7}{sup -} anion upon covalent binding to carbon. - Abstract: High level ab initio calculations were performed on the interaction of the hydride anion with benzene, a system of potential interest for modelling the interactions occurring in hydrogen rich planetary atmospheres. We investigated both non-covalent and covalent binding, exploring the complete basis set limit using highly correlated MP2 and CCSD(T) levels of theory. Two non-covalent minima on the potential energy surface have been characterized, and found to correspond to moderately strong hydrogen bonding interactions. To gain further insight on the nature of binding, the total interaction energy was decomposed into its physically meaningful components and selected sections of the potential energy surface were calculated. Moreover, we found that H{sup -} can easily covalently bind to one of the carbon atoms of benzene to form a stable C{sub 6}H{sub 7}{sup -} anion, a global minimum on the potential energy surface, characterized by a puckered geometry, with a carbon atom bending out of the benzene plane. A slightly less stable planar C{sub 6}H{sub 7}{sup -} structure was also identified, corresponding to the transition state for the flipping motion of the puckered species.

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

    International Nuclear Information System (INIS)

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

    1996-01-01

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

  12. 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

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

    Science.gov (United States)

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

    2014-06-23

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

  14. 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...

  15. 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)

  16. Anomalous dispersion and band gap reduction in UO{sub 2+x} and its possible coupling to the coherent polaronic quantum state

    Energy Technology Data Exchange (ETDEWEB)

    Conradson, Steven D. [Synchrotron Soleil, Saint-Aubin BP-48, 91192 (France); Andersson, David A. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Bagus, Paul S. [University of North Texas, Denton, TX 76203 (United States); Boland, Kevin S.; Bradley, Joseph A.; Byler, Darrin D.; Clark, David L.; Conradson, Dylan R. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Espinosa-Faller, Francisco J. [Universidad Marista de Merida, Merida, Yucatan 97300 (Mexico); Lezama Pacheco, Juan S.; Martucci, Mary B. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Nordlund, Dennis [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Seidler, Gerald T. [University of Washington, Seattle, WA 98195 (United States); Valdez, James A. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    2016-05-01

    Hypervalent UO{sub 2}, UO{sub 2(+x)} formed by both addition of excess O and photoexcitation, exhibits a number of unusual or often unique properties that point to it hosting a polaronic Bose–Einstein(-Mott) condensate. A more thorough analysis of the O X-ray absorption spectra of UO{sub 2}, U{sub 4}O{sub 9}, and U{sub 3}O{sub 7} shows that the anomalous increase in the width of the spectral features assigned to predominantly U 5f and 6d final states that points to increased dispersion of these bands occurs on the low energy side corresponding to the upper edge of the gap bordered by the conduction or upper Hubbard band. The closing of the gap by 1.5 eV is more than twice as much as predicted by calculations, consistent with the dynamical polaron found by structural measurements. In addition to fostering the excitation that is the proposed mechanism for the coherence, the likely mirroring of this effect on the occupied, valence side of the gap below the Fermi level points to increased complexity of the electronic structure that could be associated with the Fermi topology of BEC–BCS crossover and two band superconductivity.

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

    Science.gov (United States)

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

    2014-03-01

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

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

    Science.gov (United States)

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

    2018-02-06

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

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

    Science.gov (United States)

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

    2018-02-01

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

  20. 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.

  1. Optical phonon modes and polaron related parameters in GaxIn1-xP

    Science.gov (United States)

    Bouarissa, N.; Algarni, H.; Al-Hagan, O. A.; Khan, M. A.; Alhuwaymel, T. F.

    2018-02-01

    Based on a pseudopotential approach under the virtual crystal approximation that includes the effect of compositional disorder, the optical lattice vibration frequencies and polaron related parameters in zinc-blende GaxIn1-xP have been studied. Our findings showed generally reasonably good accord with data in the literature. Other case, our results are predictions. The composition dependence of longitudinal optical (LO) and transverse optical (TO) phonon modes, LO-TO splittings, Frӧhlich coupling parameter, Debye temperature of LO phonon frequency, and polaron effective mass has been analyzed and discussed. While a non-monotonic behavior has been noticed for the LO and TO phonon frequencies versus Ga concentration x, a monotonic behavior has been observed for the rest of the features of interest. The information derived from this investigation may be useful for optoelectronic technological applications.

  2. Hall effect driven by non-collinear magnetic polarons in diluted magnetic semiconductors

    Science.gov (United States)

    Denisov, K. S.; Averkiev, N. S.

    2018-04-01

    In this letter, we develop the theory of Hall effect driven by non-collinear magnetic textures (topological Hall effect—THE) in diluted magnetic semiconductors (DMSs). We show that a carrier spin-orbit interaction induces a chiral magnetic ordering inside a bound magnetic polaron (BMP). The inner structure of non-collinear BMP is controlled by the type of spin-orbit coupling, allowing us to create skyrmion- (Rashba) or antiskyrmion-like (Dresselhaus) configurations. The asymmetric scattering of itinerant carriers on polarons leads to the Hall response which exists in weak external magnetic fields and at low temperatures. We point out that DMS-based systems allow one to investigate experimentally the dependence of THE both on a carrier spin polarization and on a non-collinear magnetic texture shape.

  3. Small polaron formation and motion of holes in a-SiO2

    International Nuclear Information System (INIS)

    Hughes, R.C.; Emin, D.

    1978-01-01

    X-ray generated holes in SiO 2 are observed to be reduced to low mobility in times of the order of vibrational periods, 10 -12 s. The temperature dependence, electric field dependence and magnitude of this mobility for times up to about 100 ns are consistent with those of hole-like small polarons. The circumstances which favor the occurrence of rapid small polaron formation are a large effective mass (narrow valence band), the presence of the long-range hole-lattice interaction characteristic of an ionic material and the presence of disorder, all of which are found in amorphous SiO 2 . An alternative explanation involving trapping requires an extremely large localized state density and fortuitous temperature and field dependences of the hopping rates

  4. Impact of morphology on polaron delocalization in a semicrystalline conjugated polymer

    KAUST Repository

    Steyrleuthner, Robert

    2016-12-20

    We investigate the delocalization of holes in the semicrystalline conjugated polymer poly(2,5-bis(3-alkylthiophene-2-yl)thieno[3,2-b]thiophene) (PBTTT) by directly measuring the hyperfine coupling between photogenerated polarons and bound nuclear spins using electron nuclear double resonance spectroscopy. An extrapolation of the corresponding oligomer spectra reveals that charges tend to delocalize over 4.0-4.8 nm with delocalization strongly dependent on molecular order and crystallinity of the PBTTT polymer thin films. Density functional theory calculations of hyperfine couplings confirm that long-range corrected functionals appropriately describe the change in coupling strength with increasing oligomer size and agree well with the experimentally measured polymer limit. Our discussion presents general guidelines illustrating the various pitfalls and opportunities when deducing polaron localization lengths from hyperfine coupling spectra of conjugated polymers.

  5. Effects of hole self-trapping by polarons on transport and negative bias illumination stress in amorphous-IGZO

    Science.gov (United States)

    de Jamblinne de Meux, A.; Pourtois, G.; Genoe, J.; Heremans, P.

    2018-04-01

    The effects of hole injection in amorphous indium-gallium-zinc-oxide (a-IGZO) are analyzed by means of first-principles calculations. The injection of holes in the valence band tail states leads to their capture as a polaron, with high self-trapping energies (from 0.44 to 1.15 eV). Once formed, they mediate the formation of peroxides and remain localized close to the hole injection source due to the presence of a large diffusion energy barrier (of at least 0.6 eV). Their diffusion mechanism can be mediated by the presence of hydrogen. The capture of these holes is correlated with the low off-current observed for a-IGZO transistors, as well as with the difficulty to obtain a p-type conductivity. The results further support the formation of peroxides as being the root cause of Negative Bias Illumination Stress (NBIS). The strong self-trapping substantially reduces the injection of holes from the contact and limits the creation of peroxides from a direct hole injection. In the presence of light, the concentration of holes substantially rises and mediates the creation of peroxides, responsible for NBIS.

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

    International Nuclear Information System (INIS)

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

    1984-01-01

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

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

    International Nuclear Information System (INIS)

    Haddou El Ghazi; Anouar Jorio; Izeddine Zorkani

    2013-01-01

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

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

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

    International Nuclear Information System (INIS)

    Huxtable, B.D.

    1988-01-01

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

  10. Dynamics of the optically-induced properties of a small-polaronic glass

    International Nuclear Information System (INIS)

    Emin, D.

    1979-01-01

    The relaxation and recombination of an electronic excitation created by the absorption of a super-band-gap photon is considered for a system in which excitons and charge carriers find it energetically favorable to self-trap. The notions of a barrier to self-trapping, a short-range repulsion between electrons and holes, and the electromodulation of the small-polaron absorption band play a central role in this discussion. The results are consistent with experiments on chalcogenide glasses

  11. Excitations partition into two distinct populations in bulk perovskites due to polaron formation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lili; Brawand, Nicholas P.; Vörös, Márton; Dahlberg, Peter D.; Otto, John P.; Williams, Nicholas E.; Tiede, David M.; Galli, Giulia; Engel, Gregory S.

    2018-03-05

    Organolead halide perovskites convert optical excitations to charge carriers with remarkable efficiency in optoelectronic devices. Previous research predominantly documents dynamics in perovskite thin films; however, extensive disorder in this platform may obscure the observed carrier dynamics. Here, carrier dynamics in perovskite single-domain single crystals is examined by performing transient absorption spectroscopy in a transmissive geometry. Two distinct sets of carrier populations that coexist at the same radiation fluence, but display different decay dynamics, are observed: one dominated by second-order recombination and the other by third-order recombination. Based on ab initio simulations, this observation is found to be most consistent with the hypothesis that free carriers and localized carriers coexist due to polaron formation. The calculations suggest that polarons will form in both CH3NH3PbBr3 and CH3NH3PbI3 crystals, but that they are more pronounced in CH3NH3PbBr3. Single-crystal CH3NH3PbBr3 could represent the key to understanding the impact of polarons on the transport properties of perovskite optoelectronic devices.

  12. Hartree-Fock treatment of Fermi polarons using the Lee-Low-Pine transformation

    Science.gov (United States)

    Kain, Ben; Ling, Hong Y.

    2017-09-01

    We consider the Fermi polaron problem at zero temperature, where a single impurity interacts with noninteracting host fermions. We approach the problem starting with a Fröhlich-like Hamiltonian where the impurity is described with canonical position and momentum operators. We apply the Lee-Low-Pine (LLP) transformation to change the fermionic Fröhlich Hamiltonian into the fermionic LLP Hamiltonian, which describes a many-body system containing host fermions only. We adapt the self-consistent Hartree-Fock (HF) approach, first proposed by Edwards, to the fermionic LLP Hamiltonian in which a pair of host fermions with momenta k and k' interact with a potential proportional to k .k' . We apply the HF theory, which has the advantage of not restricting the number of particle-hole pairs, to repulsive Fermi polarons in one dimension. When the impurity and host fermion masses are equal our variational ansatz, where HF orbitals are expanded in terms of free-particle states, produces results in excellent agreement with McGuire's exact analytical results based on the Bethe ansatz. This work raises the prospect of using the HF ansatz and its time-dependent generalization as building blocks for developing all-coupling theories for both equilibrium and nonequilibrium Fermi polarons in higher dimensions.

  13. Optical Characterization of the Hole Polaron in a Series of Diketopyrrolopyrrole Polymers Used for Organic Photovoltaics

    Directory of Open Access Journals (Sweden)

    Evan L. Williams

    2014-12-01

    Full Text Available A strategy that is often used for designing low band gap polymers involves the incorporation of electron-rich (donor and electron-deficient (acceptor conjugated segments within the polymer backbone. In this paper we investigate such a series of Diketopyrrolopyrrole (DPP-based co-polymers. The co-polymers consisted of a DPP unit attached to a phenylene, naphthalene, or anthracene unit. Additionally, polymers utilizing either the thiophene-flanked DPP or the furan-flanked DPP units paired with the naphthalene comonomer were compared. As these polymers have been used as donor materials and subsequent hole transporting materials in organic solar cells, we are specifically interested in characterizing the optical absorption of the hole polaron of these DPP based copolymers. We employ chemical doping, electrochemical doping, and photoinduced absorption (PIA studies to probe the hole polaron absorption spectra. While some donor-acceptor polymers have shown an appreciable capacity to generate free charge carriers upon photoexcitation, no polaron signal was observed in the PIA spectrum of the polymers in this study. The relations between molecular structure and optical properties are discussed.

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

    Science.gov (United States)

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

    2007-11-01

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

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

    Science.gov (United States)

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

    2015-10-01

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

  16. 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.

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

    Science.gov (United States)

    Qiu, Ling; Xiao, Heming

    2009-05-15

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

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

    Science.gov (United States)

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

    2017-07-04

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

  19. 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

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

    Science.gov (United States)

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

    2011-11-23

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

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

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2015-01-01

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

  2. Finite-temperature behavior of the Bose polaron

    DEFF Research Database (Denmark)

    Levinsen, Jesper; Parish, Meera M.; Christensen, Rasmus S.

    2017-01-01

    We consider a mobile impurity immersed in a Bose gas at finite temperature. Using perturbation theory valid for weak coupling between the impurity and the bosons, we derive analytical results for the energy and damping of the impurity for low and high temperatures, as well as for temperatures close...... to the critical temperature $T_c$ for Bose-Einstein condensation. These results show that the properties of the impurity vary strongly with temperature. The energy exhibits an intriguing non-monotonic behavior close to $T_c$, and the damping rises sharply close to $T_c$. We finally discuss how these effects can...

  3. 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.

  4. Quasi-one-dimensional polaronic states due to the preferential reduction in the Li sub 1 sub + sub x V sub 3 O sub 8 insertion electrode

    CERN Document Server

    Onoda, M

    2003-01-01

    The structural and electronic properties of the Li sub 1 sub + sub x V sub 3 O sub 8 insertion electrode, where 0 sup 0.1 with nearly stoichiometric oxygen atoms, small polarons exist without carrier-creation energy at high temperatures, while at low temperatures the conduction may be of variable-range hopping (VRH) type. For x > 0.2, one-dimensional magnetic properties appear due to sizable exchange couplings and order-disorder effects of additional Li ions may lead to significant change of transport properties. For the intermediate composition 0 < x sup<= 0.1, strong randomness of the Li doping and the congenital oxygen deficiency cause VRH states even at high temperatures.

  5. Quasi-one-dimensional polaronic states due to the preferential reduction in the Li1+xV3O8 insertion electrode

    Science.gov (United States)

    Onoda, Masashige; Amemiya, Isao

    2003-05-01

    The structural and electronic properties of the Li1+xV3O8 insertion electrode, where 0 leq x 0.1 with nearly stoichiometric oxygen atoms, small polarons exist without carrier-creation energy at high temperatures, while at low temperatures the conduction may be of variable-range hopping (VRH) type. For x > 0.2, one-dimensional magnetic properties appear due to sizable exchange couplings and order-disorder effects of additional Li ions may lead to significant change of transport properties. For the intermediate composition 0 < x leq 0.1, strong randomness of the Li doping and the congenital oxygen deficiency cause VRH states even at high temperatures.

  6. 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.

  7. 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.)

  8. 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.)

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

    Science.gov (United States)

    Genheden, Samuel; Ryde, Ulf

    2011-11-08

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

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

    Science.gov (United States)

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

    2011-10-10

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

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

    Science.gov (United States)

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

    2011-11-24

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

  12. 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.

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

    Science.gov (United States)

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

    2006-08-24

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

  14. Acceptor and Excitation Density Dependence of the Ultrafast Polaron Absorption Signal in Donor-Acceptor Organic Solar Cell Blends.

    Science.gov (United States)

    Zarrabi, Nasim; Burn, Paul L; Meredith, Paul; Shaw, Paul E

    2016-07-21

    Transient absorption spectroscopy on organic semiconductor blends for solar cells typically shows efficient charge generation within ∼100 fs, accounting for the majority of the charge carriers. In this Letter, we show using transient absorption spectroscopy on blends containing a broad range of acceptor content (0.01-50% by weight) that the rise of the polaron signal is dependent on the acceptor concentration. For low acceptor content (10%) most polarons are generated within 200 fs. The rise time in blends with low acceptor content was also found to be sensitive to the pump fluence, decreasing with increasing excitation density. These results indicate that the sub-100 fs rise of the polaron signal is a natural consequence of both the high acceptor concentrations in many donor-acceptor blends and the high excitation densities needed for transient absorption spectroscopy, which results in a short average distance between the exciton and the donor-acceptor interface.

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

    Science.gov (United States)

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

    2013-10-28

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

  16. 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...

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

    DEFF Research Database (Denmark)

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

    experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated...... the free energy changes of the initial tetramer dissociation under different conditions and in the presence of thyroxine....

  18. A variational study of the self-trapped magnetic polaron formation in double-exchange model

    International Nuclear Information System (INIS)

    Liu Tao; Feng Mang; Wang Kelin

    2005-01-01

    We study the formation of self-trapped magnetic polaron (STMP) in an antiferro/ferromagnetic double-exchange model semi-analytically by variational solutions. It is shown that the Jahn-Teller effect is not essential to the STMP formation and the STMP forms in the antiferromagnetic material within the region of the order of the lattice constant. We also confirm that no ground state STMP exists in the ferromagnetic background, but the ground state bound MP could appear due to the impurity potential

  19. Polarons as stable solitary wave solutions to the Dirac-Coulomb system

    Science.gov (United States)

    Comech, Andrew; Zubkov, Mikhail

    2013-11-01

    We consider solitary wave solutions to the Dirac-Coulomb system both from physical and mathematical points of view. Fermions interacting with gravity in the Newtonian limit are described by the model of Dirac fermions with the Coulomb attraction. This model also appears in certain condensed matter systems with emergent Dirac fermions interacting via optical phonons. In this model, the classical soliton solutions of equations of motion describe the physical objects that may be called polarons, in analogy to the solutions of the Choquard equation. We develop analytical methods for the Dirac-Coulomb system, showing that the no-node gap solitons for sufficiently small values of charge are linearly (spectrally) stable.

  20. Bound magnetic polaron driven low-temperature ferromagnetism in Cu1-xMnxO compounds

    Science.gov (United States)

    Cai, J. Z.; Li, L.; Wang, S.; Zou, W. Q.; Wu, X. S.; Zhang, F. M.

    2013-09-01

    Partial Mn atoms have been confirmed to enter the CuO lattice and form the Cu1-xMnxO compounds in the case of doping with 0≤x≤0.2 by the sol-gel method. With increasing Mn content, magnetism is observed. The magnetic critical transition temperature increases with enhanced magnetism, which obeys the bound magnetic polaron theory. The electronic transportation shows an insulating behavior as the band-gap decreases. Our results may indicate that CuO may be used as a candidate of magnetic semiconductor.

  1. 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 )

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

    International Nuclear Information System (INIS)

    Birkholz, M.; Rudert, R.

    1995-01-01

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

  3. Molecular-weight dependence of interchain polaron delocalization and exciton bandwidth in high-mobility conjugated polymers

    DEFF Research Database (Denmark)

    Chang, J.F.; Clark, J.; Zhao, N.

    2006-01-01

    here a detailed study of interchain interaction effects on both charged polarons as well as neutral excitons in highly crystalline, high-mobility poly-3-hexylthiophene (P3HT) as a function of molecular weight. We find experimental evidence for reduced exciton bandwidth and increased polaron...... delocalization with increasing conjugation length and crystalline quality. From comparative studies of field-effect transistor characteristics, film morphology, and optical properties our study provides a microscopic understanding of the factors which limit the charge transport in P3HT to field-effect mobilities...

  4. 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.

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

    Science.gov (United States)

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

    2013-01-07

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

  6. 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

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

    International Nuclear Information System (INIS)

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

    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)

  8. Polaronic behavior in a weak-coupling superconductor.

    Science.gov (United States)

    Swartz, Adrian G; Inoue, Hisashi; Merz, Tyler A; Hikita, Yasuyuki; Raghu, Srinivas; Devereaux, Thomas P; Johnston, Steven; Hwang, Harold Y

    2018-02-13

    The nature of superconductivity in the dilute semiconductor SrTiO 3 has remained an open question for more than 50 y. The extremely low carrier densities ([Formula: see text]-[Formula: see text] cm -3 ) at which superconductivity occurs suggest an unconventional origin of superconductivity outside of the adiabatic limit on which the Bardeen-Cooper-Schrieffer (BCS) and Migdal-Eliashberg (ME) theories are based. We take advantage of a newly developed method for engineering band alignments at oxide interfaces and access the electronic structure of Nb-doped SrTiO 3 , using high-resolution tunneling spectroscopy. We observe strong coupling to the highest-energy longitudinal optic (LO) phonon branch and estimate the doping evolution of the dimensionless electron-phonon interaction strength ([Formula: see text]). Upon cooling below the superconducting transition temperature ([Formula: see text]), we observe a single superconducting gap corresponding to the weak-coupling limit of BCS theory, indicating an order of magnitude smaller coupling ([Formula: see text]). These results suggest that despite the strong normal state interaction with electrons, the highest LO phonon does not provide a dominant contribution to pairing. They further demonstrate that SrTiO 3 is an ideal system to probe superconductivity over a wide range of carrier density, adiabatic parameter, and electron-phonon coupling strength.

  9. Bose polaron as an instance of quantum Brownian motion

    Directory of Open Access Journals (Sweden)

    Aniello Lampo

    2017-09-01

    Full Text Available We study the dynamics of a quantum impurity immersed in a Bose-Einstein condensate as an open quantum system in the framework of the quantum Brownian motion model. We derive a generalized Langevin equation for the position of the impurity. The Langevin equation is an integrodifferential equation that contains a memory kernel and is driven by a colored noise. These result from considering the environment as given by the degrees of freedom of the quantum gas, and thus depend on its parameters, e.g. interaction strength between the bosons, temperature, etc. We study the role of the memory on the dynamics of the impurity. When the impurity is untrapped, we find that it exhibits a super-diffusive behavior at long times. We find that back-flow in energy between the environment and the impurity occurs during evolution. When the particle is trapped, we calculate the variance of the position and momentum to determine how they compare with the Heisenberg limit. One important result of this paper is that we find position squeezing for the trapped impurity at long times. We determine the regime of validity of our model and the parameters in which these effects can be observed in realistic experiments.

  10. 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).

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

    Science.gov (United States)

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

    2010-12-22

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

  12. Multi-impurity polarons in a dilute Bose-Einstein condensate

    International Nuclear Information System (INIS)

    Santamore, D H; Timmermans, Eddy

    2011-01-01

    We describe the ground state of a large, dilute, neutral atom Bose-Einstein condensate (BEC) doped with N strongly coupled mutually indistinguishable, bosonic neutral atoms (referred to as ‘impurity’) in the polaron regime where the BEC density response to the impurity atoms remains significantly smaller than the average density of the surrounding BEC. We find that N impurity atoms with N ≠ 1 can self-localize at a lower value of the impurity-boson interaction strength than a single impurity atom. When the ‘bare’ short-range impurity-impurity repulsion does not play a significant role, the self-localization of multiple bosonic impurity atoms into the same single particle orbital (which we call co-self-localization) is the nucleation process of the phase separation transition. When the short-range impurity-impurity repulsion successfully competes with co-self-localization, the system may form a stable liquid of self-localized single impurity polarons. (paper)

  13. Observation of magnetic polarons in the magnetoresistive pyrochlore Lu2V2O7

    International Nuclear Information System (INIS)

    Storchak, Vyacheslav G; Brewer, Jess H; Eshchenko, Dmitry G; Mengyan, Patrick W; Zhou Haidong; Wiebe, Christopher R

    2013-01-01

    Materials that exhibit colossal magnetoresistance (CMR) have attracted much attention due to their potential technological applications. One particularly interesting model for the magnetoresistance of low-carrier-density ferromagnets involves mediation by magnetic polarons (MP)—electrons localized in nanoscale ferromagnetic ‘droplets’ by their exchange interaction. However, MP have not previously been directly detected and their size has been difficult to determine from macroscopic measurements. In order to provide this crucial information, we have carried out muon spin rotation measurements on the magnetoresistive semiconductor Lu 2 V 2 O 7 in the temperature range from 2 to 300 K and in magnetic fields up to 7 T. Magnetic polarons with characteristic radius R ≈ 0.4 nm are detected below about 100 K, where Lu 2 V 2 O 7 exhibits CMR; at higher temperature, where the magnetoresistance vanishes, these MP also disappear. This observation confirms the MP-mediated model of CMR and reveals the microscopic size of the MP in magnetoresistive pyrochlores. (paper)

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

    Science.gov (United States)

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

    2017-09-01

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

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

    International Nuclear Information System (INIS)

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

    1995-01-01

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

  16. 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

  17. 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.

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

    Science.gov (United States)

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

    2018-01-01

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

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

    Science.gov (United States)

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

    2005-05-18

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

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    Understanding protein adsorption is a key to the development of biosensors and anti-biofouling materials. Hydration essentially controls the adsorption process on hydrophobic surfaces, but its effect is complicated by various factors. Here, we present an ideal model system to isolate hydration effects—lysozyme adsorption on a flat hydrophobic graphene surface. Our all-atom molecular dynamics and molecular-mechanics/Poisson-Boltzmann surface area computation study reveal that lysozyme on graphene displays much larger diffusivity than in bulk water. Protein's hydration free energy within the first hydration shell is dominated by the protein-water electrostatic interactions and acts as an energy barrier for protein adsorption. On the other hand, the surface tension, especially that from the hydrophobic graphene, can effectively weaken the barrier to promote adsorption

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

    Energy Technology Data Exchange (ETDEWEB)

    Nakano, C. Masato [Flintridge Preparatory School, La Canada Flintridge, California 91011 (United States); Ma, Heng; Wei, Tao, E-mail: twei@lamar.edu [Dan F. Smith Department of Chemical Engineering, Lamar University, Beaumont, Texas 77710 (United States)

    2015-04-13

    Understanding protein adsorption is a key to the development of biosensors and anti-biofouling materials. Hydration essentially controls the adsorption process on hydrophobic surfaces, but its effect is complicated by various factors. Here, we present an ideal model system to isolate hydration effects—lysozyme adsorption on a flat hydrophobic graphene surface. Our all-atom molecular dynamics and molecular-mechanics/Poisson-Boltzmann surface area computation study reveal that lysozyme on graphene displays much larger diffusivity than in bulk water. Protein's hydration free energy within the first hydration shell is dominated by the protein-water electrostatic interactions and acts as an energy barrier for protein adsorption. On the other hand, the surface tension, especially that from the hydrophobic graphene, can effectively weaken the barrier to promote adsorption.

  2. 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

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

    Science.gov (United States)

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

    2018-03-12

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Jia, Juanjuan [Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay (France); CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351, Université Paris Sud, 91405 Orsay (France); Kara, Abdelkader, E-mail: abdelkader.kara@ucf.edu, E-mail: vladimir.esaulov@u-psud.fr [Department of Physics, University of Central Florida, Orlando, Florida 32816 (United States); Pasquali, Luca [Dipartimento di Ingegneria “E. Ferrari,” Università di Modena e Reggio Emilia, Via Vignolese 905, 41125 Modena (Italy); IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste (Italy); Department of Physics, University of Johannesburg, P.O. Box 524, Auckland Park 2006 (South Africa); Bendounan, Azzedine; Sirotti, Fausto [Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48, F-91192 Gif-sur-Yvette Cedex (France); Esaulov, Vladimir A., E-mail: abdelkader.kara@ucf.edu, E-mail: vladimir.esaulov@u-psud.fr [Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay (France); CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351, Université Paris Sud, 91405 Orsay (France); IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste (Italy)

    2015-09-14

    Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S–C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments.

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

    Science.gov (United States)

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

    2018-03-22

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-12-15

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

  7. 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.

  8. 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

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

    Science.gov (United States)

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

    2012-08-01

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

  10. 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.

  11. Femtosecond dynamics of excitons and hole-polarons in composite P3HT/PCBM nanoparticles.

    Science.gov (United States)

    Clafton, Scott N; Huang, David M; Massey, William R; Kee, Tak W

    2013-04-25

    The dynamics of charge separation in aqueous suspensions of regioregular P3HT nanoparticles containing PCBM were investigated for the first time using femtosecond transient absorption spectroscopy. This investigation is supported by the recently reported use of regioregular P3HT/PCBM nanoparticles as charge trapping and storage devices. In this study, the presence of excited-state and charge-separated species, including singlet excitons, polymer polarons and free charges, generated in rr-P3HT/PCBM nanoparticles was identified through visible pump and visible/near-infrared probe femtosecond transient absorption spectroscopy at a range of electron acceptor concentrations. The decrease of the singlet exciton lifetime by charge transfer to PCBM is well described by a one-dimensional diffusion model with a P3HT domain size of approximately 5 nm for 5-50 wt % PCBM. This model also indicates that bimolecular recombination is the dominant charge recombination mechanism at 20 wt % PCBM and above.

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

    International Nuclear Information System (INIS)

    Soloviov, Maksym; Meuwly, Markus

    2015-01-01

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

  13. 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

  14. 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

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

    Science.gov (United States)

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

    2018-01-01

    Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design data resource (D3R) organizes challenges against blinded experimental data to prospectively test computational methodologies as an opportunity for improved methods and algorithms to emerge. We participated in Grand Challenge 2 to predict the crystallographic poses of 36 Farnesoid X Receptor (FXR)-bound ligands and the relative binding affinities for two designated subsets of 18 and 15 FXR-bound ligands. Here, we present our methodology for pose and affinity predictions and its evaluation after the release of the experimental data. For predicting the crystallographic poses, we used docking and physics-based pose prediction methods guided by the binding poses of native ligands. For FXR ligands with known chemotypes in the PDB, we accurately predicted their binding modes, while for those with unknown chemotypes the predictions were more challenging. Our group ranked #1st (based on the median RMSD) out of 46 groups, which submitted complete entries for the binding pose prediction challenge. For the relative binding affinity prediction challenge, we performed free energy perturbation (FEP) calculations coupled with molecular dynamics (MD) simulations. FEP/MD calculations displayed a high success rate in identifying compounds with better or worse binding affinity than the reference (parent) compound. Our studies suggest that when ligands with chemical precedent are available in the literature, binding pose predictions using docking and physics-based methods are reliable; however, predictions are challenging for ligands with completely unknown chemotypes. We also show that FEP/MD calculations hold predictive value and can nowadays be used in a high throughput mode in a lead optimization project provided that crystal structures of

  16. 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.

  17. 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.

  18. 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.

  19. 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.

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

    Science.gov (United States)

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

    2015-04-27

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

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

    Science.gov (United States)

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

    2007-03-01

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

  2. 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.

  3. 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)

  4. Investigation of the binding free energies of FDA approved drugs against subtype B and C-SA HIV PR: ONIOM approach.

    Science.gov (United States)

    Sanusi, Z K; Govender, T; Maguire, G E M; Maseko, S B; Lin, J; Kruger, H G; Honarparvar, B

    2017-09-01

    Human immune virus subtype C is the most widely spread HIV subtype in Sub-Sahara Africa and South Africa. A profound structural insight on finding potential lead compounds is therefore necessary for drug discovery. The focus of this study is to rationalize the nine Food and Drugs Administration (FDA) HIV antiviral drugs complexed to subtype B and C-SA PR using ONIOM approach. To achieve this, an integrated two-layered ONIOM model was used to optimize the geometrics of the FDA approved HIV-1 PR inhibitors for subtype B. In our hybrid ONIOM model, the HIV-1 PR inhibitors as well as the ASP 25/25' catalytic active residues were treated at high level quantum mechanics (QM) theory using B3LYP/6-31G(d), and the remaining HIV PR residues were considered using the AMBER force field. The experimental binding energies of the PR inhibitors were compared to the ONIOM calculated results. The theoretical binding free energies (?G bind ) for subtype B follow a similar trend to the experimental results, with one exemption. The computational model was less suitable for C-SA PR. Analysis of the results provided valuable information about the shortcomings of this approach. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide much improved binding energies for complex enzyme drug interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2015-01-22

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

  6. When polarons meet polaritons: Exciton-vibration interactions in organic molecules strongly coupled to confined light fields

    Science.gov (United States)

    Wu, Ning; Feist, Johannes; Garcia-Vidal, Francisco J.

    2016-11-01

    We present a microscopic semianalytical theory for the description of organic molecules interacting strongly with a cavity mode. Exciton-vibration coupling within the molecule and exciton-cavity interaction are treated on an equal footing by employing a temperature-dependent variational approach. The interplay between strong exciton-vibration coupling and strong exciton-cavity coupling gives rise to a hybrid ground state, which we refer to as the lower polaron polariton. Explicit expressions for the ground-state wave function, the zero-temperature quasiparticle weight of the lower polaron polariton, the photoluminescence line strength, and the mean number of vibrational quanta are obtained in terms of the optimal variational parameters. The dependence of these quantities upon the exciton-cavity coupling strength reveals that strong cavity coupling leads to an enhanced vibrational dressing of the cavity mode, and at the same time a vibrational decoupling of the dark excitons, which in turn results in a lower polaron polariton resembling a single-mode dressed bare lower polariton in the strong-coupling regime. Thermal effects on several observables are briefly discussed.

  7. Polaronic and bipolaronic structures in the adiabatic Hubbard-Holstein model involving 2 electrons and its extensions

    International Nuclear Information System (INIS)

    Proville, L.

    1998-01-01

    This thesis brings its contribution to the bipolaronic theory which might explain the origin of superconductivity at high temperature. A polaron is a quasiparticle made up of a localized electron and a deformation in the crystal structure. 2 electrons in singlet states localized on the same site form a bipolaron. Whenever the Coulomb repulsion between the 2 electrons is too strong bipolaron turns into 2 no bound polarons. We study the existence and the mobility of bipolarons. We describe the electron-phonon interaction by the Holstein term and the Coulomb repulsion by the Hubbard term. 2 assumptions are made: - the local electron-phonon interaction is strong and opposes the Coulomb repulsion between Hubbard type electrons - the system is close to the adiabatic limit. The system is reduced to 2 electrons in order to allow an exact treatment and the investigation of some bipolaronic bound states. At 2-dimensions the existence of bipolarons requires a very strong coupling which forbids any classical mobility. In some cases an important tunneling effect appears and we show that mobile bipolarons exist in a particular parameter range. Near the adiabatic limit we prove that polaronic and bipolaronic structures exist for a great number of electrons. (A.C.)

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

    Science.gov (United States)

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

    2017-11-01

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

  9. Large polaron tunneling, magnetic and impedance analysis of magnesium ferrite nanocrystallite

    Energy Technology Data Exchange (ETDEWEB)

    Mahato, Dev K., E-mail: drdevkumar@yahoo.com [Department of Physics, National Institute of Technology Patna, Patna 800 005 (India); Majumder, Sumit [Department of Physics, Jadavpur University, Kolkata 700032 (India); Surface Physics and Material Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700 064 (India); Banerjee, S. [Surface Physics and Material Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700 064 (India)

    2017-08-15

    Graphical abstract: The diffraction peaks corresponding to the planes (111), (220), (311), (222), (400), (422), (511), (440), (620), (533) and (444) provide a clear evidence for the formation of spinel structure of the ferrites. The lattice parameter ‘a’ determined as 8.392 Å matches well with JCPDS (73-2410) file for MgFe{sub 2}O{sub 4.} The volume of the unit cell is 591.012 Å{sup 3}. The crystallite size of the synthesized powder estimated from X-ray peak broadening of (311) highest intensity diffraction peak using Scherer formula was 56.4 nm. - Highlights: • Both the grain and grain boundaries contribution to conductivity of the Mg-ferrite has been observed. • Polydispersive nature of the material is checked using Cole – Cole relation. • The ac conductivity of magnesium ferrite followed σ{sub ac} ∝ ω{sup n} dependence. • The variation of the exponent ‘n’ with temperature suggests that overlapping large polaron tunnelling is the dominant conduction mechanism. • The superparamagnetic behavior of this Mg-ferrite has been observed for sample S1 annealed at 500 °C. - Abstract: Single phase MgFe{sub 2}O{sub 4} (MFO) ferrite was prepared through sol-gel auto-combustion route. The Rietveld analysis of X-ray patterns reveals that our samples are single phase. The increase in average particle size with annealing temperature and formation of nanoparticle agglomerates is observed in MgFe{sub 2}O{sub 4}. The structural morphology of the nanoparticles is studied using Scanning Electron Microscopy (SEM). Formation of spinel structure is confirmed using Fourier transform infrared spectroscopy (FTIR). The Zero-Field-Cooled (ZFC) and Field-Cooled (FC) magnetization measurements show the maximum irreversibility at 700 °C annealing temperature. The formation of a maximum at blocking temperature, T{sub B}∼ 180 K for sample annealed at 500 °C in the ZFC curve shows the superparamagnetic behavior of the sample. The increase of saturation magnetism (M

  10. Spin dynamics and spin-dependent recombination of a polaron pair under a strong ac drive

    Science.gov (United States)

    Malla, Rajesh K.; Raikh, M. E.

    2017-08-01

    We study theoretically the recombination within a pair of two polarons in magnetic field subject to a strong linearly polarized ac drive. Strong drive implies that the Zeeman frequencies of the pair partners are much smaller than the Rabi frequency, so that the rotating wave approximation does not apply. What makes the recombination dynamics nontrivial is that the partners recombine only when they form a singlet S . By admixing singlet to triplets, the drive induces the triplet recombination as well. We calculate the effective decay rate of all four spin modes. Our main finding is that, under the strong drive, the major contribution to the decay of the modes comes from short time intervals when the driving field passes through zero. When the recombination time in the absence of drive is short, fast recombination from S leads to anomalously slow recombination from the other spin states of the pair. We show that, with strong drive, this recombination becomes even slower. The corresponding decay rate falls off as a power law with the amplitude of the drive.

  11. Bound magnetic polaron in Zn-rich cobalt-doped ZnSe nanowires

    Science.gov (United States)

    Hou, Lipeng; Pan, Longfei; Liang, Bianbian; Liu, Yuting; Zhang, Li; Bukhtiar, Arfan; Shi, Lijie; Liu, Ruibin; Zou, Bingsuo

    2018-02-01

    The micro-luminescence spectra of the diluted magnetic semiconductor (DMS) can reflect the spin-exciton interaction and related relaxation process. Here the micro-photoluminescence (micro-PL) spectra and PL lifetime measurements have been done on an individual ferromagnetic (FM)-coupled cobalt (Co) doped zinc selenide (ZnSe) nanowire. There occurs a double-peak profile in its near bandedge emission spectrum: the first peak is from free exciton (FX) and the second comes from magnetic polaron (MP). In their temperature dependent PL spectra, the MP emission peak demonstrates obviously temperature-independent behavior, in contrast to the behaviors of FX and reported exciton MP in nanobelt. It is found that in this Co(II) doped ZnSe nanowires, this MP’s temperature-independent emission is related to the coupling between exciton and a FM nanocluster (↑↑↓). The nanocluster is likely due to the interaction of Se vacancies of the wide bandgap semiconductors with the antiferromagnetic (AFM) arrangement transition metal (TM) ions in these Se-deficient Co doped ZnSe nanowires. These results reflect that the AFM coupling TM ions pair can give rise to FM behavior with the involvement of positive charge defect, also indicating that the micro-luminescence detection can be used to study the magnetic coupling in DMS.

  12. Communication: regularizing binding energy distributions and thermodynamics of hydration: theory and application to water modeled with classical and ab initio simulations.

    Science.gov (United States)

    Weber, Valéry; Merchant, Safir; Asthagiri, D

    2011-11-14

    The high-energy tail of the distribution of solute-solvent interaction energies is poorly characterized for condensed systems, but this tail region is of principal interest in determining the excess free energy of the solute. We introduce external fields centered on the solute to modulate the short-range repulsive interaction between the solute and solvent. This regularizes the binding energy distribution and makes it easy to calculate the free energy of the solute with the field. Together with the work done to apply the field in the presence and absence of the solute, we calculate the excess chemical potential of the solute. We present the formal development of this idea and apply it to study liquid water. © 2011 American Institute of Physics

  13. Observation of core-level binding energy shifts between (100) surface and bulk atoms of epitaxial CuInSe{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, A.J. [Colorado School of Mines, Golden, CO (United States); Berry, G.; Rockett, A. [Univ. of Illinois, Urbana-Champaign, IL (United States)] [and others

    1997-04-01

    Core-level and valence band photoemission from semiconductors has been shown to exhibit binding energy differences between surface atoms and bulk atoms, thus allowing one to unambiguously distinguish between the two atomic positions. Quite clearly, surface atoms experience a potential different from the bulk due to the lower coordination number - a characteristic feature of any surface is the incomplete atomic coordination. Theoretical accounts of this phenomena are well documented in the literature for III-V and II-VI semiconductors. However, surface state energies corresponding to the equilibrium geometry of (100) and (111) surfaces of Cu-based ternary chalcopyrite semiconductors have not been calculated or experimental determined. These compounds are generating great interest for optoelectronic and photovoltaic applications, and are an isoelectronic analog of the II-VI binary compound semiconductors. Surface core-level binding energy shifts depend on the surface cohesive energies, and surface cohesive energies are related to surface structure. For ternary compound semiconductor surfaces, such as CuInSe{sub 2}, one has the possibility of variations in surface stoichiometry. Applying standard thermodynamical calculations which consider the number of individual surface atoms and their respective chemical potentials should allow one to qualitatively determine the magnitude of surface core-level shifts and, consequently, surface state energies.

  14. Dissociation kinetics of excited ions: PEPICO measurements of Os3(CO)12 — The 7-35 eV single ionization binding energy region

    Science.gov (United States)

    Schalk, Oliver; Josefsson, Ida; Geng, Ting; Richter, Robert; Sa'adeh, Hanan; Thomas, Richard D.; Mucke, Melanie

    2018-02-01

    In this article, we study the photoinduced dissociation pathways of a metallocarbonyl, Os3(CO)12, in particular the consecutive loss of CO groups. To do so, we performed photoelectron-photoion coincidence (PEPICO) measurements in the single ionization binding energy region from 7 to 35 eV using 45-eV photons. Zero-energy ion appearance energies for the dissociation steps were extracted by modeling the PEPICO data using the statistical adiabatic channel model. Upon ionization to the excited ionic states above 13 eV binding energy, non-statistical behavior was observed and assigned to prompt CO loss. Double ionization was found to be dominated by the knockout process with an onset of 20.9 ± 0.4 eV. The oscillator strength is significantly larger for energies above 26.6 ± 0.4 eV, corresponding to one electron being ejected from the Os3 center and one from the CO ligands. The cross section for double ionization was found to increase linearly up to 35 eV ionization energy, at which 40% of the generated ions are doubly charged.

  15. 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.

  16. Binding Energies of the pi-Stacked Anisole Dimer: New Molecular Beam-Laser Spectroscopy Experiments and CCSD(T) Calculations

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Nachtigallová, Dana; Mazzoni, F.; Pasquini, M.; Pietraperzia, G.; Becucci, M.; Müller-Dethlefs, K.; Hobza, Pavel

    2015-01-01

    Roč. 21, č. 18 (2015), s. 6740-6746 ISSN 0947-6539 R&D Projects: GA ČR GBP208/12/G016 Grant - others:GA MŠk(CZ) ED2.1.00/03.0058 Program:ED Institutional support: RVO:61388963 Keywords : binding energy * noncovalent interactions * pi stacking * laser spectroscopy * CCSD(T) calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.771, year: 2015

  17. Cation-pi interactions with a model for the side chain of tryptophan: structures and absolute binding energies of alkali metal cation-indole complexes.

    Science.gov (United States)

    Ruan, Chunhai; Yang, Zhibo; Hallowita, Nuwan; Rodgers, M T

    2005-12-22

    Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.

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

    Science.gov (United States)

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

    2017-04-24

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

  19. First-Principle Framework for Total Charging Energies in Electrocatalytic Materials and Charge-Responsive Molecular Binding at Gas-Surface Interfaces.

    Science.gov (United States)

    Tan, Xin; Tahini, Hassan A; Seal, Prasenjit; Smith, Sean C

    2016-05-04

    Heterogeneous charge-responsive molecular binding to electrocatalytic materials has been predicted in several recent works. This phenomenon offers the possibility of using voltage to manipulate the strength of the binding interaction with the target gas molecule and thereby circumvent thermochemistry constraints, which inhibit achieving both efficient binding and facile release of important targets such as CO2 and H2. Stability analysis of such charge-induced molecular adsorption has been beyond the reach of existing first-principle approaches. Here, we draw on concepts from semiconductor physics and density functional theory to develop a first principle theoretical approach that allows calculation of the change in total energy of the supercell due to charging. Coupled with the calculated adsorption energy of gas molecules at any given charge, this allows a complete description of the energetics of the charge-induced molecular adsorption process. Using CO2 molecular adsorption onto negatively charged h-BN (wide-gap semiconductor) and g-C4N3 (half metal) as example cases, our analysis reveals that - while adsorption is exothermic after charge is introduced - the overall adsorption processes are not intrinsically spontaneous due to the energetic cost of charging the materials. The energies needed to overcome the barriers of these processes are 2.10 and 0.43 eV for h-BN and g-C4N3, respectively. This first principle approach opens up new pathways for a more complete description of charge-induced and electrocatalytic processes.

  20. The role of extra-atomic relaxation in determining Si2p binding energy shifts at silicon/silicon oxide interfaces

    International Nuclear Information System (INIS)

    Zhang, K.Z.; Greeley, J.N.; Banaszak Holl, M.M.; McFeely, F.R.

    1997-01-01

    The observed binding energy shift for silicon oxide films grown on crystalline silicon varies as a function of film thickness. The physical basis of this shift has previously been ascribed to a variety of initial state effects (Si endash O ring size, strain, stoichiometry, and crystallinity), final state effects (a variety of screening mechanisms), and extrinsic effects (charging). By constructing a structurally homogeneous silicon oxide film on silicon, initial state effects have been minimized and the magnitude of final state stabilization as a function of film thickness has been directly measured. In addition, questions regarding the charging of thin silicon oxide films on silicon have been addressed. From these studies, it is concluded that initial state effects play a negligible role in the thickness-dependent binding energy shift. For the first ∼30 Angstrom of oxide film, the thickness-dependent binding energy shift can be attributed to final state effects in the form of image charge induced stabilization. Beyond about 30 Angstrom, charging of the film occurs. copyright 1997 American Institute of Physics

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

    International Nuclear Information System (INIS)

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

    2014-01-01

    We present and test a new approximation for the exchange-correlation (xc) energy of Kohn-Sham density functional theory. It combines exact exchange with a compatible non-local correlation functional. The functional is by construction free of one-electron self-interaction, respects constraints derived from uniform coordinate scaling, and has the correct asymptotic behavior of the xc energy density. It contains one parameter that is not determined ab initio. We investigate whether it is possible to construct a functional that yields accurate binding energies and affords other advantages, specifically Kohn-Sham eigenvalues that reliably reflect ionization potentials. Tests for a set of atoms and small molecules show that within our local-hybrid form accurate binding energies can be achieved by proper optimization of the free parameter in our functional, along with an improvement in dissociation energy curves and in Kohn-Sham eigenvalues. However, the correspondence of the latter to experimental ionization potentials is not yet satisfactory, and if we choose to optimize their prediction, a rather different value of the functional's parameter is obtained. We put this finding in a larger context by discussing similar observations for other functionals and possible directions for further functional development that our findings suggest

  2. An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles

    Science.gov (United States)

    Xu, Beisi; Yang, Yuedong; Liang, Haojun; Zhou, Yaoqi

    2009-01-01

    How to make an accurate representation of protein-DNA interactions by an energy function is a long-standing unsolved problem in structural biology. Here, we modified a statistical potential based on the distance-scaled, finite ideal-gas reference state (DFIRE) so that it is optimized for protein-DNA interactions. The changes include a volume-fraction correction to account for unmixable atom types in proteins and DNA in addition to the usage of a low-count correction, residue/base-specific atom types, and a shorter cutoff distance for protein-DNA interactions. The new statistical energy functions are tested in threading and docking decoy discriminations and prediction of protein-DNA binding affinities and transcription-factor binding profiles. Results indicate that new proposed energy functions are among the best in existing energy functions for protein-DNA interactions. The new energy functions are available as a web-server called DDNA 2.0 at http://sparks.informatics.iupui.edu. The server version was trained by the entire 212 protein-DNA complexes. PMID:19274740

  3. 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.

  4. Measurement of the resonant polaron effect in the Reststrahlen band of GaAs:Si using far-infrared two-photon excitation

    International Nuclear Information System (INIS)

    Wenckebach, W.Th.; Planken, P.C.M.; Son, P.C. van

    1995-01-01

    We present the results of photoconductivity measurements of the resonant electron-phonon interaction in the middle of the Reststrahlen band using two-photon excitation with intense picosecond pulses with frequency around 143 cm -1 (70 μm). We use two photons rather than a single photon for the excitation of the resonant-polaron to avoid the problems of strong reflection and dielectric artifacts encountered in direct single-photon excitation in the Reststrahlen band. The sample is a 10 μm thick Si-doped GaAs epitaxial layer on a 400 μm semi-insulating GaAs substrate. The electronic levels of the Si shallow donor can be tuned by the application of a magnetic field. Intense tunable picosecond pulses with a frequency of around 143 cm -1 from the Dutch free-electron laser FELIX are weakly focussed onto the sample, which is kept at 8 K. Electrons excited to the 3d +2 state via the electric-dipole allowed two-photon transition out of the 1s 0- ground state, decay to the conduction band and give rise to an increase in the photoconductivity. The figure shows the energy-peak position of the 3d +2 transition thus obtained as a function of the magnetic-field strength. The figure clearly shows the avoided crossing around the LO-phonon energy where the coupling shows the avoided crossing around the LO-phonon energy where the coupling between the 3d +2 state and the LO phonon is strongest. Note that the data between 267 cm -1 and 296 cm -1 are extremely difficult to obtain with single-photon excitation because of their position in the middle of the Reststrahlen band

  5. First-principles investigation on the electronic efficiency and binding energy of the contacts formed by graphene and poly-aromatic hydrocarbon anchoring groups

    KAUST Repository

    Li, Yang

    2015-04-28

    © 2015 AIP Publishing LLC. The electronic efficiency and binding energy of contacts formed between graphene electrodes and poly-aromatic hydrocarbon (PAH) anchoring groups have been investigated by the non-equilibrium Green\\'s function formalism combined with density functional theory. Our calculations show that PAH molecules always bind in the interior and at the edge of graphene in the AB stacking manner, and that the binding energy increases following the increase of the number of carbon and hydrogen atoms constituting the PAH molecule. When we move to analyzing the electronic transport properties of molecular junctions with a six-carbon alkyne chain as the central molecule, the electronic efficiency of the graphene-PAH contacts is found to depend on the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the corresponding PAH anchoring group, rather than its size. To be specific, the smaller is the HOMO-LUMO gap of the PAH anchoring group, the higher is the electronic efficiency of the graphene-PAH contact. Although the HOMO-LUMO gap of a PAH molecule depends on its specific configuration, PAH molecules with similar atomic structures show a decreasing trend for their HOMO-LUMO gap as the number of fused benzene rings increases. Therefore, graphene-conjugated molecule-graphene junctions with high-binding and high-conducting graphene-PAH contacts can be realized by choosing appropriate PAH anchor groups with a large area and a small HOMO-LUMO gap.

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

    Science.gov (United States)

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

    2018-02-01

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

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

    Science.gov (United States)

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

    2012-09-25

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

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

    Science.gov (United States)

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

    2008-01-01

    We revisit the reactivity of trapped pure gold (Au(n)+, n cluster cations (Ag(m)Au(n)+, m + n adsorption sites, associated vibrational frequencies) of CO to the noble metal as a function of cluster size and composition. Starting from results for pure gold cluster cations for which an overall decrease of CO binding energy with increasing cluster size was experimentally observed--from about 1.09 +/- 0.1 eV (for n = 6) to below 0.65 +/- 0.1 eV (for n > 26) we demonstrate that metal--CO bond energies correlate with the total electron density and with the energy of the lowest unoccupied molecular orbital (LUMO) on the bare metal cluster cation as obtained by density functional theory (DFT) computations. This is a consequence of the predominantly sigma-donating character of the CO-M bond. Further support for this concept is found by contrasting the predictions of binding energies to the experimental results for small alloy cluster cations (Ag(m)Au(n)+, 4 adsorption sites and pre-screen favorable isomers.

  9. Inhibitor and peptide binding to calmodulin characterized by high pressure Fourier transform infrared spectroscopy and Förster resonance energy transfer.

    Science.gov (United States)

    Cinar, Süleyman; Czeslik, Claus

    2018-03-17

    We compare the binding of an inhibitor with that of a natural peptide to Ca 2+ saturated calmodulin (holo-CaM). As inhibitor we have chosen trifluoperazine (TFP) that is inducing a huge conformational change of holo-CaM from the open dumbbell-shaped to the closed globular conformation upon binding. On the other hand, melittin is used as model peptide, which is a well-known natural binding partner of holo-CaM. The experiments are carried out as a function of pressure to reveal the contribution of volume or packing effects to the stability of the calmodulin-ligand complexes. From high-pressure Fourier transform infrared (FTIR) spectroscopy, we find that the holo-CaM/TFP complex has a much higher pressure stability than the holo-CaM/melittin complex. Although the analysis of the secondary structure of holo-CaM (without and with ligand) indicates no major changes up to several kbar, pressure-induced exposure of α-helices to water is most pronounced for holo-CaM without ligand, followed by holo-CaM/melittin and then holo-CaM/TFP. Moreover, structural pressure resistance of the holo-CaM/TFP complex in comparison with the holo-CaM/melittin complex is also clearly visible by higher Ca 2+ affinity. Förster resonance energy transfer (FRET) from the Tyr residues of holo-CaM to the Trp residue of melittin even suggests some partial dissociation of the complex under pressure which points to void volumes at the protein-ligand interface and to electrostatic binding. Thus, all results of this study show that the inhibitor TFP binds to holo-CaM with higher packing density than the peptide melittin enabling a favorable volume contribution to the inhibitor efficiency. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. Comparison of gas-solid chromatography and MM2 force field molecular binding energies for greenhouse gases on a carbonaceous surface.

    Science.gov (United States)

    Rybolt, Thomas R; Bivona, Kevin T; Thomas, Howard E; O'Dell, Casey M

    2009-10-01

    Gas-solid chromatography was used to determine B(2s) (gas-solid virial coefficient) values for eight molecular adsorbates interacting with a carbon powder (Carbopack B, Supelco). B(2s) values were determined by multiple size variant injections within the temperature range of 313-553 K. The molecular adsorbates included: carbon dioxide (CO(2)); tetrafluoromethane (CF(4)); hexafluoroethane (C(2)F(6)); 1,1-difluoroethane (C(2)H(4)F(2)); 1-chloro-1,1-difluoroethane (C(2)H(3)ClF(2)); dichlorodifluoromethane (CCl(2)F(2)); trichlorofluoromethane (CCl(3)F); and 1,1,1-trichloroethane (C(2)H(3)Cl(3)). Two of these molecules are of special interest because they are "super greenhouse gases". The global warming potential, GWP, for CF(4) is 6500 and for C(2)F(6) is 9200 relative to the reference value of 1 for CO(2). The GWP index considers both radiative blocking and molecular lifetime. For these and other industrial greenhouse gases, adsorptive trapping on a carbonaceous solid, which depends on molecule-surface binding energy, could avoid atmospheric release. The temperature variations of the gas-solid virial coefficients in conjunction with van't Hoff plots were used to find the experimental adsorption energy or binding energy values (E(*)) for each adsorbate. A molecular mechanics based, rough-surface model was used to calculate the molecule-surface binding energy (Ecal(*)) using augmented MM2 parameters. The surface model consisted of parallel graphene layers with two separated nanostructures each containing 17 benzene rings arranged in linear strips. The separation of the parallel nanostructures had been optimized in a prior study to appropriately represent molecule-surface interactions for Carbopack B. Linear regressions of E(*) versus Ecal(*) for the current data set of eight molecules and the same surface model gave E(*)=0.926 Ecal(*) and r(2)=0.956. A combined set of the current and prior Carbopack B adsorbates studied (linear alkanes, branched alkanes, cyclic alkanes

  11. Interplay of cross-plane polaronic transport and resistive switching in Pt–Pr0.67Ca0.33MnO3–Pt heterostructures

    International Nuclear Information System (INIS)

    Scherff, M; Hoffmann, J; Meyer, B; Danz, Th; Jooss, Ch

    2013-01-01

    The identification of the cross-plane electric transport mechanisms in different resistance states of metal–oxide sandwich structures is essential for gaining insights into the mechanisms of resistive switching (RS). Here, we present a systematic study of cross-plane electric transport properties of Pr 0.67 Ca 0.33 MnO 3 (PCMO) thin films sandwiched by precious Pt metal electrodes. We observe three different transport regimes: ohmic, nonlinear and RS. The nonlinear regime is associated with colossal magneto-resistance (CMR) and colossal electro-resistance (CER) effects. In contrast to RS, the CMR and CER are volatile resistance effects which persist only during application of strong magnetic or electric fields and they are restricted to low temperatures. At low current densities, the device resistance is dominated by small polaron hopping transport of the PCMO film. At higher electric current densities near the switching threshold, the interface resistance starts to dominate and remarkably also exhibits thermally activated transport properties. Our studies also shed light onto the interplay of colossal resistance effects and RS: at low temperatures, RS can be only induced by reduction of the PCMO resistivity through CMR and CER. This clearly demonstrates the key role of the current density for controlling the amplitude of non-volatile resistive changes. Conversely, the CMR can be used as a probe for the switching induced changes in disorder and correlations. At small switching amplitudes, we observe slight changes in polaron activation energy which can be attributed to changes at the interface. If the switching amplitude exceeds 1000% and more, the CMR effect in the device can be reversibly changed. This indicates persistent changes in electronic or lattice structure of large regions within the PCMO film. (paper)

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

    Science.gov (United States)

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

    2018-01-01

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

  13. Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface.

    Science.gov (United States)

    Löytynoja, T; Li, X; Jänkälä, K; Rinkevicius, Z; Ågren, H

    2016-07-14

    We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

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

    Directory of Open Access Journals (Sweden)

    Dimitrios Spiliotopoulos

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

  15. Role of polaron hopping in leakage current behavior of a SrTiO{sub 3} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Y., E-mail: yxc238@psu.edu; Randall, C. A.; Chen, L. Q. [Department of Materials Science and Engineering, Penn State University, University Park, Pennsylvania 16802 (United States); Bhattacharya, S. [Department of Materials Science and Engineering, Indian Institute of Technology Hyderabad, YM 502205 (India); Shen, J. [Department of Mathematics, Purdue University, West Lafayette, Indiana 47907 (United States)

    2013-12-14

    We studied the ionic/electronic transport and resistance degradation behavior of dielectric oxides by solving the electrochemical transport equations. Here, we took into account the non-periodical boundary conditions for the transport equations using the Chebyshev collocation algorithm. A sandwiched Ni|SrTiO{sub 3}|Ni capacitor is considered as an example under the condition of 1.0 V, 1.0 μm thickness for SrTiO{sub 3} layer, and a temperature of 150 °C. The applied voltage resulted in the migration of ionic defects (oxygen vacancies) from anode towards cathode. The simulated electric potential profile at steady state is in good agreement with the recent experimental observation. We introduced the possibility of polaron-hopping between Ti{sup 3+} and Ti{sup 4+} at the electrode interface. It is shown that both the oxygen vacancy transport and the polaron-hopping contribute to the resistance degradation of single crystal SrTiO{sub 3}, which is consistent with the experimental observations.

  16. Motif III in superfamily 2 "helicases" helps convert the binding energy of ATP into a high-affinity RNA binding site in the yeast DEAD-box protein Ded1.

    Science.gov (United States)

    Banroques, Josette; Doère, Monique; Dreyfus, Marc; Linder, Patrick; Tanner, N Kyle

    2010-03-05

    Motif III in the putative helicases of superfamily 2 is highly conserved in both its sequence and its structural context. It typically consists of the sequence alcohol-alanine-alcohol (S/T-A-S/T). Historically, it was thought to link ATPase activity with a "helicase" strand displacement activity that disrupts RNA or DNA duplexes. DEAD-box proteins constitute the largest family of superfamily 2; they are RNA-dependent ATPases and ATP-dependent RNA binding proteins that, in some cases, are able to disrupt short RNA duplexes. We made mutations of motif III (S-A-T) in the yeast DEAD-box protein Ded1 and analyzed in vivo phenotypes and in vitro properties. Moreover, we made a tertiary model of Ded1 based on the solved structure of Vasa. We used Ded1 because it has relatively high ATPase and RNA binding activities; it is able to displace moderately stable duplexes at a large excess of substrate. We find that the alanine and the threonine in the second and third positions of motif III are more important than the serine, but that mutations of all three residues have strong phenotypes. We purified the wild-type and various mutants expressed in Escherichia coli. We found that motif III mutations affect the RNA-dependent hydrolysis of ATP (k(cat)), but not the affinity for ATP (K(m)). Moreover, mutations alter and reduce the affinity for single-stranded RNA and subsequently reduce the ability to disrupt duplexes. We obtained intragenic suppressors of the S-A-C mutant that compensate for the mutation by enhancing the affinity for ATP and RNA. We conclude that motif III and the binding energy of gamma-PO(4) of ATP are used to coordinate motifs I, II, and VI and the two RecA-like domains to create a high-affinity single-stranded RNA binding site. It also may help activate the beta,gamma-phosphoanhydride bond of ATP. (c) 2009 Elsevier Ltd. All rights reserved.

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

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

    NARCIS (Netherlands)

    Dijkstra, Peter

    2016-01-01

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

  19. Ultrafast Dynamics of Localized and Delocalized Polaron Transitions in P3HT/PCBM Blend Materials: The Effects of PCBM Concentration

    Directory of Open Access Journals (Sweden)

    Alexandrou Ioannis

    2009-01-01

    Full Text Available Abstract Nowadays, organic solar cells have the interest of engineers for manufacturing flexible and low cost devices. The considerable progress of this nanotechnology area presents the possibility of investigating new effects from a fundamental science point of view. In this letter we highlight the influence of the concentration of fullerene molecules on the ultrafast transport properties of charged electrons and polarons in P3HT/PCBM blended materials which are crucial for the development of organic solar cells. Especially, we report on the femtosecond dynamics of localized (P2at 1.45 eV and delocalized (DP2at 1.76 eV polaron states of P3HT matrix with the addition of fullerene molecules as well as the free-electron relaxation dynamics of PCBM-related states. Our study shows that as PCBM concentration increases, the amplified exciton dissociation at bulk heterojunctions leads to increased polaron lifetimes. However, the increase in PCBM concentration can be directly related to the localization of polarons, creating thus two competing trends within the material. Our methodology shows that the effect of changes in structure and/or composition can be monitored at the fundamental level toward optimization of device efficiency.

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

    Science.gov (United States)

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

    2018-01-01

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

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

    Science.gov (United States)

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

    2018-01-01

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

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

    Science.gov (United States)

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

    2017-08-01

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

  3. Angle-resolved photoemission studies of lattice polaron formation in the cuprate Ca2CuO2Cl2

    Energy Technology Data Exchange (ETDEWEB)

    Shen, K.M.

    2010-05-03

    To elucidate the nature of the single-particle excitations in the undoped parent cuprates, we have performed a detailed study of Ca{sub 2}CuO{sub 2}Cl{sub 2} using photoemission spectroscopy. The photoemission lineshapes of the lower Hubbard band are found to be well-described by a polaron model. By comparing the lineshape and temperature dependence of the lower Hubbard band with additional O 2p and Ca 3p states, we conclude that the dominant broadening mechanism arises from the interaction between the photohole and the lattice. The strength of this interaction was observed to be strongly anisotropic and may have important implications for the momentum dependence of the first doped hole states.

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

    Science.gov (United States)

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

    2009-01-01

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

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

    Science.gov (United States)

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

    2010-02-01

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

  6. Magnetic field effect on state energies and transition frequency of a ...

    Indian Academy of Sciences (India)

    polaron in an anisotropic quantum dot (AQD) under an applied magnetic field along the z-direction. The effects of the magnetic field and the electron–phonon coupling strength are taken into account. It is found that the ground and the first excited state energies and the transition frequency are increas- ing functions of the ...

  7. Magnetic field effect on state energies and transition frequency of a ...

    Indian Academy of Sciences (India)

    By employing a variational method of the Pekar-type, which has different variational parameters in the – plane and the z -direction, we study the ground and the first excited state energies and transition frequency between the ground and the first excited states of a strong-coupling polaron in an anisotropic quantum dot ...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1992-02-01

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

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

    Science.gov (United States)

    Bishop, Kevin P.; Roy, Pierre-Nicholas

    2018-03-01

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

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

    Science.gov (United States)

    Bishop, Kevin P; Roy, Pierre-Nicholas

    2018-03-14

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Hoffer, P. B.

    1980-06-10

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

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

    Science.gov (United States)

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

    2017-01-19

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

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

    Science.gov (United States)

    Hallen, Mark A; Donald, Bruce R

    2016-05-01

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

  14. Degradation Mechanisms in Blue Phosphorescent Organic Light-Emitting Devices by Exciton-Polaron Interactions: Loss in Quantum Yield versus Loss in Charge Balance.

    Science.gov (United States)

    Zhang, Yingjie; Aziz, Hany

    2017-01-11

    We study the relative importance of deterioration of material quantum yield and charge balance to the electroluminescence stability of PHOLEDs, with a special emphasis on blue devices. Investigations show that the quantum yields of both host and emitter in the emission layer degrade due to exciton-polaron interactions and that the deterioration in material quantum yield plays the primary role in device degradation under operation. On the other hand, the results show that the charge balance factor is also affected by exciton-polaron interactions but only plays a secondary role in determining device stability. Finally, we show that the degradation mechanisms in blue PHOLEDs are fundamentally the same as those in green PHOLEDs. The limited stability of the blue devices is a result of faster deterioration in the quantum yield of the emitter.

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

    Science.gov (United States)

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

    2017-02-08

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

  16. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-02-28

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

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

    Science.gov (United States)

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

    2018-01-01

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

  19. Linear and non-linear infrared response of one-dimensional vibrational Holstein polarons in the anti-adiabatic limit: Optical and acoustical phonon models

    Science.gov (United States)

    Falvo, Cyril

    2018-02-01

    The theory of linear and non-linear infrared response of vibrational Holstein polarons in one-dimensional lattices is presented in order to identify the spectral signatures of self-trapping phenomena. Using a canonical transformation, the optical response is computed from the small polaron point of view which is valid in the anti-adiabatic limit. Two types of phonon baths are considered: optical phonons and acoustical phonons, and simple expressions are derived for the infrared response. It is shown that for the case of optical phonons, the linear response can directly probe the polaron density of states. The model is used to interpret the experimental spectrum of crystalline acetanilide in the C=O range. For the case of acoustical phonons, it is shown that two bound states can be observed in the two-dimensional infrared spectrum at low temperature. At high temperature, analysis of the time-dependence of the two-dimensional infrared spectrum indicates that bath mediated correlations slow down spectral diffusion. The model is used to interpret the experimental linear-spectroscopy of model α-helix and β-sheet polypeptides. This work shows that the Davydov Hamiltonian cannot explain the observations in the NH stretching range.

  20. Mobility balance in the light-emitting layer governs the polaron accumulation and operational stability of organic light-emitting diodes

    Science.gov (United States)

    Kim, Jae-Min; Lee, Chang-Heon; Kim, Jang-Joo

    2017-11-01

    Organic light-emitting diode (OLED) displays are lighter and more flexible, have a wider color gamut, and consume less power than conventional displays. Stable materials and the structural design of the device are important for OLED longevity. Control of charge transport and accumulation in the device is particularly important because the interaction of excitons and polarons results in material degradation. This research investigated the charge dynamics of OLEDs experimentally and by drift-diffusion modeling. Parallel capacitance-voltage measurements of devices provided knowledge of charge behavior at different driving voltages. A comparison of exciplex-forming co-host and single host structures established that the mobility balance in the emitting layers determined the amount of accumulated polarons in those layers. Consequently, an exciplex-forming co-host provides a superior structure in terms of device lifetime and efficiency because of its well-balanced mobility. Minimizing polaron accumulation is key to achieving long OLED device lifetimes. This is a crucial aspect of device physics that must be considered in the device design structure.

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

    Science.gov (United States)

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

    2004-06-01

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

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

    Science.gov (United States)

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

    2012-07-01

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

  3. Optimal Shell Thickness of Metal@Insulator Nanoparticles for Net Enhancement of Photogenerated Polarons in P3HT Films.

    Science.gov (United States)

    Goh, Wei-Peng; Williams, Evan L; Yang, Ren-Bin; Koh, Wee-Shing; Mhaisalkar, Subodh; Ooi, Zi-En

    2016-02-03

    Embedding metal nanoparticles in the active layer of organic solar cells has been explored as a route for improving charge carrier generation, with localized field enhancement as a proposed mechanism. However, embedded metal nanoparticles can also act as charge recombination sites. To suppress such recombination, the metal nanoparticles are commonly coated with a thin insulating shell. At the same time, this insulating shell limits the extent that the localized enhanced electric field influences charge generation in the organic medium. It is presumed that there is an optimal thickness which maximizes field enhancement effects while suppressing recombination. Atomic Layer Deposition (ALD) was used to deposit Al2O3 layers of different thicknesses onto silver nanoparticles (Ag NPs), in a thin film of P3HT. Photoinduced absorption (PIA) spectroscopy was used to study the dependence of the photogenerated P3HT(+) polaron population on the Al2O3 thickness. The optimal thickness was found to be 3-5 nm. This knowledge can be further applied in the design of metal nanoparticle-enhanced solar cells.

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

    Science.gov (United States)

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

    2016-03-01

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

  5. Solute-vacancy binding in aluminum

    International Nuclear Information System (INIS)

    Wolverton, C.

    2007-01-01

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

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

    Science.gov (United States)

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

    2017-02-01

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

  7. The effect of impurity on transition frequency of bound polaron in ...

    Indian Academy of Sciences (India)

    et al [16] used photoacoustic method to measure the optical absorption properties of as- prepared CdSe QRs. Employing scanning tunnelling microscopy technique, Talaat et al. [17] determined the energy band gap of a series of CdSe QR having different sizes at room temperature. Their results confirmed that the band ...

  8. Observation of attractive and repulsive polarons in a Bose-Einstein condensate

    DEFF Research Database (Denmark)

    Jørgensen, Nils Byg

    2016-01-01

    (BEC) has not yet been realized. Here, we use radio frequency spectroscopy of ultracold bosonic 39K atoms to experimentally demonstrate the existence of a well-defined quasiparticle state of an impurity interacting with a BEC. We measure the energy of the impurity both for attractive and repulsive...

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

    Science.gov (United States)

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

    2011-11-22

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

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

    Science.gov (United States)

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

    2011-01-01

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

  11. Energy

    International Nuclear Information System (INIS)

    Meister, F.; Ott, F.

    2002-01-01

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

  12. Energy

    International Nuclear Information System (INIS)

    Meister, F.

    2001-01-01

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

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

    Science.gov (United States)

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

    2018-04-01

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

  14. Localization-enhanced biexciton binding in semiconductors

    DEFF Research Database (Denmark)

    Langbein, Wolfgang Werner; Hvam, Jørn Märcher

    1999-01-01

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

  15. Theory of coherent resonance energy transfer

    International Nuclear Information System (INIS)

    Jang, Seogjoo; Cheng, Y.-C.; Reichman, David R.; Eaves, Joel D.

    2008-01-01

    A theory of coherent resonance energy transfer is developed combining the polaron transformation and a time-local quantum master equation formulation, which is valid for arbitrary spectral densities including common modes. The theory contains inhomogeneous terms accounting for nonequilibrium initial preparation effects and elucidates how quantum coherence and nonequilibrium effects manifest themselves in the coherent energy transfer dynamics beyond the weak resonance coupling limit of the Foerster and Dexter (FD) theory. Numerical tests show that quantum coherence can cause significant changes in steady state donor/acceptor populations from those predicted by the FD theory and illustrate delicate cooperation of nonequilibrium and quantum coherence effects on the transient population dynamics.

  16. Bound magnetic polaron driven low-temperature ferromagnetism in Cu{sub 1−x}Mn{sub x}O compounds

    Energy Technology Data Exchange (ETDEWEB)

    Cai, J.Z.; Li, L.; Wang, S.; Zou, W.Q.; Wu, X.S., E-mail: xswu@nju.edu.cn; Zhang, F.M., E-mail: fmzhang@nju.edu.cn

    2013-09-01

    Partial Mn atoms have been confirmed to enter the CuO lattice and form the Cu{sub 1−x}Mn{sub x}O compounds in the case of doping with 0≤x≤0.2 by the sol–gel method. With increasing Mn content, magnetism is observed. The magnetic critical transition temperature increases with enhanced magnetism, which obeys the bound magnetic polaron theory. The electronic transportation shows an insulating behavior as the band-gap decreases. Our results may indicate that CuO may be used as a candidate of magnetic semiconductor.

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

    Directory of Open Access Journals (Sweden)

    Zisheng Wang

    2018-01-01

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

  18. Observation of Attractive and Repulsive Polarons in a Bose-Einstein Condensate

    DEFF Research Database (Denmark)

    Jørgensen, Nils B.; Wacker, Lars; Skalmstang, Kristoffer Theis

    2016-01-01

    for an impurity interacting with a Bose-Einstein condensate (BEC). We measure the energy of the impurity both for attractive and repulsive interactions with the BEC, and find excellent agreement with theories that incorporate three-body correlations, both in the weak-coupling limits and across unitarity. Our...... results show that the spectral response consists of a well-defined quasiparticle peak at weak coupling and a continuum of excited many-body states. For increasing interaction strength, the spectrum is strongly broadened and becomes dominated by the many-body continuum, but no significant effects of three......The behavior of a mobile impurity particle interacting with a quantum-mechanical medium is of fundamental importance in physics. Due to the great flexibility of atomic gases, our understanding of the impurity problem has improved dramatically since it was realized experimentally in a particularly...

  19. Energy

    International Nuclear Information System (INIS)

    Bobin, J.L.

    1996-01-01

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

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

    International Nuclear Information System (INIS)

    Sakai, M.

    1980-01-01

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

  1. Energy

    CERN Document Server

    Foland, Andrew Dean

    2007-01-01

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

  2. Small polaron hopping conduction in samples of ceramic La1.4Sr1.6Mn2O7.06

    International Nuclear Information System (INIS)

    Nakatsugawa, H.; Iguchi, E.; Jung, W.H.; Munakata, F.

    1999-01-01

    The ceramic sample of La 1.4 Sr 1.6 Mn 2 O 7.06 exhibits the metal-insulator transition and a negative magnetoresistance in the vicinity of the Curie temperature (T C ∼ 100 K). The dc magnetic susceptibility between 100 K and 280 K is nearly constant and decreases gradually with increasing temperature above 280 K. The measurements of dc resistivity and the thermoelectric power indicate that small polaron hopping conduction takes place at T > 280 K. The spin ordering due to the two-dimensional d x 2 -y 2 state occurring at T > 280 K is directly related to the hopping conduction above 280 K, although the spin ordering due to the one-dimensional d 3z 2 -r 2 state takes place at T > T C . The two-dimensional d x 2 -y 2 state extending within the MnO 2 sheets starts to narrow and leads to the carrier localisation at 280 K. The effective number of holes in this sample estimated from the thermoelectric power is considerably smaller than the nominal value. This indicates that the small polaron hopping conduction takes place predominantly within the in-plane MnO 2 sheets. A discussion is given of the experimental results of the ceramic sample of La 2/3 Ca 1/3 MnO 2.98 . Copyright (1999) CSIRO Australia

  3. Polaronic Nonmetal-Correlated Metal Crossover System β'-CuxV2O5 with Anharmonic Copper Oscillation and Thermoelectric Conversion Performance

    Science.gov (United States)

    Onoda, Masashige; Sato, Takuma

    2017-12-01

    The crystal structures and electronic properties of β'CuxV2O5 are explored through measurements of X-ray four-circle diffraction, electrical resistivity, thermoelectric power, thermal conductivity, magnetization, and electron paramagnetic resonance. For various compositions with 0.243 ≤ x ≤ 0.587, the crystal structures are redetermined through the anharmonic approach of the copper displacement factors, where the anharmonicity is reduced with increasing Cu concentration. The electron transport for x ≤ 0.45 is nonmetallic due to polaron hopping and the random potential of Cu ions, while for x = 0.60, a correlated Fermi-liquid state appears with a Wilson ratio of 1.3 and a Kadowaki-Woods ratio close to the universal value for heavy-fermion systems. At around x = 0.50, the polaronic bandwidth may broaden so that the Hubbard subbands caused by the electron correlation will overlap. The nonmetallic composition in the proximity of the nonmetal-metal crossover shows a dimensionless thermoelectric power factor of 10-2 at 300 K, partly due to the anharmonic copper oscillation.

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

    Science.gov (United States)

    Ziaei, Vafa; Bredow, Thomas

    2018-04-18

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

  5. Energy

    CERN Document Server

    Robertson, William C

    2002-01-01

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

  6. DFT+U study of polaronic conduction in Li2O2 and Li2CO3

    DEFF Research Database (Denmark)

    García Lastra, Juan Maria; Myrdal, J.S.G.; Christensen, Rune

    2013-01-01

    The main discharge products formed at the cathode of nonaqueous Li-air batteries are known to be Li2O2 and residual Li2CO3. Recent experiments indicate that the charge transport through these materials is the main limiting factor for the battery performance. It has been also shown that the perfor......The main discharge products formed at the cathode of nonaqueous Li-air batteries are known to be Li2O2 and residual Li2CO3. Recent experiments indicate that the charge transport through these materials is the main limiting factor for the battery performance. It has been also shown...... that the performance of the battery decreases drastically when the amount of Li2CO3 at the cathode increases with respect to Li2O2. In this work, we study the formation and transport of hole and electron polarons in Li2O2 and Li2CO3 using density functional theory (DFT) within the PBE+U approximation. For both...... materials, we find that the formation of polarons (both hole and electron) is stabilized with respect to the delocalized states for all physically relevant values of U. We find a much higher mobility for hole polarons than for the electron polarons, and we show that the poor charge transport in Li2CO3...

  7. Energies

    International Nuclear Information System (INIS)

    2003-01-01

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

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

    NARCIS (Netherlands)

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

    Hydroxylations of octane and lauric acid by Cytochrome P450-BM3 (CYP102A1) wild-type and three active site mutants--F87A, L188Q/A74G, and F87V/L188Q/A74G--were rationalized using a combination of substrate orientation from docking, substrate binding statistics from molecular dynamics simulations,

  9. Influence of polaron effects on superexchange interaction. Isotopic shifts of T sub N , T sub c and T* in laminated copper oxides

    CERN Document Server

    Eremin, M V; Larionov, I A; Terzi, A V

    2002-01-01

    The compact formula for the parameter for the magnetic ions superexchange interaction through intermediate anions with an account of the polaron effects both on the magnetic ions and intermediate anions is obtained. It is applied for the analysis of the basic peculiarities of these types of temperature in the layered cuprates on the HTSC basis: the Neel temperature (T sub N), critical temperatures of the transition into the superconducting state (T sub c) and characteristic temperatures of the normal phases pseudogap state (T*). The calculations are based on the scenario of competition of the superconducting phase with the charge-current waves phase. The agreement of the calculation with the experiment testifies to the benefit of the above scenario

  10. Optical tunability of magnetic polaron stability in single-Mn doped bulk GaAs and GaAs/AlGaAs quantum dots

    Science.gov (United States)

    Qu, Fanyao; Moura, Fábio Vieira; Alves, Fabrizio M.; Gargano, Ricardo

    2013-03-01

    Optical control of magnetic property of a magnetic polaron (MP) in Mn-doped bulk GaAs and GaAs/AlGaAs quantum dots (QDs) have been studied. We have developed basis optimization technique for the method of linear combination of atomic orbitals (LCAOs), which significantly improve the accuracy of the conventional LCAO calculation. We have demonstrated that a monochromatic, linearly polarized, intense pulsed laser field induces a collapse of the MP and an ionization of Mn-acceptor in Mn-doped GaAs materials due to a dichotomy of hole wave function. We find this optical tunability of MP stability can be adjusted by confinement introduced in GaAs QDs.

  11. Degradation of blue-phosphorescent organic light-emitting devices involves exciton-induced generation of polaron pair within emitting layers.

    Science.gov (United States)

    Kim, Sinheui; Bae, Hye Jin; Park, Sangho; Kim, Wook; Kim, Joonghyuk; Kim, Jong Soo; Jung, Yongsik; Sul, Soohwan; Ihn, Soo-Ghang; Noh, Changho; Kim, Sunghan; You, Youngmin

    2018-03-23

    Degradation of organic materials is responsible for the short operation lifetimes of organic light-emitting devices, but the mechanism by which such degradation is initiated has yet to be fully established. Here we report a new mechanism for degradation of emitting layers in blue-phosphorescent devices. We investigate binary mixtures of a wide bandgap host and a series of novel Ir(III) complex dopants having N-heterocyclocarbenic ligands. Our mechanistic study reveals the charge-neutral generation of polaron pairs (radical ion pairs) by electron transfer from the dopant to host excitons. Annihilation of the radical ion pair occurs by charge recombination, with such annihilation competing with bond scission. Device lifetime correlates linearly with the rate constant for the annihilation of the radical ion pair. Our findings demonstrate the importance of controlling exciton-induced electron transfer, and provide novel strategies to design materials for long-lifetime blue electrophosphorescence devices.

  12. Neither Goodenough ionic model nor Zener polaron model for Bi 0.5Ca 0.5Mn 1- xNi xO 3- δ system

    Science.gov (United States)

    Toulemonde, O.; Skovsen, I.; Mesguich, F.; Gaudin, E.

    2008-04-01

    The magnetic susceptibilities of three Bi 0.5Ca 0.5MnO 3- δ compounds synthesised by three different methods were characterised and analysed. Large magnetic Mn x clusters ( x ≥ 4) were considered to explain the high value of the Curie-Weiss constant. Unlike previous studies on similar systems, Goodenough ionic model or Zener polaron model is not suitable. In all cases, cluster behaviour is observed at low field and at low temperature. The influence of the oxygen stoichiometry and the homogeneity of the cation distribution depending on the method of the synthesis used is discussed. Finally, the effects of nickel doping on the magnetic properties were studied and the cluster behaviour was confirmed. The distribution in size of the clusters depends on the amount of nickel and it induces a glassy magnetic behaviour.

  13. 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.)

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-04-09

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

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

    Science.gov (United States)

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

    2000-08-01

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

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

    Czech Academy of Sciences Publication Activity Database

    Haldar, Susanta; Gnanasekaran, Ramachandran; Hobza, Pavel

    2015-01-01

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

  17. Experimental manifestations of the Nb.sup.4+./sup.-O.sup.-./sup. polaronic excitons in KTa.sub.0.988./sub.Nb.sub.0.012./sub.O.sub.3./sub..

    Czech Academy of Sciences Publication Activity Database

    Yusupov, R.V.; Gracheva, I.N.; Rodionov, A.A.; Syrnikov, P. P.; Gubaev, A. I.; Dejneka, Alexandr; Jastrabík, Lubomír; Trepakov, V.A.; Salakhov, M.K.

    2011-01-01

    Roč. 84, č. 17 (2011), 174118/1-174118/7 ISSN 1098-0121 R&D Projects: GA MŠk(CZ) 1M06002 Institutional research plan: CEZ:AV0Z10100522 Keywords : photoinduced EPR * Nb 4+ -O - polaronic excitons * KTa 0.988 Nb 0.012 O 3 Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.691, year: 2011

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

    Science.gov (United States)

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

    2016-06-01

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

  19. Polaronic and bipolaronic structures in the adiabatic Hubbard-Hostein model involving 2 electrons and in its extensions; Structures polaroniques et bipolaroniques dans le modele de hostein hubbard adiabatique a deux electrons et ses extensions

    Energy Technology Data Exchange (ETDEWEB)

    Proville, L

    1998-03-30

    This thesis brings its contribution to the bipolaronic theory which might explain the origin of superconductivity at high temperature. A polaron is a quasiparticle made up of a localized electron and a deformation in the crystal structure. 2 electrons in singlet states localized on the same site form a bipolaron. Whenever the Coulomb repulsion between the 2 electrons is too strong bipolaron turns into 2 no bound polarons. We study the existence and the mobility of bipolarons. We describe the electron-phonon interaction by the Holstein term and the Coulomb repulsion by the Hubbard term. 2 assumptions are made: - the local electron-phonon interaction is strong and opposes the Coulomb repulsion between Hubbard type electrons - the system is close to the adiabatic limit. The system is reduced to 2 electrons in order to allow an exact treatment and the investigation of some bipolaronic bound states. At 2-dimensions the existence of bipolarons requires a very strong coupling which forbids any classical mobility. In some cases an important tunneling effect appears and we show that mobile bipolarons exist in a particular parameter range. Near the adiabatic limit we prove that polaronic and bipolaronic structures exist for a great number of electrons. (A.C.) 33 refs.

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

    International Nuclear Information System (INIS)

    Hoffer, P.B.

    1981-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Kirovski Danijela

    2012-01-01

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

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

    Science.gov (United States)

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

    2017-03-01

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

  3. Binding thermodynamics of a glutamate transporter homologue

    Science.gov (United States)

    Reyes, Nicolas; Oh, SeCheol; Boudker, Olga

    2013-01-01

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

  4. Monte Carlo study of efficiency roll-off of phosphorescent organic light-emitting diodes: Evidence for dominant role of triplet-polaron quenching

    Energy Technology Data Exchange (ETDEWEB)

    Eersel, H. van, E-mail: h.v.eersel@tue.nl; Coehoorn, R. [Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands); Philips Research Laboratories, High Tech Campus 4, 5656 AE Eindhoven (Netherlands); Bobbert, P. A.; Janssen, R. A. J. [Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands)

    2014-10-06

    We present an advanced molecular-scale organic light-emitting diode (OLED) model, integrating both electronic and excitonic processes. Using this model, we can reproduce the measured efficiency roll-off for prototypical phosphorescent OLED stacks based on the green dye tris[2-phenylpyridine]iridium (Ir(ppy){sub 3}) and the red dye octaethylporphine platinum (PtOEP) and study the cause of the roll-off as function of the current density. Both the voltage versus current density characteristics and roll-off agree well with experimental data. Surprisingly, the results of the simulations lead us to conclude that, contrary to what is often assumed, not triplet-triplet annihilation but triplet-polaron quenching is the dominant mechanism causing the roll-off under realistic operating conditions. Simulations for devices with an optimized recombination profile, achieved by carefully tuning the dye trap depth, show that it will be possible to fabricate OLEDs with a drastically reduced roll-off. It is envisaged that J{sub 90}, the current density at which the efficiency is reduced to 90%, can be increased by almost one order of magnitude as compared to the experimental state-of-the-art.

  5. Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test

    Science.gov (United States)

    Pandey, Preeti; Srivastava, Rakesh; Bandyopadhyay, Pradipta

    2018-03-01

    The relative performance of MM-PBSA and MM-3D-RISM methods to estimate the binding free energy of protein-ligand complexes is investigated by applying these to three proteins (Dihydrofolate Reductase, Catechol-O-methyltransferase, and Stromelysin-1) differing in the number of metal ions they contain. None of the computational methods could distinguish all the ligands based on their calculated binding free energies (as compared to experimental values). The difference between the two comes from both polar and non-polar part of solvation. For charged ligand case, MM-PBSA and MM-3D-RISM give a qualitatively different result for the polar part of solvation.

  6. Bloch oscillations in organic and inorganic polymers

    Science.gov (United States)

    Ribeiro, Luiz Antonio; Ferreira da Cunha, Wiliam; de Almeida Fonseca, Antonio Luciano; e Silva, Geraldo Magela

    2017-04-01

    The transport of polarons above the mobility threshold in organic and inorganic polymers is theoretically investigated in the framework of a one-dimensional tight-binding model that includes lattice relaxation. The computational approach is based on parameters for which the model Hamiltonian suitably describes different polymer lattices in the presence of external electric fields. Our findings show that, above critical field strengths, a dissociated polaron moves through the polymer lattice as a free electron performing Bloch oscillations. These critical electric fields are considerably smaller for inorganic lattices in comparison to organic polymers. Interestingly, for inorganic lattices, the free electron propagates preserving charge and spin densities' localization which is a characteristic of a static polaron. Moreover, in the turning points of the spatial Bloch oscillations, transient polaron levels are formed inside the band gap, thus generating a fully characterized polaron structure. For the organic case, on the other hand, no polaron signature is observed: neither in the shape of the distortion—those polaron profile signatures are absent—nor in the energy levels—as no such polaron levels are formed during the simulation. These results solve controversial aspects concerning Bloch oscillations recently reported in the literature and may enlighten the understanding about the charge transport mechanism in polymers above their mobility edge.

  7. Total iron binding capacity

    Science.gov (United States)

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

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

    Science.gov (United States)

    Tarcsay, Ákos; Keserű, György M

    2015-01-01

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

  9. Effect of Förster-mediated triplet-polaron quenching and triplet-triplet annihilation on the efficiency roll-off of organic light-emitting diodes

    Energy Technology Data Exchange (ETDEWEB)

    Eersel, H. van [Simbeyond B.V., P.O. Box 513, NL-5600 MB Eindhoven (Netherlands); Bobbert, P. A.; Janssen, R. A. J.; Coehoorn, R., E-mail: r.coehoorn@tue.nl [Department of Applied Physics and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, NL-5600 MB Eindhoven (Netherlands)

    2016-04-28

    We report the results of a systematic study of the interplay of triplet-polaron quenching (TPQ) and triplet-triplet annihilation (TTA) on the efficiency roll-off of organic light-emitting diodes (OLEDs) with increasing current density. First, we focus on OLEDs based on the green phosphorescent emitter tris[2-phenylpyridine]iridium(III) (Ir(ppy){sub 3}) and the red phosphorescent dye platinum octaethylporphyrin. It is found that the experimental data can be reproduced using kinetic Monte Carlo (kMC) simulations within which TPQ and TTA are due to a nearest-neighbor (NN) interaction, or due to a more long-range Förster-type process. Furthermore, we find a subtle interplay between TPQ and TTA: decreasing the contribution of one process can increase the contribution of the other process, so that the roll-off is not significantly reduced. Furthermore, we find that just analyzing the shape of the roll-off is insufficient for determining the relative role of TPQ and TTA. Subsequently, we investigate the wider validity of this picture using kMC simulations for idealized but realistic symmetric OLEDs, with an emissive layer containing a small concentration of phosphorescent dye molecules in a matrix material. Whereas for NN-interactions the roll-off can be reduced when the dye molecules act as shallow hole and electron traps, we find that such an approach becomes counterproductive for long-range TTA and TPQ. Developing well-founded OLED design rules will thus require that more quantitative information is available on the rate and detailed mechanism of the TPQ and TTA processes.

  10. K- nuclear states: Binding energies and widths

    Czech Academy of Sciences Publication Activity Database

    Hrtánková, Jaroslava; Mareš, Jiří

    2017-01-01

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

  11. Feature Binding in Zebrafish

    Directory of Open Access Journals (Sweden)

    P Neri

    2012-07-01

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

  12. DNS & Bind Cookbook

    CERN Document Server

    Liu, Cricket

    2011-01-01

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

  13. Energies; Energies

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-07-01

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

  14. DNS BIND Server Configuration

    Directory of Open Access Journals (Sweden)

    Radu MARSANU

    2011-01-01

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

  15. DNS BIND Server Configuratio

    OpenAIRE

    Radu MARSANU

    2011-01-01

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

  16. DNS BIND Server Configuration

    OpenAIRE

    Radu MARSANU

    2011-01-01

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

  17. Melanin-binding radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

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

    1980-01-01

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

  18. Melanin-binding radiopharmaceuticals

    International Nuclear Information System (INIS)

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

    1980-01-01

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

  19. Quantum versus semiclassical description of selftrapping: anharmonic effects

    International Nuclear Information System (INIS)

    Raghavan, S.; Bishop, A.R.; Kenkre, V.M.

    1998-09-01

    Selftrapping has been traditionally studied on the assumption that quasiparticles interact with harmonic phonons and that this interaction is linear in the displacement of the phonon. To complement recent semiclassical studies of anharmonicity and nonlinearity in this context, we present below a fully quantum mechanical analysis of a two-site system, where the oscillator is described by a tunably anharmonic potential, with a square well with infinite walls and the harmonic potential as its extreme limits, and wherein the interaction is nonlinear in the oscillator displacement. We find that even highly anharmonic polarons behave similar to their harmonic counterparts in that selftrapping is preserved for long times in the limit of strong coupling, and that the polaronic tunneling time scale depends exponentially on the polaron binding energy. Further, in agreement with earlier results related to harmonic polarons, the semiclassical approximation agrees with the full quantum result in the massive oscillator limit of small oscillator frequency and strong quasiparticle-oscillator coupling. (author)

  20. Computational search for aflatoxin binding proteins

    Science.gov (United States)

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

    2017-10-01

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

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

    DEFF Research Database (Denmark)

    1995-01-01

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

  2. Disentangling overlapping high-field EPR spectra of organic radicals: Identification of light-induced polarons in the record fullerene-free solar cell blend PBDB-T:ITIC

    Science.gov (United States)

    Van Landeghem, Melissa; Maes, Wouter; Goovaerts, Etienne; Van Doorslaer, Sabine

    2018-03-01

    We present a combined high-field EPR and DFT study of light-induced radicals in the bulk heterojunction blend of PBDB-T:ITIC, currently one of the highest efficiency non-fullerene donor:acceptor combinations in organic photovoltaics. We demonstrate two different approaches for disentangling the strongly overlapping high-field EPR spectra of the positive and negative polarons after charge separation: (1) relaxation-filtered field-swept EPR based on the difference in T1 spin-relaxation times and (2) field-swept EDNMR-induced EPR by exploiting the presence of 14N hyperfine couplings in only one of the radical species, the small molecule acceptor radical. The approach is validated by light-induced EPR spectra on related blends and the spectral assignment is underpinned by DFT computations. The broader applicability of the spectral disentangling methods is discussed.

  3. Tension-induced binding of semiflexible biopolymers

    International Nuclear Information System (INIS)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Bitter István

    2010-10-01

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

  5. Thermodynamic Characterization of New Positive Allosteric Modulators Binding to the Glutamate Receptor A2 Ligand-Binding Domain

    DEFF Research Database (Denmark)

    Nørholm, Ann-Beth; Francotte, Pierre; Goffin, Eric

    2014-01-01

    ,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxides. Measurements of ligand binding by isothermal titration calorimetry (ITC) showed similar binding affinities for the modulator series at the GluA2 LBD but differences in the thermodynamic driving forces. Binding of 5c (7-F) and 6 (no-F) is enthalpy driven......, and combined with the shorter total simulation time, we found the OSP method to be more effective for this setup. Furthermore, from the molecular dynamics simulations, we extracted the enthalpies and entropies, and along with the ITC data, this suggested that the differences in binding free energies...

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

    Science.gov (United States)

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

    2017-04-01

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

  7. binding protein (HABP1)

    Indian Academy of Sciences (India)

    Unknown

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

  8. Sequential memory: Binding dynamics

    Science.gov (United States)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

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

  9. binding protein (HABP1)

    Indian Academy of Sciences (India)

    Unknown

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

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

    OpenAIRE

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

    2013-01-01

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

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

    DEFF Research Database (Denmark)

    Birn, Henrik; Zhai, Xiaoyue; Holm, Jan

    2005-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Wu Y

    2011-01-01

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

  13. Carboplatin binding to histidine

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-08-29

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

  14. Optical Binding of Nanowires

    Czech Academy of Sciences Publication Activity Database

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

    2017-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Huiying Zhao

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

  16. IGF binding proteins.

    Science.gov (United States)

    Bach, Leon A

    2017-12-18

    Insulin-like growth factor binding proteins (IGFBPs) 1-6 bind IGFs but not insulin with high affinity. They were initially identified as serum carriers and passive inhibitors of IGF actions. However, subsequent studies showed that, although IGFBPs inhibit IGF actions in many circumstances, they may also potentiate these actions. IGFBPs are widely expressed in most tissues, and they are flexible endocrine and autocrine/paracrine regulators of IGF activity, which is essential for this important physiological system. More recently, individual IGFBPs have been shown to have IGF-independent actions. Mechanisms underlying these actions include (i) interaction with non-IGF proteins in compartments including the extracellular space and matrix, the cell surface and intracellularly; (ii) interaction with and modulation of other growth factor pathways including EGF, TGF- and VEGF; and (iii) direct or indirect transcriptional effects following nuclear entry of IGFBPs. Through these IGF-dependent and IGF-independent actions, IGFBPs modulate essential cellular processes including proliferation, survival, migration, senescence, autophagy and angiogenesis. They have been implicated in a range of disorders including malignant, metabolic, neurological and immune diseases. A more complete understanding of their cellular roles may lead to the development of novel IGFBP-based therapeutic opportunities.

  17. Ultrafast energy transfer within the photosystem II core complex.

    Science.gov (United States)

    Pan, Jie; Gelzinis, Andrius; Chorošajev, Vladimir; Vengris, Mikas; Senlik, S Seckin; Shen, Jian-Ren; Valkunas, Leonas; Abramavicius, Darius; Ogilvie, Jennifer P

    2017-06-14

    We report 2D electronic spectroscopy on the photosystem II core complex (PSII CC) at 77 K under different polarization conditions. A global analysis of the high time-resolution 2D data shows rapid, sub-100 fs energy transfer within the PSII CC. It also reveals the 2D spectral signatures of slower energy equilibration processes occurring on several to hundreds of picosecond time scales that are consistent with previous work. Using a recent structure-based model of the PSII CC [Y. Shibata, S. Nishi, K. Kawakami, J. R. Shen and T. Renger, J. Am. Chem. Soc., 2013, 135, 6903], we simulate the energy transfer in the PSII CC by calculating auxiliary time-resolved fluorescence spectra. We obtain the observed sub-100 fs evolution, even though the calculated electronic energy shows almost no dynamics at early times. On the other hand, the electronic-vibrational interaction energy increases considerably over the same time period. We conclude that interactions with vibrational degrees of freedom not only induce population transfer between the excitonic states in the PSII CC, but also reshape the energy landscape of the system. We suggest that the experimentally observed ultrafast energy transfer is a signature of excitonic-polaron formation.

  18. Thermodynamics of sequence-specific binding of PNA to DNA

    DEFF Research Database (Denmark)

    Ratilainen, T; Holmén, A; Tuite, E

    2000-01-01

    For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes) and seq......For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes......) and sequence specificity of binding (singly mismatched duplexes) using mainly absorption hypochromicity melting curves and isothermal titration calorimetry. For perfectly sequence-matched duplexes of varying lengths (6-20 bp), the average free energy of binding (DeltaG degrees ) was determined to be -6...... relative to that of the perfectly matched sequence with a corresponding free energy penalty of about 15 kJ mol(-1) bp(-1). The average cost of a single mismatch is therefore estimated to be on the order of or larger than the gain of two matched base pairs, resulting in an apparent binding constant of only...

  19. Some Effective Tight-Binding Models for Electrons in DNA Conduction: A Review

    International Nuclear Information System (INIS)

    Yamada, H.; Iguchi, K.

    2010-01-01

    Quantum transport for DNA conduction has been widely studied with interest in application as a candidate in making nanowires as well as interest in the scientific mechanism. In this paper, we review recent works concerning the electronic states and the conduction/transfer in DNA polymers. We have mainly investigated the energy-band structure and the correlation effects of localization property in the two- and three-chain systems (ladder model) with long-range correlation as a simple model for electronic property in a double strand of DNA by using the tight-bindingmodel. In addition, we investigated the localization properties of electronic states in several actual DNA sequences such as bacteriophages of Escherichia coli, human-chromosome 22, compared with those of the artificial disordered sequences with correlation. The charge-transfer properties for poly(dA)-poly(dT) and poly(dG)-poly(dC) DNA polymers are also presented in terms of localization lengths within the frameworks of the polaron models due to the coupling between the charge carriers and the lattice vibrations of the double strand of DNA

  20. Temperature and composition dependent density of states extracted using overlapping large polaron tunnelling model in MnxCo1-xFe2O4 (x=0.25, 0.5, 0.75) nanoparticles

    Science.gov (United States)

    Jamil, Arifa; Afsar, M. F.; Sher, F.; Rafiq, M. A.

    2017-03-01

    We report detailed ac electrical and structural characterization of manganese cobalt ferrite nanoparticles, prepared by coprecipitation technique. X-ray diffraction (XRD) confirmed single-phase cubic spinel structure of the nanoparticles. Tetrahedral (A) and octahedral (B) group complexes were present in the spinel lattice as determined by Fourier Transform Infrared Spectroscopy (FTIR). Scanning Electron Microscope (SEM) images revealed presence of spherical shape nanoparticles having an average diameter 50-80 nm. Composition, temperature and frequency dependent ac electrical study of prepared nanoparticles interpreted the role of cationic distribution between A and B sites. Overlapping large polaron tunnelling (OLPT) conduction mechanism was observed from 290 to 200 K. Frequency exponent s was fitted theoretically using OLPT model. High values of Density of States (DOS) of the order of 1022-1024 eV-1 cm-3 were extracted from ac conductivity for different compositions. We found that DOS was dependent on distribution of cations in the tunnel-type cavities along the a and b axis.

  1. Modeling Shear Induced Von Willebrand Factor Binding to Collagen

    Science.gov (United States)

    Dong, Chuqiao; Wei, Wei; Morabito, Michael; Webb, Edmund; Oztekin, Alparslan; Zhang, Xiaohui; Cheng, Xuanhong

    2017-11-01

    Von Willebrand factor (vWF) is a blood glycoprotein that binds with platelets and collagen on injured vessel surfaces to form clots. VWF bioactivity is shear flow induced: at low shear, binding between VWF and other biological entities is suppressed; for high shear rate conditions - as are found near arterial injury sites - VWF elongates, activating its binding with platelets and collagen. Based on parameters derived from single molecule force spectroscopy experiments, we developed a coarse-grain molecular model to simulate bond formation probability as a function of shear rate. By introducing a binding criterion that depends on the conformation of a sub-monomer molecular feature of our model, the model predicts shear-induced binding, even for conditions where binding is highly energetically favorable. We further investigate the influence of various model parameters on the ability to predict shear-induced binding (vWF length, collagen site density and distribution, binding energy landscape, and slip/catch bond length) and demonstrate parameter ranges where the model provides good agreement with existing experimental data. Our results may be important for understanding vWF activity and also for achieving targeted drug therapy via biomimetic synthetic molecules. National Science Foundation (NSF),Division of Mathematical Sciences (DMS).

  2. Cross-modality deep learning-based prediction of TAP binding and naturally processed peptide.

    Science.gov (United States)

    Besser, Hanan; Louzoun, Yoram

    2018-02-28

    Epitopes presented on MHC class I molecules pass multiple processing stages before their presentation on MHC molecules, the main ones being proteasomal cleavage and TAP binding. Transporter associated with antigen processing (TAP) binding is a necessary stage for most, but not all, MHC-I-binding peptides. The molecular determinants of TAP-binding peptides can be experimentally estimated from binding experiments and from the properties of peptides inducing a CD8 T cell response. We here propose novel optimization formalisms to combine binding and activation experimental results to produce a classifier for TAP binding using dual-output kernel and deep learning approaches. The application of these algorithms to the human and murine TAP binding leads to predictors that are much more precise than current state of the art methods. Moreover, the computed score is highly correlated with the observed binding energy. The new predictors show that TAP binding may be much more selective than previously assumed in humans and mice and sensitive to the properties of most positions of the peptides. Beyond the improved precision for TAP binding, we propose that the same approach holds in most molecular binding problems, where functional and binding measures are simultaneously available, and can be used to significantly improve the precision of binding prediction algorithms in general and immune system molecules specifically.

  3. Hydrolysis at One of the Two Nucleotide-binding Sites Drives the Dissociation of ATP-binding Cassette Nucleotide-binding Domain Dimers*

    Science.gov (United States)

    Zoghbi, Maria E.; Altenberg, Guillermo A.

    2013-01-01

    The functional unit of ATP-binding cassette (ABC) transporters consists of two transmembrane domains and two nucleotide-binding domains (NBDs). ATP binding elicits association of the two NBDs, forming a dimer in a head-to-tail arrangement, with two nucleotides “sandwiched” at the dimer interface. Each of the two nucleotide-binding sites is formed by residues from the two NBDs. We recently found that the prototypical NBD MJ0796 from Methanocaldococcus jannaschii dimerizes in response to ATP binding and dissociates completely following ATP hydrolysis. However, it is still unknown whether dissociation of NBD dimers follows ATP hydrolysis at one or both nucleotide-binding sites. Here, we used luminescence resonance energy transfer to study heterodimers formed by one active (donor-labeled) and one catalytically defective (acceptor-labeled) NBD. Rapid mixing experiments in a stop-flow chamber showed that NBD heterodimers with one functional and one inactive site dissociated at a rate indistinguishable from that of dimers with two hydrolysis-competent sites. Comparison of the rates of NBD dimer dissociation and ATP hydrolysis indicated that dissociation followed hydrolysis of one ATP. We conclude that ATP hydrolysis at one nucleotide-binding site drives NBD dimer dissociation. PMID:24129575

  4. Full momentum- and energy-resolved spectral function of a 2D electronic system

    Science.gov (United States)

    Jang, Joonho; Yoo, Heun Mo; Pfeiffer, L. N.; West, K. W.; Baldwin, K. W.; Ashoori, Raymond C.

    2017-11-01

    The single-particle spectral function measures the density of electronic states in a material as a function of both momentum and energy, providing central insights into strongly correlated electron phenomena. Here we demonstrate a high-resolution method for measuring the full momentum- and energy-resolved electronic spectral function of a two-dimensional (2D) electronic system embedded in a semiconductor. The technique remains operational in the presence of large externally applied magnetic fields and functions even for electronic systems with zero electrical conductivity or with zero electron density. Using the technique on a prototypical 2D system, a GaAs quantum well, we uncover signatures of many-body effects involving electron-phonon interactions, plasmons, polarons, and a phonon analog of the vacuum Rabi splitting in atomic systems.

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

    Science.gov (United States)

    Zhang, Yue; Wright, Edward; Zhong, Qixin

    2013-01-30

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

  6. DNA-binding cytotoxic alkaloids: comparative study of the energetics of binding of berberine, palmatine, and coralyne.

    Science.gov (United States)

    Bhadra, Kakali; Maiti, Motilal; Kumar, Gopinatha Suresh

    2008-12-01

    Deoxyribonucleic acid is the site of storage and retrieval of genetic information through interaction with proteins and other small molecules. In the present study, the interaction of two natural cytotoxic protoberberine plant alkaloids, berberine and palmatine, and a synthetic derivative, coralyne, with mammalian herring testis DNA was investigated using a combination of isothermal titration calorimetry, differential scanning calorimetry, and optical melting experiments to characterize the energetics of their binding. The binding constants of these alkaloids to DNA under identical conditions were evaluated from the UV melting data, and the enthalpy of binding was elucidated from isothermal titration studies. The binding constants of berberine, palmatine, and coralyne to DNA were found to be 1.15 x 10(4), 2.84 x 10(4), and 3.5 x 10(6) M(-1) at 20 degrees C in buffer of 20 mM [Na+]. Parsing of the free energy change of the interaction observed into polyelectrolytic and nonpolyelectrolytic components suggested that although these alkaloids are charged, the major contributor of about 75% of the binding free energy arises from the nonpolyelectrolytic forces. The binding in case of palmatine and coralyne was predominantly enthalpy driven with favoring smaller entropy terms, while that of berberine was favored by both negative enthalpy and positive entropy changes. Temperature dependence of the binding enthalpies determined from ITC studies in the range 20-40 degrees C was used to calculate the binding-induced change in heat capacity (DeltaC(o)(p)) values as -117, -135, and -157 cal/mol K, respectively, for berberine, palmatine, and coralyne. Taken together, the results suggest that the DNA binding of the planar synthetic coralyne is stronger and thermodynamically more favored compared to the buckled natural berberine and palmatine.

  7. Pictorial binding: endeavor to classify

    Directory of Open Access Journals (Sweden)

    Zinchenko S.

    2015-01-01

    Full Text Available The article is devoted to the classification of bindings of the 1-19th centuries with a unique and untypical book binding decoration technique (encaustic, tempera and oil paintings. Analysis of design features, materials and techniques of art decoration made it possible to identify them as a separate type - pictorial bindings and divide them into four groups. The first group consists of Coptic bindings, decorated with icon-painting images in encaustic technique. The second group is made up of leather Western bindings of the 13-14th centuries, which have the decoration and technique of ornamentation close to iconography. The third group involves parchment bindings, ornamentation technique of which is closer to the miniature. The last group comprises bindings of East Slavic origin of the 15-19th centuries, decorated with icon-painting pictures made in the technique of tempera or oil painting. The proposed classification requires further basic research as several specific kinds of bindings have not yet been investigated

  8. Defining Starch Binding by Glucan Phosphatases

    DEFF Research Database (Denmark)

    Auger, Kyle; Raththagala, Madushi; Wilkens, Casper

    2015-01-01

    Starch is a vital energy molecule in plants that has a wide variety of uses in industry, such as feedstock for biomaterial processing and biofuel production. Plants employ a three enzyme cyclic process utilizing kinases, amylases, and phosphatases to degrade starch in a diurnal manner. Starch...... is comprised of the branched glucan amylopectin and the more linear glucan amylose. Our lab has determined the first structures of these glucan phosphatases and we have defined their enzymatic action. Despite this progress, we lacked a means to quickly and efficiently quantify starch binding to glucan...

  9. Metal binding by food components

    DEFF Research Database (Denmark)

    Tang, Ning

    For calcium binding: Electrochemical method (calcium ion selective electrode) combined with quantum mechanical calculations (density functional theory) were used to investigate the calcium binding affinity of the amino acids and small glycine peptides. The effects of the ionic strength and p......, synergistic effect in calcium binding was found for the small glycine peptide rather than amino acids mixtures with the enhanced driving force up to -6 kJ/mol. Such study provides useful information for the future development of calcium supplements. For zinc binding: Isothermal titration calorimetry...... titration calorimetry and quantum mechanical calculations. This is due to the zinc binding affinity of the relatively softer ligands (investigated food components) will become much stronger than citrate or phytate when they present together in aqueous solution. This mechanism indicates these food components...

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

    Science.gov (United States)

    Piłat, Zofia; Antosiewicz, Jan M

    2008-11-27

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

  11. A theoretical investigation of tight-binding thermolysin inhibitors.

    Science.gov (United States)

    Shen, J

    1997-08-29

    A tight-binding thermolysin inhibitor, Cbz-Phe-psi[PO2NH]-Leu-Ala (ZFpLA, Ki = 0.068 nM), and its analogs, ZRp(O)LA (R = Ala, Leu or Phe) have been studied using the finite difference solution to the linearized Poisson-Boltzmann equation (FDPB) and solvation entropy correction (SEC). The binding energy difference between conformationally different thermolysin inhibitors ZFpLA and ZGpLL is estimated using three approaches. Two of approaches use the X-ray structures of ZFpLA-thermolysin and ZGpLL-thermolysin structures. The third one uses both X-ray structures to calculate binding energy differences from ZFpLA and ZGpLL to a hypothetical intermediate MepLA. All the results are qualitatively correct with one closely reproducing the experimental value. The enhancement of the ZFpLA binding is attributed largely to the solvation entropy or "hydrophobic force". The binding mode of the ZGpLR N-terminal moiety appears to be electrostatically unfavorable. Reducing the polarity of that moiety is predicted to enhance binding affinity. The binding trends due to the hydrophobic variation of ZRp(O)LA are calculated within 1 kcal/mol of the experimental values. Increasing lipophilicity of a ligand favors the binding due to the difference of surface area change between the free state and the bound state. The analysis of energetic components shows that these trends are not specific for the binding of phosphorus-containing inhibitors but are generally true for protein-ligand interactions. The electrostatic calculation does not support the involvement of the second protonation of ZFpLA in binding. Therefore, reexamining the second protonation of ZFpLA or seeking further experimental support seems appropriate. The structural sensitivity of the FDPB calculation was assessed by using ligand and receptor structures from different X-ray studies of thermolysin. The small deviations (< 0.3 A) in the receptor structures do not cause significant changes in electrostatic binding energy if there

  12. Iodide Binding in Sodium-Coupled Cotransporters.

    Science.gov (United States)

    Vergara-Jaque, Ariela; Fong, Peying; Comer, Jeffrey

    2017-12-26

    Several apical iodide translocation pathways have been proposed for iodide efflux out of thyroid follicular cells, including a pathway mediated by the sodium-coupled monocarboxylate transporter 1 (SMCT1), which remains controversial. Herein, we evaluate structural and functional similarities between SMCT1 and the well-studied sodium-iodide symporter (NIS) that mediates the first step of iodide entry into the thyroid. Free-energy calculations using a force field with electronic polarizability verify the presence of a conserved iodide-binding pocket between the TM2, TM3, and TM7 segments in hNIS, where iodide is coordinated by Phe67, Gln72, Cys91, and Gln94. We demonstrate the mutation of residue Gly93 of hNIS to a larger amino acid expels the side chain of a critical tryptophan residue (Trp255) into the interior of the binding pocket, partially occluding the iodide binding site and reducing iodide affinity, which is consistent with previous reports associating mutation of this residue with iodide uptake deficiency and hypothyroidism. Furthermore, we find that the position of Trp255 in this hNIS mutant mirrors that of Trp253 in wild-type hSMCT1, where a threonine (Thr91) occupies the position homologous to that occupied by glycine in wild-type hNIS (Gly93). Correspondingly, mutation of Thr91 to glycine in hSMCT1 makes the pocket structure more like that of wild-type hNIS, increasing its iodide affinity. These results suggest that wild-type hSMCT1 in the inward-facing conformation may bind iodide only very weakly, which may have implications for its ability to transport iodide.

  13. Pro DNS and BIND 10

    CERN Document Server

    Aitchison, Ron

    2011-01-01

    Pro DNS and BIND 10 guides you through the challenging array of features surrounding DNS with a special focus on the latest release of BIND, the world's most popular DNS implementation. This book unravels the mysteries of DNS, offering insight into origins, evolution, and key concepts like domain names and zone files. This book focuses on running DNS systems based on BIND 10, the first stable release that includes support for the latest DNSSEC standards. Whether you administer a DNS system, are thinking about running one, or you simply want to understand the DNS system, then this book for you.

  14. Protein binding of psychotropic agents

    International Nuclear Information System (INIS)

    Hassan, H.A.

    1990-01-01

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

  15. Predicting the binding modes and sites of metabolism of xenobiotics.

    Science.gov (United States)

    Mukherjee, Goutam; Lal Gupta, Pancham; Jayaram, B

    2015-07-01

    Metabolism studies are an essential integral part of ADMET profiling of drug candidates to evaluate their safety and efficacy. Cytochrome P-450 (CYP) metabolizes a wide variety of xenobiotics/drugs. The binding modes of these compounds with CYP and their intrinsic reactivities decide the metabolic products. We report here a novel computational protocol, which comprises docking of ligands to heme-containing CYPs and prediction of binding energies through a newly developed scoring function, followed by analyses of the docked structures and molecular orbitals of the ligand molecules, for predicting the sites of metabolism (SOM) of ligands. The calculated binding free energies of 121 heme-containing protein-ligand docked complexes yielded a correlation coefficient of 0.84 against experiment. Molecular orbital analyses of the resultant top three unique poses of the docked complexes provided a success rate of 87% in identifying the experimentally known sites of metabolism of the xenobiotics. The SOM prediction methodology is freely accessible at .

  16. Decomposition of the factors that govern binding site preference in a multiple rotaxane.

    Science.gov (United States)

    Angelo, Joseph P; Sohlberg, Karl

    2009-06-18

    A particularly interesting class of multiple rotaxanes consists of complexes where one long shaft threads two rings. If the shaft contains three or more potential binding sites for the rings, multiple co-conformations are possible. Such a complex is a molecular topological analogue to an abacus. Here we address the question, how does strength of ring binding to the shaft vary with respect to position on the shaft? Previous studies have found that a shaft with three binding sites exhibits strongest ring binding at the center site. Here a five-binding-site shaft is studied. We employ a novel method to partition the total energy of the system into contributions from intercomponent binding and intracomponent distortion. The method uses the output of quantum mechanical electronic structure calculations to determine fitting parameters in a set of coupled equations. The solution of the equations yields the energy partitioning and reveals the influence of long-range intercomponent interactions.

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

    Directory of Open Access Journals (Sweden)

    Lovorka Perić-Hassler

    2013-12-01

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

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

    Science.gov (United States)

    Luque, Irene; Freire, Ernesto

    2002-11-01

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

  19. Metal ion binding with dehydroannulenes – Plausible two ...

    Indian Academy of Sciences (India)

    WINTEC

    has highest interaction energy of –50∙6 kcal/mol at. B3LYP/6-311++G** level and is 128∙0 kcal/mol more than 1′-K+ complex. Understandably, the binding energy of metal complexes decreases with increase in the size of the metal ion, in accordance with ear- lier results.16,21. Placement of the metal ions at the centroid of ...

  20. Fluorescence spectroscopic studies on binding of a flavonoid ...

    Indian Academy of Sciences (India)

    Unknown

    Human serum albumin; bovine serum albumin; quercetin; energy transfer; binding constant. 1. Introduction. Serum albumins are abundantly found in blood plasma and are often termed transport proteins.1–4 They are circulated in the body several times and act as carri- ers for numerous exogenous and endogenous com-.