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Sample records for polaron binding energy

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

    Czech Academy of Sciences Publication Activity Database

    Nožár, Juraj; Nešpůrek, Stanislav; Šebera, Jakub

    2012-01-01

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

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-01

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

  4. Polaron interaction energies in reduced tungsten trioxide

    International Nuclear Information System (INIS)

    Iguchi, E.; Salje, E.; Tilley, R.J.D.

    1981-01-01

    Consideration of the properties of reduced tungsten trioxide suggest that the mobile charge carriers are polarons. As it is uncertain how the presence of polarons will influence the microstructures of the crystallographic shear (CS) planes present in reduced tungsten trioxide we have calculated both the polaron-CS plane and polaron-polaron interaction energy for a variety of circumstances. Three CS plane geometries were considered, (102), (103), and (001) CS plane arrays, and the nominal compositions of the crystals ranged from WO 2 70 to WO 3 0 . The polarons were assumed to have radii from 0.6 to 1.0 nm and the polaron-CS plane electrostatic interaction was assumed to be screened. The results suggest that for the most part the total interaction energy is small and is unlikely to be of major importance in controlling the microstructures found in CS planes. However, at very high polaron densities the interaction energy could be appreciable and may have some influence on the existence range of CS phases

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  6. Quantitative measurements of magnetic polaron binding on acceptors in CdMnTe alloys

    Science.gov (United States)

    Nhung, Tran Hong; Planel, R.

    1983-03-01

    The acceptor binding energy is measured as a function of Temperature and composition in Cd1-x Mnx Te alloys, by time resolved spectroscopy. The Bound magnetic polaron effect is measured and compared with a theory accouting for magnetic saturation and fluctuations.

  7. Ground state energy of a polaron in a superlattice

    International Nuclear Information System (INIS)

    Mensah, S.Y.; Allotey, F.K.A.; Nkrumah, G.; Mensah, N.G.

    2000-10-01

    The ground state energy of a polaron in a superlattice was calculated using the double-time Green functions. The effective mass of the polaron along the planes perpendicular to the superlattice axis was also calculated. The dependence of the ground state energy and the effective mass along the planes perpendicular to the superlattice axis on the electron-phonon coupling constant α and on the superlattice parameters (i.e. the superlattice period d and the bandwidth Δ) were studied. It was observed that if an infinite square well potential is assumed, the ground state energy of the polaron decreases (i.e. becomes more negative) with increasing α and d, but increases with increasing Δ. For small values of α, the polaron ground state energy varies slowly with Δ, becoming approximately constant for large Δ. The effective mass along the planes perpendicular to the superlattice axis was found to be approximately equal to the mass of an electron for all typical values of α, d and Δ. (author)

  8. 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 ...

  9. 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.

  10. Strong-coupling polaron effect in quantum dots

    International Nuclear Information System (INIS)

    Zhu Kadi; Gu Shiwei

    1993-11-01

    Strong-coupling polaron in a parabolic quantum dot is investigated by the Landau-Pekar variational treatment. The polaron binding energy and the average number of virtual phonons around the electron as a function of the effective confinement length of the quantum dot are obtained in Gaussian function approximation. It is shown that both the polaron binding energy and the average number of virtual phonons around the electron decrease by increasing the effective confinement length. The results indicate that the polaronic effects are more pronounced in quantum dots than those in two-dimensional and three-dimensional cases. (author). 15 refs, 4 figs

  11. 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.

  12. Zero-Magnetic-Field Spin Splitting of Polaron's Ground State Energy Induced by Rashba Spin-Orbit Interaction

    International Nuclear Information System (INIS)

    Liu Jia; Xiao Jingling

    2006-01-01

    We study theoretically the ground state energy of a polaron near the interface of a polar-polar semiconductor by considering the Rashba spin-orbit (SO) coupling with the Lee-Low-Pines intermediate coupling method. Our numerical results show that the Rashba SO interaction originating from the inversion asymmetry in the heterostructure splits the ground state energy of the polaron. The electron areal density and vector dependence of the ratio of the SO interaction to the total ground state energy or other energy composition are obvious. One can see that even without any external magnetic field, the ground state energy can be split by the Rashba SO interaction, and this split is not a single but a complex one. Since the presents of the phonons, whose energy gives negative contribution to the polaron's, the spin-splitting states of the polaron are more stable than electron's.

  13. Energy Migration in Organic Thin Films--From Excitons to Polarons

    Science.gov (United States)

    Mullenbach, Tyler K.

    The rise of organic photovoltaic devices (OPVs) and organic light-emitting devices has generated interest in the physics governing exciton and polaron dynamics in thin films. Energy transfer has been well studied in dilute solutions, but there are emergent properties in thin films and greater complications due to complex morphologies which must be better understood. Despite the intense interest in energy transport in thin films, experimental limitations have slowed discoveries. Here, a new perspective of OPV operation is presented where photovoltage, instead of photocurrent, plays the fundamental role. By exploiting this new vantage point the first method of measuring the diffusion length (LD) of dark (non-luminescent) excitons is developed, a novel photodetector is invented, and the ability to watch exciton arrival, in real-time, at the donor-acceptor heterojunction is presented. Using an enhanced understanding of exciton migration in thin films, paradigms for enhancing LD by molecular modifications are discovered, and the first exciton gate is experimentally and theoretically demonstrated. Generation of polarons from exciton dissociation represents a second phase of energy migration in OPVs that remains understudied. Current approaches are capable of measuring the rate of charge carrier recombination only at open-circuit. To enable a better understanding of polaron dynamics in thin films, two new approaches are presented which are capable of measuring both the charge carrier recombination and transit rates at any OPV operating voltage. These techniques pave the way for a more complete understanding of charge carrier kinetics in molecular thin films.

  14. Full-counting statistics of energy transport of molecular junctions in the polaronic regime

    International Nuclear Information System (INIS)

    Tang, Gaomin; Yu, Zhizhou; Wang, Jian

    2017-01-01

    We investigate the full-counting statistics (FCS) of energy transport carried by electrons in molecular junctions for the Anderson–Holstein model in the polaronic regime. Using the two-time quantum measurement scheme, the generating function (GF) for the energy transport is derived and expressed as a Fredholm determinant in terms of Keldysh nonequilibrium Green’s function in the time domain. Dressed tunneling approximation is used in decoupling the phonon cloud operator in the polaronic regime. This formalism enables us to analyze the time evolution of energy transport dynamics after a sudden switch-on of the coupling between the dot and the leads towards the stationary state. The steady state energy current cumulant GF in the long time limit is obtained in the energy domain as well. Universal relations for steady state energy current FCS are derived under a finite temperature gradient with zero bias and this enabled us to express the equilibrium energy current cumulant by a linear combination of lower order cumulants. The behaviors of energy current cumulants in steady state under temperature gradient and external bias are numerically studied and explained. The transient dynamics of energy current cumulants is numerically calculated and analyzed. Universal scaling of normalized transient energy cumulants is found under both temperature gradient and external bias. (paper)

  15. The ground state energy of a bound polaron in the presence of a magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    Zorkani, I [International Centre for Theoretical Physics, Trieste (Italy); Belhissi, R [Faculte des Sciences Dhar Mahraz, Fes (Morocco). Dept. de Physique

    1995-09-01

    A theoretical calculation for the ground state energy of a bound polaron as a function of the magnetic field is presented. The theory is based on a variational approach using a trial wave function proposed by Devreese et al. in the absence of the magnetic field. It was shown that his function is adequate for all electron - phonon coupling {alpha} and all parameter {gamma}{sub 0} which is the ratio between the L.O. phonon energy and the Colombian one. Analytical results are obtained in the weak coupling limit. (author). 27 refs, 4 figs, 1 tab.

  16. Continual integration method in the polaron model

    International Nuclear Information System (INIS)

    Kochetov, E.A.; Kuleshov, S.P.; Smondyrev, M.A.

    1981-01-01

    The article is devoted to the investigation of a polaron system on the base of a variational approach formulated on the language of continuum integration. The variational method generalizing the Feynman one for the case of the system pulse different from zero has been formulated. The polaron state has been investigated at zero temperature. A problem of the bound state of two polarons exchanging quanta of a scalar field as well as a problem of polaron scattering with an external field in the Born approximation have been considered. Thermodynamics of the polaron system has been investigated, namely, high-temperature expansions for mean energy and effective polaron mass have been studied [ru

  17. 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

  18. Hole polaron-polaron interaction in transition metal oxides and its limit to p-type doping

    Science.gov (United States)

    Chen, Shiyou; Wang, Lin-Wang

    2014-03-01

    Traditionally the origin of the poor p-type conductivity in some transition metal oxides (TMOs) was attributed to the limited hole concentration: the charge-compensating donor defects, such as oxygen vacancies and cation interstitials, can form spontaneously as the Fermi energy shifts down to near the valence band maximum. Besides the thermodynamic limit to the hole concentration, the limit to the hole mobility can be another possible reason, e.g., the hole carrier can form self-trapped polarons with very low carrier mobility. Although isolated hole polarons had been found in some TMOs, the polaron-polaron interaction is not well-studied. Here we show that in TMOs such as TiO2 and V2O5, the hole polarons prefer to bind with each other to form bipolarons, which are more stable than free hole carriers or separated polarons. This pushes the hole states upward into the conduction band and traps the holes. The rise of the Fermi energy suppresses the spontaneous formation of the charge-compensating donor defects, so the conventional mechanism becomes ineffective. Since it can happen in the impurity-free TMO lattices, independent of any extrinsic dopant, it acts as an intrinsic and general limit to the p-type conductivity in these TMOs. This material is based upon work performed by the JCAP, a US DOE Energy Innovation Hub, the NSFC (No. 61106087 and 91233121) and special funds for major state basic research (No. 2012CB921401).

  19. First-principles supercell calculations of small polarons with proper account for long-range polarization effects

    Science.gov (United States)

    Kokott, Sebastian; Levchenko, Sergey V.; Rinke, Patrick; Scheffler, Matthias

    2018-03-01

    We present a density functional theory (DFT) based supercell approach for modeling small polarons with proper account for the long-range elastic response of the material. Our analysis of the supercell dependence of the polaron properties (e.g., atomic structure, binding energy, and the polaron level) reveals long-range electrostatic effects and the electron–phonon (el–ph) interaction as the two main contributors. We develop a correction scheme for DFT polaron calculations that significantly reduces the dependence of polaron properties on the DFT exchange-correlation functional and the size of the supercell in the limit of strong el–ph coupling. Using our correction approach, we present accurate all-electron full-potential DFT results for small polarons in rocksalt MgO and rutile TiO2.

  20. Determining a hopping polaron's bandwidth from its Seebeck coefficient: Measuring the disorder energy of a non-crystalline semiconductor

    International Nuclear Information System (INIS)

    Emin, David

    2016-01-01

    Charge carriers that execute multi-phonon hopping generally interact strongly enough with phonons to form polarons. A polaron's sluggish motion is linked to slowly shifting atomic displacements that severely reduce the intrinsic width of its transport band. Here a means to estimate hopping polarons' bandwidths from Seebeck-coefficient measurements is described. The magnitudes of semiconductors' Seebeck coefficients are usually quite large (>k/|q| = 86 μV/K) near room temperature. However, in accord with the third law of thermodynamics, Seebeck coefficients must vanish at absolute zero. Here, the transition of the Seebeck coefficient of hopping polarons to its low-temperature regime is investigated. The temperature and sharpness of this transition depend on the concentration of carriers and on the width of their transport band. This feature provides a means of estimating the width of a polaron's transport band. Since the intrinsic broadening of polaron bands is very small, less than the characteristic phonon energy, the net widths of polaron transport bands in disordered semiconductors approach the energetic disorder experienced by their hopping carriers, their disorder energy

  1. Optical transition energy of magneto-polaron in a GaAs{sub 0.9}P{sub 0.1}/GaAs{sub 0.6}P{sub 0.4} quantum dot

    Energy Technology Data Exchange (ETDEWEB)

    Vinolin, Ada [Dept. of Physics, Madurai Kamaraj University College, Alagarkoil Road, Madurai-625002. India (India); Peter, A. John, E-mail: a.john.peter@gmail.com [Dept. of Physics, Govt. Arts College, Melur-625106. Madurai. India (India)

    2015-06-24

    Magneto-LO-polaron in a cylindrical GaAs{sub 0.9} P{sub 0.1} / GaAs{sub 0.6} P{sub 0.4} quantum dot is investigated taking into consideration of geometrical confinement effect. The effects of phonon on the exciton binding energy and the interband emission energy as a function of dot radius are found. The calculations are performed within the single band effective mass approximation using the variational method based on the Lee-Low-Pine LLP transformation.

  2. 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.

  3. 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.

  4. 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)

  5. 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

  6. Polaron crossover in molecular solids

    International Nuclear Information System (INIS)

    Zoli, Marco; Das, A N

    2004-01-01

    An analytical variational method is applied to the molecular Holstein Hamiltonian in which the dispersive features of the dimension dependent phonon spectrum are taken into account by a force constant approach. The crossover between a large and a small size polaron is monitored, in one, two and three dimensions and for different values of the adiabatic parameter, through the behaviour of the effective mass as a function of the electron-phonon coupling. By increasing the strength of the intermolecular forces the crossover becomes smoother and occurs at higher e-ph couplings. These effects are more evident in three dimensions. We show that our modified Lang-Firsov method starts to capture the occurrence of a polaron self-trapping transition when the electron energies become of order of the phonon energies. The self-trapping event persists in the fully adiabatic regime. At the crossover we estimate polaron effective masses of order ∼ 5-40 times the bare band mass according to the dimensionality and the value of the adiabatic parameter. Modified Lang-Firsov polaron masses are substantially reduced in two and three dimensions. There is no self-trapping in the antiadiabatic regime

  7. Binding energies of cluster ions

    International Nuclear Information System (INIS)

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

    2002-01-01

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

  8. Effects of Polaron and Quantum Confinement on the Nonlinear Optical Properties in a GaAs/Ga1-xAlxAs Quantum Well Wire

    Directory of Open Access Journals (Sweden)

    L. Caroline Sugirtham

    2014-01-01

    Full Text Available The binding energy of a polaron confined in a GaAs/Ga1-xAlxAs quantum well wire is calculated within the framework of the variational technique and Lee-Low Pines approach. The polaron-induced photoionization cross section as a function of normalized photon energy for a on-centre donor impurity in the quantum wire is investigated. The oscillator strength with the geometrical effect is studied taking into account the polaron effects in a GaAs/Ga0.8Al0.2As quantum well wire. The effect of polaron on the third-order susceptibility of third harmonic generation is studied. Our theoretical results are shown to be in good agreement with previous investigations.

  9. Explanation for the temperature dependence of plasma frequencies in SrTiO3 using mixed-polaron theory

    International Nuclear Information System (INIS)

    Eagles, D.M.; Georgiev, M.; Petrova, P.C.

    1996-01-01

    A theory of mixed polarons is used to interpret the published experimental results of Gervais et al. on temperature-dependent plasma frequencies in Nb-doped SrTiO 3 . For given polaron masses before mixing, the appropriate average mixed-polaron mass at any temperature T depends on two quantities, δ and b, which are measures of the separation between the bottoms of large and nearly small polaron bands before mixing and of a mixing matrix element; δ and b are assumed to have arbitrary linear dependences on T, probably related to a T dependence of the bare mass, and a term quadratic in T is included in δ, determined from the T dependence of large-polaron binding energies. Including a constraint on the ratio δ/|b| at low T from known masses from specific-heat data, satisfactory agreement is obtained with masses determined from plasma frequencies. This gives further support for the theory of mixed polarons in SrTiO 3 in addition to that already published. copyright 1996 The American Physical Society

  10. Energy and contact of the one-dimensional Fermi polaron at zero and finite temperature.

    Science.gov (United States)

    Doggen, E V H; Kinnunen, J J

    2013-07-12

    We use the T-matrix approach for studying highly polarized homogeneous Fermi gases in one dimension with repulsive or attractive contact interactions. Using this approach, we compute ground state energies and values for the contact parameter that show excellent agreement with exact and other numerical methods at zero temperature, even in the strongly interacting regime. Furthermore, we derive an exact expression for the value of the contact parameter in one dimension at zero temperature. The model is then extended and used for studying the temperature dependence of ground state energies and the contact parameter.

  11. 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

  12. Skyrmions with low binding energies

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-06-15

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

  13. Skyrmions with low binding energies

    International Nuclear Information System (INIS)

    Gillard, Mike; Harland, Derek; Speight, Martin

    2015-01-01

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

  14. Skyrmions with low binding energies

    Directory of Open Access Journals (Sweden)

    Mike Gillard

    2015-06-01

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

  15. Polarons in acetanilide

    Science.gov (United States)

    Scott, Alwyn C.; Bigio, Irving J.; Johnston, Clifford T.

    1989-06-01

    The best available data are presented of the integrated intensity of the 1650-cm-1 band in crystalline acetanilide as a function of temperature. A concise theory of polaron states is presented and used to interpret the data.

  16. Big magnetoresistance: magnetic polarons

    International Nuclear Information System (INIS)

    Teresa, J.M. de; Ibarra, M.R.

    1997-01-01

    By using several macro and microscopic experimental techniques we have given evidence for magnetoresistance in manganese oxides caused by the effect of the magnetic field on the magnetic polarons. (Author) 3 refs

  17. 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

  18. Polaron as the extended particle model

    International Nuclear Information System (INIS)

    Kochetov, E.A.; Kuleshov, S.P.; Smondyrev, M.A.

    1977-01-01

    The polaron (a moving electron with concomitant lattice distortion) mass and energy are calculated. The problem of finding the Green function in the polaron model is solved. A number of the simplest approximations corresponding to the approximation in the picture of straight-line paths is considered. The case of strong coupling requires more detailed study of the particle motion in the effective field, caused by the significant polarization of vacuum near the particle. As a consequence, a more complex approximation of functional integrals is required. A variation method is used in this case. The bound state of a polaron interacting not only with photons, but also with some external classical field is investigated as well. A classical potential is considered as an example

  19. Polaron in the dilute critical Bose condensate

    Science.gov (United States)

    Pastukhov, Volodymyr

    2018-05-01

    The properties of an impurity immersed in a dilute D-dimensional Bose gas at temperatures close to its second-order phase transition point are considered. Particularly by means of the 1/N-expansion, we calculate the leading-order polaron energy and the damping rate in the limit of vanishing boson–boson interaction. It is shown that the perturbative effective mass and the quasiparticle residue diverge logarithmically in the long-length limit, signalling the non-analytic behavior of the impurity spectrum and pole-free structure of the polaron Green’s function in the infrared region, respectively.

  20. Chiral plaquette polaron theory of cuprate superconductivity

    Science.gov (United States)

    Tahir-Kheli, Jamil; Goddard, William A., III

    2007-07-01

    Ab initio density functional calculations on explicitly doped La2-xSrxCuO4 find that doping creates localized holes in out-of-plane orbitals. A model for cuprate superconductivity is developed based on the assumption that doping leads to the formation of holes on a four-site Cu plaquette composed of the out-of-plane A1 orbitals apical Opz , planar Cud3z2-r2 , and planar Opσ . This is in contrast to the assumption of hole doping into planar Cudx2-y2 and Opσ orbitals as in the t-J model. Allowing these holes to interact with the d9 spin background leads to chiral polarons with either a clockwise or anticlockwise charge current. When the polaron plaquettes percolate through the crystal at x≈0.05 for La2-xSrxCuO4 , a Cudx2-y2 and planar Opσ band is formed. The computed percolation doping of x≈0.05 equals the observed transition to the “metallic” and superconducting phase for La2-xSrxCuO4 . Spin exchange Coulomb repulsion with chiral polarons leads to d -wave superconducting pairing. The equivalent of the Debye energy in phonon superconductivity is the maximum energy separation between a chiral polaron and its time-reversed partner. This energy separation is on the order of the antiferromagnetic spin coupling energy, Jdd˜0.1eV , suggesting a higher critical temperature. An additive skew-scattering contribution to the Hall effect is induced by chiral polarons and leads to a temperature dependent Hall effect that fits the measured values for La2-xSrxCuO4 . The integrated imaginary susceptibility, observed by neutron spin scattering, satisfies ω/T scaling due to chirality and spin-flip scattering of polarons along with a uniform distribution of polaron energy splittings. The derived functional form is compatible with experiments. The static spin structure factor for chiral spin coupling of the polarons to the undoped antiferromagnetic Cud9 spins is computed for classical spins on large two-dimensional lattices and is found to be incommensurate with a

  1. Polaron scattering by an external field

    International Nuclear Information System (INIS)

    Kochetov, E.A.

    1980-01-01

    The problem of polaron scattering by an external field is studied. The problem is solved using the stationary scattering theory formalism based on two operators: the G Green function operator and the T scattering operator. The dependence of the scattering amplitude on the quasi particle structure is studied. The variation approach is used for estimation of the ground energy level

  2. Method of T-products in polaron theory

    International Nuclear Information System (INIS)

    Bogolubov, N.N. Jr.; Kurbatov, A.M.; Kireev, A.N.

    1985-11-01

    T-products method is used for the investigation of equilibrium thermodynamic properties of Frohlich's model in polaron theory. Polaron free energy at finite temperatures is calculated on the basis of Bogolubov's variational principle. A trial function is chosen in the most general form corresponding to arbitrary number of oscillators harmonically interacting with electron. The upper bound to the polaron ground state energy in limiting case of weak interaction and low temperatures is obtained and investigated in detail. It is shown that the result becomes more exact by increasing the number of oscillators. (author)

  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. Tracking polaron generation in electrochemically doped polyaniline thin films

    Science.gov (United States)

    Kalagi, S. S.; Patil, P. S.

    2018-04-01

    Electrochemically deposited polyaniline films on ITO substrates have been studied for their optical properties. π-π*transitions inducing the formation of polarons and bipolarons have been studied from the optical spectra. The generation of these quasiparticles and the corresponding quantum of energy stored has been analysed and calculated from the experimental data. The evolution of polaron with increased levels of protonation has been identified and the necessary energy required for the transitions have been explained with the help of band structure diagram.

  6. Screening effect on the polaron by surface plasmons

    Science.gov (United States)

    Xu, Xiaoying; Xu, Xiaoshan; Seal, Katyayani; Guo, Hangwen; Shen, Jian; Low Dimensional Materials Physics, Oak Ridge National Lab Team; University of Tennessee Team; Physics Department, Fudan University Team

    2011-03-01

    Surface plasmons occur when the conduction electrons at a metal/dielectric interface resonantly interact with external electromagnetic fields. While surface plasmons in vicinity of a polaron in the dielectric material, a strong screening effect on polaron characteristics is introduced. In this work, we observed the reduction of polarons in multiferroic LuFe2O4, which is mainly contributed by surface plasmons. Research sponsored by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the U. S. Department of Energy.

  7. 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

  8. 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

  9. Polaron-Driven Surface Reconstructions

    Directory of Open Access Journals (Sweden)

    Michele Reticcioli

    2017-09-01

    Full Text Available Geometric and electronic surface reconstructions determine the physical and chemical properties of surfaces and, consequently, their functionality in applications. The reconstruction of a surface minimizes its surface free energy in otherwise thermodynamically unstable situations, typically caused by dangling bonds, lattice stress, or a divergent surface potential, and it is achieved by a cooperative modification of the atomic and electronic structure. Here, we combined first-principles calculations and surface techniques (scanning tunneling microscopy, non-contact atomic force microscopy, scanning tunneling spectroscopy to report that the repulsion between negatively charged polaronic quasiparticles, formed by the interaction between excess electrons and the lattice phonon field, plays a key role in surface reconstructions. As a paradigmatic example, we explain the (1×1 to (1×2 transition in rutile TiO_{2}(110.

  10. Theory of super-para-electric large polaron for gigantic photo-enhancements of dielectric constant and electronic conductivity in SrTiO3

    International Nuclear Information System (INIS)

    Yu Qiu; Nasu, Keiichiro

    2005-01-01

    In connection with the recent experimental discoveries on gigantic photoenhancements of the electronic conductivity and the quasi-static dielectric susceptibility in SrTiO 3 , we theoretically study a photo-generation mechanism of a charged ferroelectric domain in this quantum dielectric. The photo-generated electron, being quite itinerant in the 3d band of Ti 4+ , is assumed to couple weakly but quadratically with soft-anharmonic T 1u phonons in this quantum dielectric. The photo-generated electron is also assumed to couple strongly but linearly with the breathing type high energy phonons. Using a tight binding model for electron, we will show that these two types of electron-phonon couplings result in two types of polarons, a 'super-para-electric (SPE) large polaron' with a quasi-global parity violation, and an 'off-centre type self-trapped polaron' with only a local parity violation. We will also show that this SPE large polaron is nothing else but a singly charged (e - ) and conductive ferroelectric (or SPE) domain with a quasi macroscopic size. This polaron or domain is also shown to have a high mobility and a large quasi-static dielectric susceptibility

  11. P-shell hyperon binding energies

    International Nuclear Information System (INIS)

    Koetsier, D.; Amos, K.

    1991-01-01

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

  12. Multiphonon contribution to the polaron formation in cuprates with strong electron correlations and strong electron-phonon interaction

    Science.gov (United States)

    Ovchinnikov, Sergey G.; Makarov, Ilya A.; Kozlov, Peter A.

    2017-03-01

    In this work dependences of the electron band structure and spectral function in the HTSC cuprates on magnitude of electron-phonon interaction (EPI) and temperature are investigated. We use three-band p-d model with diagonal and offdiagonal EPI with breathing and buckling phonon mode in the frameworks of polaronic version of the generalized tight binding (GTB) method. The polaronic quasiparticle excitation in the system with EPI within this approach is formed by a hybridization of the local multiphonon Franck-Condon excitations with lower and upper Hubbard bands. Increasing EPI leads to transfer of spectral weight to high-energy multiphonon excitations and broadening of the spectral function. Temperature effects are taken into account by occupation numbers of local excited polaronic states and variations in the magnitude of spin-spin correlation functions. Increasing the temperature results in band structure reconstruction, spectral weight redistribution, broadening of the spectral function peak at the top of the valence band and the decreasing of the peak intensity. The effect of EPI with two phonon modes on the polaron spectral function is discussed.

  13. 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)

  14. Exciton Binding Energy of Monolayer WS2

    Science.gov (United States)

    Zhu, Bairen; Chen, Xi; Cui, Xiaodong

    2015-03-01

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

  15. Binding energy of two-dimensional biexcitons

    DEFF Research Database (Denmark)

    Singh, Jai; Birkedal, Dan; Vadim, Lyssenko

    1996-01-01

    Using a model structure for a two-dimensional (2D) biexciton confined in a quantum well, it is shown that the form of the Hamiltonian of the 2D biexciton reduces into that of an exciton. The binding energies and Bohr radii of a 2D biexciton in its various internal energy states are derived...... analytically using the fractional dimension approach. The ratio of the binding energy of a 2D biexciton to that of a 2D exciton is found to be 0.228, which agrees very well with the recent experimental value. The results of our approach are compared with those of earlier theories....

  16. Binding energies of hypernuclei and hypernuclear interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R. [Argonne National Lab., IL (United States)]|[Univ. of Illinois, Chicago, IL (United States). Dept. of Physics; Murali, S.; Usmani, Q.N. [Jamia Millia Islamia, New Delhi (India). Dept. of Physics

    1996-05-01

    In part 1 the effect of nuclear core dynamics on the binding energies of {Lambda} hypernuclei is discussed in the framework of variational correlated wave functions. In particular, the authors discuss a new rearrangement energy contribution and its effect on the core polarization. In part 2 they consider the interpretation of the {Lambda} single-particle energy in terms of basic {Lambda}-nuclear interactions using a local density approximation based on a Fermi hypernetted chain calculation of the A binding to nuclear matter. To account for the data strongly repulsive 3-body {Lambda}NN forces are required. Also in this framework they discuss core polarization for medium and heavier hypernuclei.

  17. Binding energies of hypernuclei and hypernuclear interactions

    International Nuclear Information System (INIS)

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

    1996-01-01

    In part 1 the effect of nuclear core dynamics on the binding energies of Λ hypernuclei is discussed in the framework of variational correlated wave functions. In particular, the authors discuss a new rearrangement energy contribution and its effect on the core polarization. In part 2 they consider the interpretation of the Λ single-particle energy in terms of basic Λ-nuclear interactions using a local density approximation based on a Fermi hypernetted chain calculation of the A binding to nuclear matter. To account for the data strongly repulsive 3-body ΛNN forces are required. Also in this framework they discuss core polarization for medium and heavier hypernuclei

  18. 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

  19. Impact of D2O/H2O Solvent Exchange on the Emission of HgTe and CdTe Quantum Dots: Polaron and Energy Transfer Effects.

    Science.gov (United States)

    Wen, Qiannan; Kershaw, Stephen V; Kalytchuk, Sergii; Zhovtiuk, Olga; Reckmeier, Claas; Vasilevskiy, Mikhail I; Rogach, Andrey L

    2016-04-26

    We have studied light emission kinetics and analyzed carrier recombination channels in HgTe quantum dots that were initially grown in H2O. When the solvent is replaced by D2O, the nonradiative recombination rate changes highlight the role of the vibrational degrees of freedom in the medium surrounding the dots, including both solvent and ligands. The contributing energy loss mechanisms have been evaluated by developing quantitative models for the nonradiative recombination via (i) polaron states formed by strong coupling of ligand vibration modes to a surface trap state (nonresonant channel) and (ii) resonant energy transfer to vibration modes in the solvent. We conclude that channel (i) is more important than (ii) for HgTe dots in either solution. When some of these modes are removed from the relevant spectral range by the H2O to D2O replacement, the polaron effect becomes weaker and the nonradiative lifetime increases. Comparisons with CdTe quantum dots (QDs) served as a reference where the resonant energy loss (ii) a priori was not a factor, also confirmed by our experiments. The solvent exchange (H2O to D2O), however, is found to slightly increase the overall quantum yield of CdTe samples, probably by increasing the fraction of bright dots in the ensemble. The fundamental study reported here can serve as the foundation for the design and optimization principles of narrow bandgap quantum dots aimed at applications in long wavelength colloidal materials for infrared light emitting diodes and photodetectors.

  20. 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)

  1. Al-bound hole polarons in TiO2

    International Nuclear Information System (INIS)

    Stashans, Arvids; Bermeo, Sthefano

    2009-01-01

    Changes in the structural and electronic properties of TiO 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 ΔSCF approach.

  2. Quantum transition and decoherence of levitating polaron on helium film thickness under an electromagnetic field

    Science.gov (United States)

    Kenfack, S. C.; Fotue, A. J.; Fobasso, M. F. C.; Djomou, J.-R. D.; Tiotsop, M.; Ngouana, K. S. L.; Fai, L. C.

    2017-12-01

    We have studied the transition probability and decoherence time of levitating polaron in helium film thickness. By using a variational method of Pekar type, the ground and the first excited states of polaron are calculated above the liquid-helium film placed on the polar substrate. It is shown that the polaron transits from the ground to the excited state in the presence of an external electromagnetic field in the plane. We have seen that, in the helium film, the effects of the magnetic and electric fields on the polaron are opposite. It is also shown that the energy, transition probability and decoherence time of the polaron depend sensitively on the helium film thickness. We found that decoherence time decreases as a function of increasing electron-phonon coupling strength and the helium film thickness. It is seen that the film thickness can be considered as a new confinement in our system and can be adjusted in order to reduce decoherence.

  3. Size dependent polaronic conduction in hematite

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Monika; Banday, Azeem; Murugavel, Sevi [Department of Physics and Astrophysics, University of Delhi, Delhi – 110 007 (India)

    2016-05-23

    Lithium Ion Batteries have been attracted as the major renewable energy source for all portable electronic devices because of its advantages like superior energy density, high theoretical capacity, high specific energy, stable cycling and less memory effects. Recently, α-Fe{sub 2}O{sub 3} has been considered as a potential anode material due to high specific capacity, low cost, high abundance and environmental benignity. We have synthesized α-Fe{sub 2}O{sub 3} with various sizes by using the ball milling and sol-gel procedure. Here, we report the dc conductivity measurement for the crystallite size ranging from 15 nm to 50 nm. It has been observed that the enhancement in the polaronic conductivity nearly two orders in magnitude while reducing the crystallite size from bulk into nano scale level. The enhancement in the conductivity is due to the augmented to compressive strain developed in the material which leads to pronounced decrease in the hopping length of polarons. Thus, nanocrystaline α-Fe{sub 2}O{sub 3} may be a better alternative anode material for lithium ion batteries than earlier reported systems.

  4. Size dependent polaronic conduction in hematite

    International Nuclear Information System (INIS)

    Sharma, Monika; Banday, Azeem; Murugavel, Sevi

    2016-01-01

    Lithium Ion Batteries have been attracted as the major renewable energy source for all portable electronic devices because of its advantages like superior energy density, high theoretical capacity, high specific energy, stable cycling and less memory effects. Recently, α-Fe_2O_3 has been considered as a potential anode material due to high specific capacity, low cost, high abundance and environmental benignity. We have synthesized α-Fe_2O_3 with various sizes by using the ball milling and sol-gel procedure. Here, we report the dc conductivity measurement for the crystallite size ranging from 15 nm to 50 nm. It has been observed that the enhancement in the polaronic conductivity nearly two orders in magnitude while reducing the crystallite size from bulk into nano scale level. The enhancement in the conductivity is due to the augmented to compressive strain developed in the material which leads to pronounced decrease in the hopping length of polarons. Thus, nanocrystaline α-Fe_2O_3 may be a better alternative anode material for lithium ion batteries than earlier reported systems.

  5. 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.

  6. 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.

  7. Trapping, self-trapping and the polaron family

    International Nuclear Information System (INIS)

    Stoneham, A M; Gavartin, J; Shluger, A L; Kimmel, A V; Ramo, D Munoz; Roennow, H M; Aeppli, G; Renner, C

    2007-01-01

    The earliest ideas of the polaron recognized that the coupling of an electron to ionic vibrations would affect its apparent mass and could effectively immobilize the carrier (self-trapping). We discuss how these basic ideas have been generalized to recognize new materials and new phenomena. First, there is an interplay between self-trapping and trapping associated with defects or with fluctuations in an amorphous solid. In high dielectric constant oxides, like HfO 2 , this leads to oxygen vacancies having as many as five charge states. In colossal magnetoresistance manganites, this interplay makes possible the scanning tunnelling microscopy (STM) observation of polarons. Second, excitons can self-trap and, by doing so, localize energy in ways that can modify the material properties. Third, new materials introduce new features, with polaron-related ideas emerging for uranium dioxide, gate dielectric oxides, Jahn-Teller systems, semiconducting polymers and biological systems. The phonon modes that initiate self-trapping can be quite different from the longitudinal optic modes usually assumed to dominate. Fourth, there are new phenomena, like possible magnetism in simple oxides, or with the evolution of short-lived polarons, like muons or excitons. The central idea remains that of a particle whose properties are modified by polarizing or deforming its host solid, sometimes profoundly. However, some of the simpler standard assumptions can give a limited, indeed misleading, description of real systems, with qualitative inconsistencies. We discuss representative cases for which theory and experiment can be compared in detail

  8. Polaron-mediated surface reconstruction in the reduced Rutile TiO2 (110) surface

    Science.gov (United States)

    Reticcioli, Michele; Setvin, Martin; Hao, Xianfeng; Diebold, Ulrike; Franchini, Cesare

    The role of polarons is of key importance for the understanding of the fundamental properties and functionalities of TiO2. We use density functional theory with an on-site Coulomb interaction and molecular dynamics to study the formation and dynamics of small polarons in the reduced rutile (110) surface. We show that excess electrons donated by oxygen-vacancies (VO) form mobile small polarons that hop easily in subsurface and surface Ti-sites. The polaron formation becomes more favorable by increasing the VO concentration level (up to 20%) due to the progressively lower energy cost needed to distort the lattice. However, at higher VO concentration the shortening of the averaged polaron-polaron distance leads to an increased Coulomb repulsion among the trapped charges at the Ti-sites, which weakens this trend. This instability is overtaken by means of a structural 1 × 2 surface reconstruction, characterized by a distinctively more favorable polaron distribution. The calculations are validated by a direct comparison with experimental AFM and STM data. Our study identifies a fundamentally novel mechanism to drive surface reconstructions and resolves a long standing issue on the origin of the reconstruction in rutile (110) surface.

  9. First calculation of the deuteron binding energy

    International Nuclear Information System (INIS)

    Schaegger, B.

    2012-01-01

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

  10. Measuring Intermolecular Binding Energies by Laser Spectroscopy.

    Science.gov (United States)

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

    2017-02-22

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

  11. Fitting theories of nuclear binding energies

    International Nuclear Information System (INIS)

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

    2005-01-01

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

  12. Binding-energy distribution and dephasing of localized biexcitons

    DEFF Research Database (Denmark)

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

    1997-01-01

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

  13. 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

  14. 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...

  15. Implicit ligand theory for relative binding free energies

    Science.gov (United States)

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

    2018-03-01

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

  16. 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 ...

  17. 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...

  18. 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

  19. 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.

  20. On binding energy of trions in bulk materials

    Science.gov (United States)

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

    2018-03-01

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

  1. 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.

  2. 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

  3. 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...

  4. 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

  5. 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.

  6. 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.

  7. Predicting accurate absolute binding energies in aqueous solution

    DEFF Research Database (Denmark)

    Jensen, Jan Halborg

    2015-01-01

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

  8. 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...... polarized (ferromagnetic) domains are then examined for a binary mixture of atoms with a general mass ratio. Our results indicate that mass imbalance lowers the critical interaction strength for phase-separation, but that very short quasiparticle decay times will complicate the experimental observation...

  9. 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

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

    Indian Academy of Sciences (India)

    Orifjon Ganiev

    2017-05-30

    May 30, 2017 ... sizes and effective masses are large polarons. According ... nating metallic and insulating domains with mobile ... The mobile polaronic carriers are con- ..... [51] T Kondo, Y Hamaya, A D Palczewski, T Takeuchi, J S Wen,.

  11. A new DFT approach to model small polarons in oxides with proper account for long-range polarization

    Science.gov (United States)

    Kokott, Sebastian; Levchenko, Sergey V.; Scheffler, Matthias; Theory Department Team

    In this work, we address two important challenges in the DFT description of small polarons (excess charges localized within one unit cell): sensitivity to the errors in exchange-correlation (XC) treatment and finite-size effects in supercell calculations. The polaron properties are obtained using a modified neutral potential-energy surface (PES). Using the hybrid HSE functional and considering the whole range 0 Deutsche Forschungsgemeinschaft).

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

    International Nuclear Information System (INIS)

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

    2004-01-01

    In this paper we present the binding energy of 16 O together with single-particle energies in the oxygen region by folding together a Hamiltonian in the rest-frame of the nucleus with two-body correlation functions based on the Nijmegen potential. We have found that the binding energies are very sensitive to the core radius rc and that the effects of tensor correlations are non-negligible.Our calculated binding energy, E B = - 127.8 MeV with r c = 0.241 fm compares well with the experimental binding energy, E B = - 127.6 MeV

  13. Observation of Spin Polarons in a Tunable Fermi Liquid of Ultracold Atoms

    Science.gov (United States)

    Zwierlein, Martin

    2009-05-01

    We have observed spin polarons, dressed spin down impurities in a spin up Fermi sea of ultracold atoms via 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- or Fermi 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 spectra allow us to directly measure the polaron energy and the quasi-particle residue Z. The polarons are found to be only weakly interacting with each other, and can thus be identified with the quasi-particles of Landau's Fermi liquid theory. At a critical interaction strength, we observe a transition from spin one-half polarons to spin zero molecules. At this point the Fermi liquid undergoes a phase transition into a superfluid Bose liquid.

  14. Gross–Tulub polaron functional in the region of intermediate and strong coupling

    Directory of Open Access Journals (Sweden)

    N.I. Kashirina

    2017-10-01

    Full Text Available Properties of the polaron functional obtained as a result of averaging the Fröhlich Hamiltonian on the translation-invariant function have been investigated. The polaron functional can be represented in two different forms. It has been shown that the functional of translationally invariant Gross–Tulub polaron cannot be applied in the strong coupling region, where the real part of the complex quantity takes negative values. The function coincides in its structure with the dynamic susceptibility of degenerate electron gas. The necessary condition for obtaining correct results is investigation of the region of admissible values of the Gross–Tulub functional depending on properties of the function , variational parameters, and the electron-phonon interaction parameter α (Fröhlich coupling constant. A simple and exact formula for the recoil energy of the translationally invariant polaron has been derived, which makes it possible to extend the range of admissible values of the parameters of the electron-phonon interaction to the region of extremely strong coupling (α > 10, where . Numerical investigation of different forms of polaron functionals obtained using the field theory methods has been carried out.

  15. Small polaron hopping conduction mechanism in LiFePO4 glass and crystal

    Science.gov (United States)

    Banday, Azeem; Murugavel, Sevi

    2017-01-01

    The optimization of a cathode material is the most important criterion of lithium ion battery technology, which decides the power density. In order to improve the rate capability, a cathode material must possess high electronic and ionic conductivities. Therefore, it is important to understand the charge transport mechanism in such an advanced cathode material in its intrinsic state before modifying it by various means. In this work, we report the thermal, structural, and electrical conductivity studies on lithium iron phosphate, LiFePO4, both in its polycrystalline (LFPC) and glassy (LFPG) counterpart states. The vibrational spectroscopic measurements reveal the characteristic vibrational modes, which are the intrinsic part of LFPC, whereas in LFPG, the phonon modes become broader and overlap with each other due to the lattice disorder. The electrical conductivity measurements reveal that LFPG exhibits a higher polaronic conductivity of 1.6 orders than the LFPC sample. The temperature dependent dc conductivity has been analyzed with the Mott model of polarons and reveals the origin of enhanced polaronic conductivity in LFPG. Based on the analysis, the enhanced polaronic conductivity in LFPG has been attributed to the combined effect of reduced hopping length, decreased activation energy, and enhanced polaron concentration.

  16. The polaron problem and the Boltzmann equation

    International Nuclear Information System (INIS)

    Devreese, J.

    1979-01-01

    A mobility theory for the Feynman polaron is developed. It is shown that the Boltzmann equation for polarons is valid for weak coupling and not too high electric fields. The analytical results indicate that for E → 0 the relaxation time approximation is valid. A comparison is made of three methods to calculate the mobility in a linear electron transport theory. An approximation to the Kubo formula, a mobility calculation using path integrals by Feynman and a calculation based on the displaced Maxwell distribution function are considered. The three methods lead to equivalent results in the weak scattering and small electric field limit

  17. Binding energy effects in cascade evolution and sputtering

    International Nuclear Information System (INIS)

    Robinson, M.T.

    1995-06-01

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

  18. 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

  19. Non-canonical distribution and non-equilibrium transport beyond weak system-bath coupling regime: A polaron transformation approach

    Science.gov (United States)

    Xu, Dazhi; Cao, Jianshu

    2016-08-01

    The concept of polaron, emerged from condense matter physics, describes the dynamical interaction of moving particle with its surrounding bosonic modes. This concept has been developed into a useful method to treat open quantum systems with a complete range of system-bath coupling strength. Especially, the polaron transformation approach shows its validity in the intermediate coupling regime, in which the Redfield equation or Fermi's golden rule will fail. In the polaron frame, the equilibrium distribution carried out by perturbative expansion presents a deviation from the canonical distribution, which is beyond the usual weak coupling assumption in thermodynamics. A polaron transformed Redfield equation (PTRE) not only reproduces the dissipative quantum dynamics but also provides an accurate and efficient way to calculate the non-equilibrium steady states. Applications of the PTRE approach to problems such as exciton diffusion, heat transport and light-harvesting energy transfer are presented.

  20. Exciton binding energy in a pyramidal quantum dot

    Indian Academy of Sciences (India)

    A ANITHA

    2018-03-27

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

  1. 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.

  2. Inapplicability of small-polaron model for the explanation of infrared absorption spectrum in acetanilide.

    Science.gov (United States)

    Zeković, Slobodan; Ivić, Zoran

    2009-01-01

    The applicability of small-polaron model for the interpretation of infrared absorption spectrum in acetanilide has been critically reexamined. It is shown that the energy difference between the normal and anomalous peak, calculated by means of small-polaron theory, displays pronounced temperature dependence which is in drastic contradiction with experiment. It is demonstrated that self-trapped states, which are recently suggested to explain theoretically the experimental absorption spectrum in protein, cannot cause the appearance of the peaks in absorption spectrum for acetanilide.

  3. 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

  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. Small polarons in 2D perovskites

    KAUST Repository

    Cortecchia, Daniele; Yin, Jun; Birowosuto, Muhammad D.; Lo, Shu-Zee A.; Gurzadyan, Gagik G.; Bruno, Annalisa; Bredas, Jean-Luc; Soci, Cesare

    2017-01-01

    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.

  6. Quantum vibrational polarons: Crystalline acetanilide revisited

    Science.gov (United States)

    Hamm, Peter; Edler, Julian

    2006-03-01

    We discuss a refined theoretical description of the peculiar spectroscopy of crystalline acetanilide (ACN). Acetanilide is a molecular crystal with quasi-one-dimensional chains of hydrogen-bonded units, which is often regarded as a model system for the vibrational spectroscopy of proteins. In linear spectroscopy, the CO stretching (amide I) band of ACN features a double-peak structure, the lower of which shows a pronounced temperature dependence which has been discussed in the context of polaron theory. In nonlinear spectroscopy, both of these peaks respond distinctly differently. The lower-frequency band exhibits the anharmonicity expected from polaron theory, while the higher-frequency band responds as if it were quasiharmonic. We have recently related the response of the higher-frequency band to that of a free exciton [J. Edler and P. Hamm, J. Chem. Phys. 117, 2415 (2002)]. However, as discussed in the present paper, the free exciton is not an eigenstate of the full quantum version of the Holstein polaron Hamiltonian, which is commonly used to describe these phenomena. In order to resolve this issue, we present a numerically exact solution of the Holstein polaron Hamiltonian in one dimension (1D) and 3D. In 1D, we find that the commonly used displaced oscillator picture remains qualitatively correct, even for relatively large exciton coupling. However, the result is not in agreement with the experiment, as it fails to explain the free-exciton band. In contrast, when taking into account the 3D nature of crystalline acetanilide, certain parameter regimes exist where the displaced oscillator picture breaks down and states appear in the spectrum that indeed exhibit the characteristics of a free exciton. The appearance of these states is a speciality of vibrational polarons, whose source of exciton coupling is transition dipole coupling which is expected to have opposite signs of interchain and intrachain coupling.

  7. 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.

  8. Decay of Polarons and Molecules in a Strongly Polarized Fermi Gas

    DEFF Research Database (Denmark)

    Bruun, Georg; Massignan, P.

    2010-01-01

    , and that it vanishes much faster than the energy difference between the two states, thereby confirming the first order nature of the polaron-molecule transition. In the regime where each state is metastable, we find quasiparticle lifetimes which are much longer than what is expected for a usual Fermi liquid. Our...

  9. 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

  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. 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…

  12. 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

  13. Alternate Energy Sources for Thermalplastic Binding Agent Consolidation

    Energy Technology Data Exchange (ETDEWEB)

    Frame, B.J.

    1999-01-01

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

  14. 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

  15. 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.

  16. Spectrally resolved hyperfine interactions between polaron and nuclear spins in organic light emitting diodes: Magneto-electroluminescence studies

    Energy Technology Data Exchange (ETDEWEB)

    Crooker, S. A.; Kelley, M. R.; Martinez, N. J. D.; Nie, W.; Mohite, A.; Nayyar, I. H.; Tretiak, S.; Smith, D. L. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Liu, F.; Ruden, P. P. [University of Minnesota, Minneapolis, Minnesota 55455 (United States)

    2014-10-13

    We use spectrally resolved magneto-electroluminescence (EL) measurements to study the energy dependence of hyperfine interactions between polaron and nuclear spins in organic light-emitting diodes. Using layered devices that generate bright exciplex emission, we show that the increase in EL emission intensity I due to small applied magnetic fields of order 100 mT is markedly larger at the high-energy blue end of the EL spectrum (ΔI/I ∼ 11%) than at the low-energy red end (∼4%). Concurrently, the widths of the magneto-EL curves increase monotonically from blue to red, revealing an increasing hyperfine coupling between polarons and nuclei and directly providing insight into the energy-dependent spatial extent and localization of polarons.

  17. 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.

  18. Magnon Polarons in the Spin Seebeck Effect.

    Science.gov (United States)

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

    2016-11-11

    Sharp structures in the magnetic field-dependent spin Seebeck effect (SSE) voltages of Pt/Y_{3}Fe_{5}O_{12} at low temperatures are attributed to the magnon-phonon interaction. Experimental results are well reproduced by a Boltzmann theory that includes magnetoelastic coupling. The SSE anomalies coincide with magnetic fields tuned to the threshold of magnon-polaron formation. The effect gives insight into the relative quality of the lattice and magnetization dynamics.

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

  20. Transport through a vibrating quantum dot: Polaronic effects

    International Nuclear Information System (INIS)

    Koch, T; Alvermann, A; Fehske, H; Loos, J; Bishop, A R

    2010-01-01

    We present a Green's function based treatment of the effects of electron-phonon coupling on transport through a molecular quantum dot in the quantum limit. Thereby we combine an incomplete variational Lang-Firsov approach with a perturbative calculation of the electron-phonon self energy in the framework of generalised Matsubara Green functions and a Landauer-type transport description. Calculating the ground-state energy, the dot single-particle spectral function and the linear conductance at finite carrier density, we study the low-temperature transport properties of the vibrating quantum dot sandwiched between metallic leads in the whole electron-phonon coupling strength regime. We discuss corrections to the concept of an anti-adiabatic dot polaron and show how a deformable quantum dot can act as a molecular switch.

  1. Evaluation of binding energies by using quantum mechanical methods

    International Nuclear Information System (INIS)

    Postolache, Cristian; Matei, Lidia; Postolache, Carmen

    2002-01-01

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

  2. Experimental electron binding energies for thulium in different matrices

    Czech Academy of Sciences Publication Activity Database

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

    2015-01-01

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

  3. Two Impurities in a Bose-Einstein Condensate: From Yukawa to Efimov Attracted Polarons

    Science.gov (United States)

    Naidon, Pascal

    2018-04-01

    The well-known Yukawa and Efimov potentials are two different mediated interaction potentials. The first one arises in quantum field theory from the exchange of virtual particles. The second one is mediated by a real particle resonantly interacting with two other particles. This Letter shows how two impurities immersed in a Bose-Einstein condensate can exhibit both phenomena. For a weak attraction with the condensate, the two impurities form two polarons that interact through a weak Yukawa attraction mediated by virtual excitations. For a resonant attraction with the condensate, the exchanged excitation becomes a real boson and the mediated interaction changes to a strong Efimov attraction that can bind the two polarons. The resulting bipolarons turn into in-medium Efimov trimers made of the two impurities and one boson. Evidence of this physics could be seen in ultracold mixtures of atoms.

  4. Second order approximation for optical polaron in the strong coupling case

    International Nuclear Information System (INIS)

    Bogolubov, N.N. Jr.

    1993-11-01

    Here we propose a method of construction second order approximation for ground state energy for class of model Hamiltonian with linear type interaction on Bose operators in strong coupling case. For the application of the above method we have considered polaron model and propose construction set of nonlinear differential equations for definition ground state energy in strong coupling case. We have considered also radial symmetry case. (author). 10 refs

  5. A polaronic model of superconductivity in doped fulleride systems

    International Nuclear Information System (INIS)

    Tiwari, S.C.

    2007-01-01

    Full text: A polaronic model of superconductivity in doped fulleride systems is presented. The normal and anomalous one-particle Green's functions are derived for a system with strong electron phonon coupling. The study of collapse of the electron band and the phonon vacuum is presented within the mean-field approximation. Self consistent equation for the superconducting order parameter is derived using Green's function technique and following Lang and Firsov transformations. Expressions for specific heat, density of states, free energy and critical field based on this model have been derived. The theory is applied to explain the experimental results in the systems K 3 C 60 and Rb 3 C 6 O. These results are in good agreement with the available experimental data. (authors)

  6. One dimensional polaron effects and current inhomogeneities in sequential phonon emission

    Energy Technology Data Exchange (ETDEWEB)

    Hellman, E.S.; Harris, J.S.; Hanna, C.; Laughlin, R.B.

    1985-07-01

    We have constructed a physical model to explain the tunneling current oscillations reported by Hickmott et al., for GaAs/AlGaAs heterostructures in high magnetic fields. We propose that the periodic structure observed is due to space charge which builds up in the undepleted layer when electrons enter it with energy just below the phonon emission threshold. Such electrons interact with the lattice to form polarons whose energy is pinned to the phonon energy, and thus has a very small group velocity. The polaron effect is strongly enhanced by the confinement of the electrons by the strong magnetic field. We infer from the current-voltage data that most of the tunneling current flows through a small area of the sample. The combined model gives reasonable quantitative agreement with experiment. 6 refs., 6 figs.

  7. One dimensional polaron effects and current inhomogeneities in sequential phonon emission

    International Nuclear Information System (INIS)

    Hellman, E.S.; Harris, J.S.; Hanna, C.; Laughlin, R.B.

    1985-07-01

    We have constructed a physical model to explain the tunneling current oscillations reported by Hickmott et al., for GaAs/AlGaAs heterostructures in high magnetic fields. We propose that the periodic structure observed is due to space charge which builds up in the undepleted layer when electrons enter it with energy just below the phonon emission threshold. Such electrons interact with the lattice to form polarons whose energy is pinned to the phonon energy, and thus has a very small group velocity. The polaron effect is strongly enhanced by the confinement of the electrons by the strong magnetic field. We infer from the current-voltage data that most of the tunneling current flows through a small area of the sample. The combined model gives reasonable quantitative agreement with experiment. 6 refs., 6 figs

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

    International Nuclear Information System (INIS)

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

    1982-01-01

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

  9. Neutron diffuse scattering in magnetite due to molecular polarons

    International Nuclear Information System (INIS)

    Yamada, Y.; Wakabayashi, N.; Nicklow, R.M.

    1980-01-01

    A detailed neutron diffuse scattering study has been carried out in order to verify a model which describes the property of valence fluctuations in magnetite above T/sub V/. This model assumes the existence of a complex which is composed of two excess electrons and a local displacement mode of oxygens within the fcc primitive cell. The complex is called a molecular polaron. It is assumed that at sufficiently high temperatures there is a random distribution of molecular polarons, which are fluctuating independently by making hopping motions through the crystal or by dissociating into smaller polarons. The lifetime of each molecular polaron is assumed to be long enough to induce an instantaneous strain field around it. Based on this model, the neutron diffuse scattering cross section due to randomly distributed dressed molecular polarons has been calculated. A precise measurement of the quasielastic scattering of neutrons has been carried out at 150 K. The observed results definitely show the characteristics which are predicted by the model calculation and, thus, give evidence for the existence of the proposed molecular polarons. From this standpoint, the Verwey transition of magnetite may be viewed as the cooperative ordering process of dressed molecular polarons. Possible extensions of the model to describe the ordering and the dynamical behavior of the molecular polarons are discussed

  10. 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

  11. 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.

  12. 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)

  13. 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).

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

    Science.gov (United States)

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

    2015-06-09

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

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

    Science.gov (United States)

    2016-01-01

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

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

    African Journals Online (AJOL)

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

  17. Measurement of Exciton Binding Energy of Monolayer WS2

    Science.gov (United States)

    Chen, Xi; Zhu, Bairen; Cui, Xiaodong

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

  18. Mechanism of small-polaron formation in the biferroic YCrO{sub 3} doped with calcium

    Energy Technology Data Exchange (ETDEWEB)

    Duran, A., E-mail: dural@cnyn.unam.mx [Universidad Nacional Autonoma de Mexico, Centro de Nanociencias y Nanotecnologia, Apartado Postal 41, C.P. 22800, Ensenada, B.C. (Mexico); Verdin, E. [Universidad de Sonora, Departamento de Fisica, Apartado Postal 1626, Hermosillo, Sonora C.P. 8300 (Mexico); Escamilla, R.; Morales, F.; Escudero, R. [Universidad Nacional Autonoma de Mexico, Instituto de Investigaciones en Materiales, Apartado Postal 70-360, Mexico D.F. 04510 (Mexico)

    2012-04-16

    Highlights: Black-Right-Pointing-Pointer The Ca doped in the YCrO3 matrix was analyzed by means of complete structural, magnetic and electric properties. Black-Right-Pointing-Pointer E{sub act} deduced by Arrhenius' Law suggests small-polarons as conduction mechanisms in pristine and doped sample. Black-Right-Pointing-Pointer Local non-centrosymmetry in pristine sample is proposed as responsible of small polarons formation. Black-Right-Pointing-Pointer A mechanism of formation of small polarons is proposed supported by experimental evidence. Black-Right-Pointing-Pointer The structural distortion caused by the Ca doped in the YCrO3 matrix is harmful to the Ferroic properties. - Abstract: The effects of Ca substitutions on the structure, magnetism and electrical properties of YCrO{sub 3} ceramics are investigated by X-ray diffraction, magnetic susceptibility and electrical conductivity measurements. The cell volume decrease occurs through the change from Cr(III) to Cr(IV) as a result of the charge compensation of the Ca doping. No changes are observed in the antiferromagnetic transition temperature while strong changes are observed in the transport measurements due to Ca content. The increase of the electrical conductivity as well as the decrease of the activation energy is caused by the formation of the small-polarons localized in the O-Cr-O lattice distortion. The origin of small-polarons in the undoped sample is different in nature from the calcium doped. 'Local non-centrosymmetry' is the source of the small-polaron formation in undoped sample, while the change from Cr(III) to Cr(IV) through the charge compensation of Ca(II) in the Y(III) site is the source of small-polarons formations. The decrease of the average bond length Cr-O as well as effective moments in the paramagnetic state and the increase of the electrical conductivity are clear evidence that the Ca doping induces localized polarons, which in turn, these quasiparticles move from site to

  19. Charge compensation and binding energy referencing in XPS analysis

    International Nuclear Information System (INIS)

    Metson, J.B.

    1999-01-01

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

  20. Magnetic Polarons in Anisotropic Quantum Dots

    Science.gov (United States)

    Oszwaldowski, Rafal; Petukhov, Andre; Zutic, Igor

    2010-03-01

    Tunability of confinement in magnetically-doped quantum dots (QDs) allows to tailor magnetism to an extent not available in bulk semiconductors. Versatile control of magnetic ordering, along with piezomagnetism, has been predicted even at a fixed number of carriers [1]. Recent experiments on colloidal QDs revealed strongly bound magnetic polarons (MPs) [2]. Previous studies of MPs in bulk semiconductors showed that the mean-field theory predicts a spurious magnetic phase transition, which is removed by taking into account spin fluctuations [3]. Here we present our theoretical results for MPs forming in QDs with pronounced magnetic anisotropy, which influences the spin fluctuations. We apply our findings to explain some peculiarities of the magnetic behavior of type-II ZnSe/(Zn,Mn)Te QDs, where magnetic polarons are found to persist to at least 200K [4]. Supported by ONR, AFOSR, and NSF-ECCS CAREER. [4pt] [1] R. M. Abolfath, A. G. Petukhov, and I. Zutic, Phys. Rev. Lett. 101, 207202 (2008); I. Zutic and A. G. Petukhov, Nature Mater.4, 623 (2009). [0pt] [2] R. Beaulac et al., Science 325, 973 (2009). [0pt] [3] T. Dietl and J. Spalek, Phys. Rev. Lett. 48, 355 (1982). [0pt] [4] I. R. Sellers, R. Oszwaldowski, et al., preprint; I. R. Sellers et al., Phys. Rev. Lett. 100, 136405 (2008).

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

    Science.gov (United States)

    2014-01-01

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

  2. 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}-...

  3. 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.

  4. Non-abelian binding energies from the lightcone bootstrap

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-02-23

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

  5. Bi-Polaron Condensation in High Tc Superconductors

    International Nuclear Information System (INIS)

    Ranninger, J.

    1995-01-01

    On the basis of optical measurements-, photoemission-, EXAFS- and neutron scattering-experiments we conclude that itinerant valence electrons coexist with localized bi-polarons.Entering the metallic phase upon chemical doping, a charge transfer between the two electronic subsystems is triggered off. We show that as the temperature is lowered towards Tc this process leads to a delocalization of bi-polarons due to a precursor effect of superfluidity of those bi-polarons. Upon entering the superconducting phase, these bipolarons ultimately condense into a superfluid state which is expected to largely determine the superconducting properties of high Tc materials. (authors)

  6. Transport and ordering of polarons in CER manganites PrCaMnO

    International Nuclear Information System (INIS)

    Schramm, S; Hoffmann, J; Jooss, Ch

    2008-01-01

    The temperature-dependent resistivity and the colossal resistance effect induced by strong electric fields of the small-band Pr 1-x Ca x MnO 3 (PCMO) manganites are analysed with respect to the influence of the Ca doping, post-annealing, the prehistory of the electric stimulation, and the physical dimensions of the sample. Despite the phase separation between charge and orbital ordered and disordered phases, PCMO reveals the properties of a homogeneous medium with a conductivity governed by the hopping of small polarons if the electric field is not too strong. In contrast, high electric fields induce a structural transition which gives rise to a glassy behaviour in the transient regime. In the low resistance state the small activation energy of charge carrier hopping implies a transition to large polaron hopping

  7. Semiclassical and quantum polarons in crystalline acetanilide

    Science.gov (United States)

    Hamm, P.; Tsironis, G. P.

    2007-08-01

    Crystalline acetanilide is a an organic solid with peptide bond structure similar to that of proteins. Two states appear in the amide I spectral region having drastically different properties: one is strongly temperature dependent and disappears at high temperatures while the other is stable at all temperatures. Experimental and theoretical work over the past twenty five years has assigned the former to a selftrapped state while the latter to an extended free exciton state. In this article we review the experimental and theoretical developments on acetanilide paying particular attention to issues that are still pending. Although the interpretation of the states is experimentally sound, we find that specific theoretical comprehension is still lacking. Among the issues that that appear not well understood is the effective dimensionality of the selftrapped polaron and free exciton states.

  8. 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.

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2014-02-05

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

  11. An accurate redetermination of the 118Sn binding energy

    International Nuclear Information System (INIS)

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

    2001-01-01

    The energy of well-known strong γ-line from 198 Au, the 'gold standard', has been modified in the light of new adjustments in the fundamental constants and the value of 411.80176(12) keV was determined which is 0.29 eV lower than the latest 1999 value. An energy calibration procedure for determining the neutron binding energy, B n , from complicated (n,γ)-spectra has been developed. A mathematically simple minimization function consisting only of terms having as parameters the coefficients of the energy calibration curve (polynomial) is used. A priori information about the relationships among the energies of different peaks on the spectrum was taken into account by a Monte Carlo simulation. The procedure was used in obtaining of B n for 118 Sn and 64 Cu. The γ-ray spectrum from thermal neutron radiative capture by 117 Sn has been measured on the IBR-2 pulsed reactor. γ-rays were detected by a 72 cm 2 HPGe-detector. B n for 64 Cu was obtained from two γ-spectra. One spectrum was measured on the IBR-2 by the same detector. The other spectrum was measured with a pair spectrometer at the Brookhaven High Flux Beam Reactor. From these two spectra B n for 64 Cu was determined equal to 7915.52(8) keV. The mean value of two most precise results of B n for 118 Sn was determined to be 9326.35(9) keV. The B n for 57Fe was determined to be 7646.08(9) keV

  12. Influence of impurities on the polaron effective mass

    International Nuclear Information System (INIS)

    Lima, R.A.T. de.

    1975-01-01

    Using the Green Function formalism, it is verified the Rodriguez's model for the effective mass of the polaron at finite temperature in the presence of 'traps'. Some aspects of this model were discussed. (M.W.O.) [pt

  13. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-07-01

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

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

    International Nuclear Information System (INIS)

    Haddad, S.

    2011-04-01

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

  16. First-Principles Modeling of Polaron Formation in TiO2 Polymorphs.

    Science.gov (United States)

    Elmaslmane, A R; Watkins, M B; McKenna, K P

    2018-06-21

    We present a computationally efficient and predictive methodology for modeling the formation and properties of electron and hole polarons in solids. Through a nonempirical and self-consistent optimization of the fraction of Hartree-Fock exchange (α) in a hybrid functional, we ensure the generalized Koopmans' condition is satisfied and self-interaction error is minimized. The approach is applied to model polaron formation in known stable and metastable phases of TiO 2 including anatase, rutile, brookite, TiO 2 (H), TiO 2 (R), and TiO 2 (B). Electron polarons are predicted to form in rutile, TiO 2 (H), and TiO 2 (R) (with trapping energies ranging from -0.02 eV to -0.35 eV). In rutile the electron localizes on a single Ti ion, whereas in TiO 2 (H) and TiO 2 (R) the electron is distributed across two neighboring Ti sites. Hole polarons are predicted to form in anatase, brookite, TiO 2 (H), TiO 2 (R), and TiO 2 (B) (with trapping energies ranging from -0.16 eV to -0.52 eV). In anatase, brookite, and TiO 2 (B) holes localize on a single O ion, whereas in TiO 2 (H) and TiO 2 (R) holes can also be distributed across two O sites. We find that the optimized α has a degree of transferability across the phases, with α = 0.115 describing all phases well. We also note the approach yields accurate band gaps, with anatase, rutile, and brookite within six percent of experimental values. We conclude our study with a comparison of the alignment of polaron charge transition levels across the different phases. Since the approach we describe is only two to three times more expensive than a standard density functional theory calculation, it is ideally suited to model charge trapping at complex defects (such as surfaces and interfaces) in a range of materials relevant for technological applications but previously inaccessible to predictive modeling.

  17. Raman and optical spectroscopic studies of small-to-large polaron crossover in the perovskite manganese oxides

    International Nuclear Information System (INIS)

    Yoon, S.; Liu, H.L.; Schollerer, G.; Cooper, S.L.; Han, P.D.; Payne, D.A.; Cheong, S.; Fisk, Z.

    1998-01-01

    We present an optical reflectance and Raman-scattering study of the A 1-x A ' x MnO 3 system as a function of temperature and doping (0.2≤x≤0.5). The metal-semiconductor transition in the A 1-x A ' x MnO 3 system is characterized by a change from a diffusive electronic Raman-scattering response in the high-temperature paramagnetic phase, to a flat continuum scattering response in the low-temperature ferromagnetic phase. We interpret this change in the scattering response as a crossover from a small-polaron-dominated regime at high temperatures to a large-polaron-dominated low-temperature regime. Interestingly, we observe evidence for the coexistence of large and small polarons in the low-temperature ferromagnetic phase. We contrast these results with those obtained for EuB 6 , which is a low-T c magnetic semiconductor with similar properties to the manganites, but with a substantially reduced carrier density and polaron energy. copyright 1998 The American Physical Society

  18. 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

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

    International Nuclear Information System (INIS)

    Mian, M.

    1987-01-01

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

  20. 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 .

  1. Effects of compositional defects on small polaron hopping in micas.

    Science.gov (United States)

    Rosso, Kevin M; Ilton, Eugene S

    2005-06-22

    Hartree-Fock calculations and electron transfer (ET) theory were used to model the effects of compositional defects on ET in the brucite-like octahedral sheet of mica. ET was modeled as an Fe(IIIII) valence interchange reaction across shared octahedral edges of the M2-M2 iron sublattice. The model entails the hopping of localized electrons and small polaron behavior. Hartree-Fock calculations indicate that substitution of F for structural OH bridges increases the reorganization energy lambda, decreases the electronic coupling matrix element V(AB), and thereby substantially decreases the hopping rate. The lambda increase arises from modification of the metal-ligand bond force constants, and the V(AB) decrease arises from reduction of superexchange interaction through anion bridges. Deprotonation of an OH bridge, consistent with a possible mechanism of maintaining charge neutrality during net oxidation, yields a net increase in the ET rate. Although substitution of Al or Mg for Fe in M1 sites distorts the structure of adjacent Fe-occupied M2 sites, the distortion has little net impact on ET rates through these M2 sites. Hence the main effect of Al or Mg substitution for Fe, should it occur in the M2 sublattice, is to block ET pathways. Collectively, these findings pave the way for larger-scale oxidation/reduction models to be constructed for realistic, compositionally diverse micas.

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

    Science.gov (United States)

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

    2016-04-15

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

  3. 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.

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

    KAUST Repository

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

    2016-01-01

    experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S

  5. 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.

  6. 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.

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

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

    Science.gov (United States)

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

    2006-07-01

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

  9. Small-polaron model of light atom diffusion

    International Nuclear Information System (INIS)

    Emin, D.

    1977-01-01

    A number of researchers have treated the diffusion of light interstitials in metals in strict analogy with the theory for the hopping diffusion of electrons in low-mobility insulators. In other words, these authors view the diffusion of light atoms as simply being an example of small-polaron hopping motion. In this paper the motion of a small polaron is introduced, and the mechanism of its motion is described. The experimental results are then succinctly presented. Next the physical assumptions implicit in the theory are compared with the situation which is believed to characterize the existence and motion of light interstitial atoms in metals. Concomitantly, the modifications of the small-polaron theory required in applying it to light atom diffusion are ennumerated

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

    Science.gov (United States)

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

    2018-01-01

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

  11. Logarithmic corrections in a quantization rule. The polaron spectrum

    International Nuclear Information System (INIS)

    Karasev, M.V.; Pereskokov, A.V.

    1994-01-01

    A nonlinear integrodifferential equation that arises in polaron theory is considered. The integral nonlinearity is given by a convolution with the Coulomb potential. Radially symmetric solutions are sought. In the semiclassical limit, an equation for the self-consistent potential is found and studied. The potential has a logarithmic singularity at the origin, and also a turning point at 1. The phase shifts at these points are determined. The quantization rule that takes into account the logarithmic corrections gives a simple asymptotic formula for the polaron spectrum. Global semiclassical solutions of the original nonlinear equation are constructed. 18 refs., 1 tab

  12. Polaronic and dressed molecular states in orbital Feshbach resonances

    Science.gov (United States)

    Xu, Junjun; Qi, Ran

    2018-04-01

    We consider the impurity problem in an orbital Feshbach resonance (OFR), with a single excited clock state | e ↑⟩ atom immersed in a Fermi sea of electronic ground state | g ↓⟩. We calculate the polaron effective mass and quasi-particle residue, as well as the polaron to molecule transition. By including one particle-hole excitation in the molecular state, we find significant correction to the transition point. This transition point moves toward the BCS side for increasing particle densities, which suggests that the corresponding many-body physics is similar to a narrow resonance.

  13. 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

  14. 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...

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

    Science.gov (United States)

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

    2005-01-01

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

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

    Science.gov (United States)

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

    2005-01-01

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

  17. Exciton binding energy in GaAsBiN spherical quantum dot heterostructures

    Science.gov (United States)

    Das, Subhasis; Dhar, S.

    2017-03-01

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

  18. Localized polarons and doorway vibrons in finite quantum structures

    Czech Academy of Sciences Publication Activity Database

    Fehske, H.; Wellein, G.; Loos, Jan; Bishop, A. R.

    2008-01-01

    Roč. 77, č. 8 (2008), 085117/1-085117/6 ISSN 1098-0121 Institutional research plan: CEZ:AV0Z10100521 Keywords : quantum dots * electron - phonon interaction * polarons Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.322, year: 2008

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

    Science.gov (United States)

    Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

    2018-03-14

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

  20. 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 ...

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

    Indian Academy of Sciences (India)

    Abstract. The effect of external magnetic field on the excited state energies in a spher- ical quantum dot was studied. The impurity energy and binding energy were calculated using the variational method within the effective mass approximation and finite barrier potential. The results showed that by increasing the magnetic ...

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

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  3. 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

  4. Anisotropic small-polaron hopping in W:BiVO4 single crystals

    International Nuclear Information System (INIS)

    Rettie, Alexander J. E.; Chemelewski, William D.; Zhou, Jianshi; Lindemuth, Jeffrey; McCloy, John S.; Marshall, Luke G.; Emin, David; Mullins, C. Buddie

    2015-01-01

    DC electrical conductivity, Seebeck and Hall coefficients are measured between 300 and 450 K on single crystals of monoclinic bismuth vanadate that are doped n-type with 0.3% tungsten donors (W:BiVO 4 ). Strongly activated small-polaron hopping is implied by the activation energies of the Arrhenius conductivities (about 300 meV) greatly exceeding the energies characterizing the falls of the Seebeck coefficients' magnitudes with increasing temperature (about 50 meV). Small-polaron hopping is further evidenced by the measured Hall mobility in the ab-plane (10 −1  cm 2  V −1  s −1 at 300 K) being larger and much less strongly activated than the deduced drift mobility (about 5 × 10 −5  cm 2  V −1  s −1 at 300 K). The conductivity and n-type Seebeck coefficient is found to be anisotropic with the conductivity larger and the Seebeck coefficient's magnitude smaller and less temperature dependent for motion within the ab-plane than that in the c-direction. These anisotropies are addressed by considering highly anisotropic next-nearest-neighbor (≈5 Å) transfers in addition to the somewhat shorter (≈4 Å), nearly isotropic nearest-neighbor transfers

  5. 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/.

  6. Ion Binding Energies Determining Functional Transport of ClC Proteins

    Science.gov (United States)

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

    2014-06-01

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

  7. Implications of the formation of small polarons in Li2O2 for Li-air batteries

    Science.gov (United States)

    Kang, Joongoo; Jung, Yoon Seok; Wei, Su-Huai; Dillon, Anne C.

    2012-01-01

    Lithium-air batteries (LABs) are an intriguing next-generation technology due to their high theoretical energy density of ˜11 kWh/kg. However, LABs are hindered by both poor rate capability and significant polarization in cell voltage, primarily due to the formation of Li2O2 in the air cathode. Here, by employing hybrid density functional theory, we show that the formation of small polarons in Li2O2 limits electron transport. Consequently, the low electron mobility μ = 10-10-10-9 cm2/V s contributes to both the poor rate capability and the polarization that limit the LAB power and energy densities. The self-trapping of electrons in the small polarons arises from the molecular nature of the conduction band states of Li2O2 and the strong spin polarization of the O 2p state. Our understanding of the polaronic electron transport in Li2O2 suggests that designing alternative carrier conduction paths for the cathode reaction could significantly improve the performance of LABs at high current densities.

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

    Science.gov (United States)

    Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

    2014-02-01

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

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

    Science.gov (United States)

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

    2017-09-14

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

  10. Singlet and triplet polaron relaxation in doubly charged self-assembled quantum dots

    International Nuclear Information System (INIS)

    Grange, T; Zibik, E A; Ferreira, R; Bastard, G; Carpenter, B A; Phillips, P J; Stehr, D; Winnerl, S; Helm, M; Steer, M J; Hopkinson, M; Cockburn, J W; Skolnick, M S; Wilson, L R

    2007-01-01

    Polaron relaxation in self-assembled InAs/GaAs quantum dot samples containing 2 electrons per dot is studied using far-infrared, time-resolved pump-probe measurements for transitions between the s-like ground and p-like first excited conduction band states. Spin-flip transitions between singlet and triplet states are observed experimentally in the decay of the absorption bleaching, which shows a clear biexponential dependence. The initial fast decay (∼30 ps) is associated with the singlet polaron decay, while the decay component with the longer time constant (∼5 ns) corresponds to the excited state triplet lifetime. The results are explained by considering the intrinsic Dresselhaus spin-orbit interaction, which induces spin-flip transitions by acoustic phonon emission or phonon anharmonicity. We have calculated the spin-flip decay times, and good agreement is obtained between the experiment and the simulation of the pump-probe signal. Our results demonstrate the importance of spin-mixing effects for intraband energy relaxation in InAs/GaAs quantum dots

  11. 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.

  12. 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.

  13. 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.

  14. Madelung and Hubbard interactions in polaron band model of doped organic semiconductors

    Science.gov (United States)

    Png, Rui-Qi; Ang, Mervin C.Y.; Teo, Meng-How; Choo, Kim-Kian; Tang, Cindy Guanyu; Belaineh, Dagmawi; Chua, Lay-Lay; Ho, Peter K.H.

    2016-01-01

    The standard polaron band model of doped organic semiconductors predicts that density-of-states shift into the π–π* gap to give a partially filled polaron band that pins the Fermi level. This picture neglects both Madelung and Hubbard interactions. Here we show using ultrahigh workfunction hole-doped model triarylamine–fluorene copolymers that Hubbard interaction strongly splits the singly-occupied molecular orbital from its empty counterpart, while Madelung (Coulomb) interactions with counter-anions and other carriers markedly shift energies of the frontier orbitals. These interactions lower the singly-occupied molecular orbital band below the valence band edge and give rise to an empty low-lying counterpart band. The Fermi level, and hence workfunction, is determined by conjunction of the bottom edge of this empty band and the top edge of the valence band. Calculations are consistent with the observed Fermi-level downshift with counter-anion size and the observed dependence of workfunction on doping level in the strongly doped regime. PMID:27582355

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

    International Nuclear Information System (INIS)

    Asghari, M.

    2006-01-01

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

  17. Bound magnetic polaron in a semimagnetic double quantum well

    Science.gov (United States)

    Kalpana, P.; Jayakumar, K.

    2017-09-01

    The effect of different combinations of the concentration of Mn2+ ion in the Quantum well Cd1-xinMnxin Te and the barrier Cd1-xoutMnxout Te on the Bound Magnetic Polaron (BMP) in a Diluted Magnetic Semiconductors (DMS) Double Quantum Well (DQW) has been investigated. The Schrodinger equation is solved variationally in the effective mass approximation through which the Spin Polaronic Shift (SPS) due to the formation of BMP has been estimated for various locations of the donor impurity in the DQW. The results show that the effect of the increase of Mn2+ ion composition with different combinations on SPS is predominant for On Centre Well (OCW) impurity when compared to all other impurity locations when there is no application of magnetic field (γ = 0), γ being a dimensionless parameter for the magnetic field, and the same is predominant for On Centre Barrier (OCB) impurity with the application of external magnetic field (γ = 0.15).

  18. 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

  19. 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.

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

    Science.gov (United States)

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

    2018-03-26

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

  1. 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

  2. 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

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

    Science.gov (United States)

    Irwin, Benedict W J; Huggins, David J

    2018-05-08

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

  4. Binding energies of hypernuclei and Λ-nuclear interactions

    International Nuclear Information System (INIS)

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

    1984-01-01

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

  5. 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

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    C. Ruben Vosmeer

    2014-01-01

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

  8. 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.

  9. 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.

  10. 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

  11. 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.

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

    DEFF Research Database (Denmark)

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

    2002-01-01

    The biexciton binding energy E-XX is investigated in ZnSe/ZnMgSe quantum wells and quantum wires as a function of the lateral confinement by transient four-wave mixing. In the quantum wells one observes for decreasing well width a significant increase in the relative binding energy, saturating...... for well widths less than 8 nm. In the quantum wires an increase of 30% is found in the smallest quantum wire structures compared to the corresponding quantum well value. A simple analytical model taking into account the quantum confinement in these low-dimensional systems is used to explain...

  13. 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

  14. 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.

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

    Science.gov (United States)

    Felfli, Zineb; Msezane, Alfred

    2017-04-01

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

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

    Science.gov (United States)

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

    2003-08-01

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

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

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

    International Nuclear Information System (INIS)

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

    1996-01-01

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

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

    International Nuclear Information System (INIS)

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

    1991-01-01

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

  20. 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

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

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

    International Nuclear Information System (INIS)

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

    1977-01-01

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

  3. 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 ...

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

    International Nuclear Information System (INIS)

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

    1995-01-01

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

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

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  6. 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

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

    International Nuclear Information System (INIS)

    Li, Xiao-xue; Chen, Gang

    2017-01-01

    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.

  8. 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.

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

    Science.gov (United States)

    Steinbrecher, Thomas; Labahn, Andreas

    2010-01-01

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

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

    Science.gov (United States)

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

    2013-08-15

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

  11. 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

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

    Science.gov (United States)

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

    2018-06-01

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

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

    Science.gov (United States)

    Olsson, Martin A.; Söderhjelm, Pär

    2016-01-01

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

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

    DEFF Research Database (Denmark)

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

    1997-01-01

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

  16. 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.

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

    Science.gov (United States)

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

    2018-05-01

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

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

    Science.gov (United States)

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

    2018-05-01

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

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

    Science.gov (United States)

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

    2018-05-01

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

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

    Science.gov (United States)

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

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

  2. 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.

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-01-01

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

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

    Science.gov (United States)

    Cournia, Zoe; Allen, Bryce; Sherman, Woody

    2017-12-26

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

  6. 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.

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

    International Nuclear Information System (INIS)

    Koepf, W.; Barreiro, L.A.

    1996-01-01

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

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

    International Nuclear Information System (INIS)

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

    1993-01-01

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

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

    International Nuclear Information System (INIS)

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

    1977-01-01

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

  10. 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.

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

    International Nuclear Information System (INIS)

    Lai Zuyou; Gu Shiwei

    1991-09-01

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

  12. 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.

  13. 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

  14. 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.

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

    International Nuclear Information System (INIS)

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

    1981-06-01

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

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

    International Nuclear Information System (INIS)

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

    1995-01-01

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

  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. Faraday rotation by the undisturbed bulk and by photoinduced giant polarons in EuTe

    Science.gov (United States)

    Henriques, A. B.; Usachev, P. A.

    2017-11-01

    A quantum mechanical model is developed for the Faraday effect in europium telluride, for photons of energy within the transparency gap. The model is based on the well known band edge electronic energy states in EuTe. A concise expression for the Verdet constant is obtained, determined by few parameters already available in the literature. The Verdet constant adopted here, defined by the ratio between the Faraday rotation angle and the magnetization, is in effect temperature independent. Its dependence on the photon energy and applied magnetic field is in excellent agreement with published results. Below 3 T the Verdet constant is also nearly independent on field, but above 3 T at low temperatures it increases due to the band gap redshift. The model is used to calculate the photoinduced Faraday rotation associated with photoinduced giant magnetic polarons in EuTe. The theoretical photoinduced Faraday rotation excitation describes quite well the main features seen experimentally. Due to the common band-edge electronic energy structure, the model reported here could be extended to all other europium chalcogenides.

  19. Effects of polarons on static polarizabilities and second order hyperpolarizabilities of conjugated polymers

    International Nuclear Information System (INIS)

    Wang Ya-Dong; Meng Yan; Di Bing; Wang Shu-Ling; An Zhong

    2010-01-01

    According to the one-dimensional tight-binding Su—Schrieffer—Heeger model, we have investigated the effects of charged polarons on the static polarizability, α xx , and the second order hyperpolarizabilities, γ xxxx , of conjugated polymers. Our results are consistent qualitatively with previous ab initio and semi-empirical calculations. The origin of the universal growth is discussed using a local-view formalism that is based on the local atomic charge derivatives. Furthermore, combining the Su-Schrieffer-Heeger model and the extended Hubbard model, we have investigated systematically the effects of electron-electron interactions on α xx and γ xxxx of charged polymer chains. For a fixed value of the nearest-neighbour interaction V, the values of α xx and γ xxxx increase as the on-site Coulomb interaction U increases for U c and decrease with U for U > U c , where U c is a critical value of U at which the static polarizability or the second order hyperpolarizability reaches a maximal value of α max or γ max . It is found that the effect of the e-e interaction on the value of α xx is dependent on the ratio between U and V for either a short or a long charged polymer. Whereas, that effect on the value of γ xxxx is sensitive both to the ratio of U to V and to the size of the molecule. (rapid communication)

  20. 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.

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

    International Nuclear Information System (INIS)

    Arredondo, Y.; Navarro, O.; Vallejo, E.

    2014-01-01

    We study numerically the formation of spin-polarons in low-dimensional systems. We consider a ferromagnetic Kondo lattice model with Hund coupling J 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 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

  2. Proton impurity in the neutron matter: a nuclear polaron problem

    Energy Technology Data Exchange (ETDEWEB)

    Kutschera, M [Institute of Nuclear Physics, Cracow (Poland); Wojcik, W [Politechnika Krakowska, Cracow (Poland)

    1992-10-01

    We study interactions of a proton impurity with density oscillations of the neutron matter in a Debye approximation. The proton-phonon coupling is of the deformation-potential type at long wavelengths. It is weak at low density and increases with the neutron matter density. We calculate the proton`s effective mass perturbatively for a weak coupling, and use a canonical transformation technique for stronger couplings. The proton`s effective mass grows significantly with density, and at higher densities the proton impurity can be localized. This behaviour is similar to that of the polaron in solids. We obtain properties of the localized proton in the strong coupling regime from variational calculations, treating the neutron in the Thomas-Fermi approximation. (author). 14 refs, 8 figs.

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

    KAUST Repository

    Cortecchia, Daniele; Yin, Jun; Bruno, Annalisa; Lo, Shu Zee Alencious; Gurzadyan, Gagik G.; Mhaisalkar, Subodh; Bredas, Jean-Luc; Soci, Cesare

    2017-01-01

    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

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

    KAUST Repository

    Yin, Jun; Li, Hong; Cortecchia, Daniele; Soci, Cesare; Bredas, Jean-Luc

    2017-01-01

    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

  5. 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.

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

    International Nuclear Information System (INIS)

    Marcos, S.; Lombard, R.J.

    1997-01-01

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

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

    Science.gov (United States)

    Zwanziger, Ch.; Reinhold, J.

    1980-02-01

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

  8. 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.

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

    KAUST Repository

    Zhang, Qianfan; Cui, Yi; Wang, Enge

    2011-01-01

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

  10. 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.

  11. Polaron-electron assisted giant dielectric dispersion in SrZrO{sub 3} high-k dielectric

    Energy Technology Data Exchange (ETDEWEB)

    Borkar, Hitesh; Barvat, Arun; Pal, Prabir; Kumar, Ashok, E-mail: ashok553@nplindia.org [CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012 (India); Academy of Scientific and Innovative Research (AcSIR), CSIR-National Physical Laboratory (CSIR-NPL) Campus, Dr. K S Krishnan Marg, New Delhi 110012 (India); Shukla, A. K. [CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012 (India); Pulikkotil, J. J. [CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012 (India); Academy of Scientific and Innovative Research (AcSIR), CSIR-National Physical Laboratory (CSIR-NPL) Campus, Dr. K S Krishnan Marg, New Delhi 110012 (India); Computation and Networking Facility, CSIR-National Physical Laboratory, New Delhi 110012 (India)

    2016-06-07

    The SrZrO{sub 3} is a well known high-k dielectric constant (∼22) and high optical bandgap (∼5.8 eV) material and one of the potential candidates for future generation nanoelectronic logic elements (8 nm node technology) beyond silicon. Its dielectric behavior is fairly robust and frequency independent till 470 K; however, it suffers a strong small-polaron based electronic phase transition (T{sub e}) linking 650 to 750 K. The impedance spectroscopy measurements revealed the presence of conducting grains and grain boundaries at elevated temperature which provide energetic mobile charge carriers with activation energy in the range of 0.7 to 1.2 eV supporting the oxygen ions and proton conduction. X-ray photoemission spectroscopy measurements suggest the presence of weak non-stoichiometric O{sup 2−} anions and hydroxyl species bound to different sites at the surface and bulk. These thermally activated charge carriers at elevated temperature significantly contribute to the polaronic based dielectric anomaly and conductivity. Our dielectric anomaly supports pseudo phase transition due to high degree of change in ZrO{sub 6} octahedral angle in the temperature range of 650–750 K, where electron density and phonon vibration affect the dielectric and conductivity properties.

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

    Science.gov (United States)

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

    2008-03-01

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

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

    Science.gov (United States)

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

    2009-03-01

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

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

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

    International Nuclear Information System (INIS)

    Takahata, Yuji; Marques, Alberto Dos Santos

    2010-01-01

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

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

    DEFF Research Database (Denmark)

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

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

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

    International Nuclear Information System (INIS)

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

    1988-02-01

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

  18. 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.

  19. Observation of semiconductor to metallic transition and polaron hopping in double perovskite Pr{sub 2}CoTiO{sub 6} ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Mahato, Dev K., E-mail: drdevkumar@yahoo.com [Department of Physics, National Institute of Technology Patna, Patna 800005 (India); Sinha, T.P. [Department of Physics, Bose Institute, 93/1, APC Road, Kolkata 700009 (India)

    2017-05-01

    This paper describes semiconductor to metal transition and polaron conduction in double perovskite Pr{sub 2}CoTiO{sub 6} (PCTO) ceramics. The XRD pattern recorded at room temperature confirmed the pure phase, single crystalline structure. The semicircle arc in the impedance plot at each temperature can be attributed to the grain boundary contribution, indicating one dominating response in the measurement frequency range. The semiconductor to metallic transition was also confirmed by the variation of grain boundary resistance (R{sub gb}) with temperature. The activation energy estimated from the imaginary part of electrical modulus and impedance are found to be the characteristic of polaron conduction in PCTO. Ac conductivity followed power law dependence σ{sub ac} = Bω{sup n}. The observed variation of the exponent ‘n’ with temperature suggests the typical of charge transport assisted by a hopping process. The observed minimum in the temperature dependence of frequency exponent ‘n’ strongly suggests that the large polaron tunneling is the dominant transport process.

  20. 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...

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

    Science.gov (United States)

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

    2006-08-31

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

  2. 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

  3. 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

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

    Science.gov (United States)

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

    2015-09-01

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

  5. 4He binding energy calculation including full tensor-force effects

    Science.gov (United States)

    Fonseca, A. C.

    1989-09-01

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

  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. 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...

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

    Science.gov (United States)

    Liu, Hui; Hou, Tingjun

    2016-07-15

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

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

    International Nuclear Information System (INIS)

    Heide, P.A.W. van der

    2006-01-01

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

  10. Small polaron conduction in lead modified lanthanum ferrite ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Bhargav, K.K.; Ram, S.; Majumder, S.B., E-mail: subhasish@matsc.iitkgp.ernet.in

    2015-07-25

    Highlights: • La{sub 0.8}Pb{sub 0.2}FeO{sub 3} (ε{sub r} ∼ 30,000) shows higher dielectric constant than LaFeO{sub 3} (∼14,000). • Lower A-site dopant content, the dielectric maxima shift to higher temperature. • The frequency dependence of ε{sub r} and tan δ vs. temperature exhibit CDC like behavior. • R{sub g} and R{sub gb} of Pb modified LaFeO{sub 3} follow small polaron hopping conduction model. - Abstract: In the present work we have illustrated the physics of the electrical characteristics of nanocrystalline La{sub 1−x}Pb{sub x}FeO{sub 3,} (0 ⩽ x ⩽ 0.2) powder prepared using auto-combustion synthesis. The effect of lead doping on the dielectric, impedance and ac conductivity characteristics of lanthanum ferrite has systematically been investigated. The synthesized powders were phase pure and crystallized into centro-symmetric Pnma space group. As compared to pure LaFeO{sub 3} ceramics (dielectric constant ∼ 14,000), the dielectric constant is grossly increased (∼30,000) in Pb doped LaFeO{sub 3}. The temperature dependence of dielectric constant of 10.0 at.% Pb doped LaFeO{sub 3} exhibits dielectric maxima similar to that observed in ferroelectric ceramics with non-centrosymmetric point group. For La{sub 0.8}Pb{sub 0.2}FeO{sub 3} ceramics, the frequency dependence of the dielectric constant and loss tangent at various temperatures (300–450 K) exhibit typical colossal dielectric constant (CDC) like behavior. From the impedance spectroscopy we have estimated the grain and grain boundary resistance and capacitance of Pb doped LaFeO{sub 3} that follow a small polaron hopping conduction model. Long range movement of the charge carriers govern the CDC behavior.

  11. 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

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

    Science.gov (United States)

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

    2016-05-04

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

  13. Charge Transport in 4 nm Molecular Wires with Interrupted Conjugation: Combined Experimental and Computational Evidence for Thermally Assisted Polaron Tunneling.

    Science.gov (United States)

    Taherinia, Davood; Smith, Christopher E; Ghosh, Soumen; Odoh, Samuel O; Balhorn, Luke; Gagliardi, Laura; Cramer, Christopher J; Frisbie, C Daniel

    2016-04-26

    We report the synthesis, transport measurements, and electronic structure of conjugation-broken oligophenyleneimine (CB-OPI 6) molecular wires with lengths of ∼4 nm. The wires were grown from Au surfaces using stepwise aryl imine condensation reactions between 1,4-diaminobenzene and terephthalaldehyde (1,4-benzenedicarbaldehyde). Saturated spacers (conjugation breakers) were introduced into the molecular backbone by replacing the aromatic diamine with trans-1,4-diaminocyclohexane at specific steps during the growth processes. FT-IR and ellipsometry were used to follow the imination reactions on Au surfaces. Surface coverages (∼4 molecules/nm(2)) and electronic structures of the wires were determined by cyclic voltammetry and UV-vis spectroscopy, respectively. The current-voltage (I-V) characteristics of the wires were acquired using conducting probe atomic force microscopy (CP-AFM) in which an Au-coated AFM probe was brought into contact with the wires to form metal-molecule-metal junctions with contact areas of ∼50 nm(2). The low bias resistance increased with the number of saturated spacers, but was not sensitive to the position of the spacer within the wire. Temperature dependent measurements of resistance were consistent with a localized charge (polaron) hopping mechanism in all of the wires. Activation energies were in the range of 0.18-0.26 eV (4.2-6.0 kcal/mol) with the highest belonging to the fully conjugated OPI 6 wire and the lowest to the CB3,5-OPI 6 wire (the wire with two saturated spacers). For the two other wires with a single conjugation breaker, CB3-OPI 6 and CB5-OPI 6, activation energies of 0.20 eV (4.6 kcal/mol) and 0.21 eV (4.8 kcal/mol) were found, respectively. Computational studies using density functional theory confirmed the polaronic nature of charge carriers but predicted that the semiclassical activation energy of hopping should be higher for CB-OPI molecular wires than for the OPI 6 wire. To reconcile the experimental and

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

    Science.gov (United States)

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

    2008-10-21

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

  15. The pairing theory of polarons in real- and impulse spaces

    International Nuclear Information System (INIS)

    Dzhumanov, S.; Abboudy, S.; Baratov, A.A.

    1995-07-01

    A consistent pairing theory of carriers in real- and impulse spaces is developed. The pairing of different free (F), delocalized (D) and self-trapped (S) carriers in real-space, leading to the formation of various bipolaronic states are considered within the continuum model and adiabatic approximation taking into account the combined effect of the short- and long-range components of electron-lattice interaction with and without electron correlation. The formation possibility of D- and S-bipolarons as a function of ε ∞ /ε 0 are shown. The pairing scenarios of carriers in k-space leading to the formation of different bipolarons (including also Cooper pairs dynamic bipolarons) are considered within the generalized BCS-like model taking into account the combined phonon and polaron-bag mediated processes. It is shown that the pure BCS pairing picture is the particular case of the general BCS-like one. The possible relevance of the obtained results to high-T c superconductors is discussed in details in the framework of a novel two-stage Fermi-Bose-liquid scenarios of superconductivity which is caused by single particle and pair condensation of an attracting bipolarons. (author). 51 refs, 6 figs

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

    International Nuclear Information System (INIS)

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

    1981-01-01

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

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

    Science.gov (United States)

    Borodin, Oleg

    2009-09-10

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

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

    Science.gov (United States)

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

    2017-09-01

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

  19. 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

  20. 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.

  1. 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.

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

    International Nuclear Information System (INIS)

    Zhao, Junhua; Lu, Lixin; Rabczuk, Timon

    2014-01-01

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

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

    Science.gov (United States)

    Kroonblawd, Matthew; Goldman, Nir

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

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

    Science.gov (United States)

    Kroonblawd, Matthew; Goldman, Nir

    2017-06-01

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

  6. 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.

  7. 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.

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

    Science.gov (United States)

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

    2007-10-01

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

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

    International Nuclear Information System (INIS)

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

    1987-08-01

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

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

    International Nuclear Information System (INIS)

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

    1988-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1977-11-15

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

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

    CERN Document Server

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

    1995-01-01

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

  13. Excitonic polarons in quasi-one-dimensional LH1 and LH2 bacteriochlorophyll a antenna aggregates from photosynthetic bacteria: A wavelength-dependent selective spectroscopy study

    International Nuclear Information System (INIS)

    Freiberg, Arvi; Raetsep, Margus; Timpmann, Kou; Trinkunas, Gediminas

    2009-01-01

    Spectral characteristics of the optically excited states in the ring-shaped quasi-one-dimensional aggregates comprising 18 and 32 tightly coupled bacteriochlorophyll a molecules have been investigated using selective spectroscopy methods and theoretical modelling of the data. Distinguished by the lowest electronic transition energies in the LH2 and LH1 antenna complexes these aggregates govern the functionally important ultrafast funneling of solar excitation energy in the photosynthetic membranes of purple bacteria. It was found by using a sophisticated differential fluorescence line narrowing method that exciton-phonon coupling in terms of the dimensionless Huang-Rhys factor is strong in these systems, justifying an excitonic polaron theoretical approach for the data analysis. Although we reached this qualitative conclusion already previously, in this work essential dependence of the exciton-phonon coupling strength and reorganization energy on excitation wavelength as well as on excitation light fluence has been established. We then show that these results corroborate with the properties of excitonic polarons in diagonally disordered ensembles of the aggregates. Furthermore, the weighted density of states of the phonon modes, which is an important characteristic of dynamical systems interacting with their surroundings, was derived. Its shape, being similar for all studied circular aggregates, deviates significantly from a reference profile describing local response of a protein to the Q y electronic transition in a single bacteriochlorophyll a molecule. Similarities of the data for regular and B800 deficient mutant LH2 complexes indicate that the B800 pigments have no direct influence on the electronic states of the B850 aggregate system. Consistent set of model parameters was determined, unambiguously implying that excitonic polarons, rather than bare excitons are proper lowest-energy optical excitations in the LH1 and LH2 antenna complexes

  14. Excitonic polarons in quasi-one-dimensional LH1 and LH2 bacteriochlorophyll a antenna aggregates from photosynthetic bacteria: A wavelength-dependent selective spectroscopy study

    Energy Technology Data Exchange (ETDEWEB)

    Freiberg, Arvi [Institute of Physics, University of Tartu, Riia 142, 51014 Tartu (Estonia); Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu (Estonia)], E-mail: arvi.freiberg@ut.ee; Raetsep, Margus; Timpmann, Kou [Institute of Physics, University of Tartu, Riia 142, 51014 Tartu (Estonia); Trinkunas, Gediminas [Insitute of Physics, Savanoriu pr. 231, LT-02300 Vilnius (Lithuania)

    2009-02-23

    Spectral characteristics of the optically excited states in the ring-shaped quasi-one-dimensional aggregates comprising 18 and 32 tightly coupled bacteriochlorophyll a molecules have been investigated using selective spectroscopy methods and theoretical modelling of the data. Distinguished by the lowest electronic transition energies in the LH2 and LH1 antenna complexes these aggregates govern the functionally important ultrafast funneling of solar excitation energy in the photosynthetic membranes of purple bacteria. It was found by using a sophisticated differential fluorescence line narrowing method that exciton-phonon coupling in terms of the dimensionless Huang-Rhys factor is strong in these systems, justifying an excitonic polaron theoretical approach for the data analysis. Although we reached this qualitative conclusion already previously, in this work essential dependence of the exciton-phonon coupling strength and reorganization energy on excitation wavelength as well as on excitation light fluence has been established. We then show that these results corroborate with the properties of excitonic polarons in diagonally disordered ensembles of the aggregates. Furthermore, the weighted density of states of the phonon modes, which is an important characteristic of dynamical systems interacting with their surroundings, was derived. Its shape, being similar for all studied circular aggregates, deviates significantly from a reference profile describing local response of a protein to the Q{sub y} electronic transition in a single bacteriochlorophyll a molecule. Similarities of the data for regular and B800 deficient mutant LH2 complexes indicate that the B800 pigments have no direct influence on the electronic states of the B850 aggregate system. Consistent set of model parameters was determined, unambiguously implying that excitonic polarons, rather than bare excitons are proper lowest-energy optical excitations in the LH1 and LH2 antenna complexes.

  15. 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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-08-01

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

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  18. 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

  19. Possibility of observation of polaron normal modes at the far-infrared spectrum of acetanilide and related organics

    Science.gov (United States)

    Kalosakas, G.; Aubry, S.; Tsironis, G. P.

    1998-10-01

    We use a stationary and normal mode analysis of the semiclassical Holstein model in order to connect the low-frequency linear polaron modes to low-lying far-infrared lines of the acetanilide spectrum and through parameter fitting we comment on the validity of the polaron results in this system.

  20. Giant Optical Polarization Rotation Induced by Spin-Orbit Coupling in Polarons

    Science.gov (United States)

    Casals, Blai; Cichelero, Rafael; García Fernández, Pablo; Junquera, Javier; Pesquera, David; Campoy-Quiles, Mariano; Infante, Ingrid C.; Sánchez, Florencio; Fontcuberta, Josep; Herranz, Gervasi

    2016-07-01

    We have uncovered a giant gyrotropic magneto-optical response for doped ferromagnetic manganite La2 /3Ca1 /3MnO3 around the near room-temperature paramagnetic-to-ferromagnetic transition. At odds with current wisdom, where this response is usually assumed to be fundamentally fixed by the electronic band structure, we point to the presence of small polarons as the driving force for this unexpected phenomenon. We explain the observed properties by the intricate interplay of mobility, Jahn-Teller effect, and spin-orbit coupling of small polarons. As magnetic polarons are ubiquitously inherent to many strongly correlated systems, our results provide an original, general pathway towards the generation of magnetic-responsive gigantic gyrotropic responses that may open novel avenues for magnetoelectric coupling beyond the conventional modulation of magnetization.

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-07-15

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

  3. 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

  4. 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

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

    Science.gov (United States)

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

    2011-01-01

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

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

    Science.gov (United States)

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

    2018-02-01

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

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

    International Nuclear Information System (INIS)

    Sivakami, A.; Mahendran, M.

    2010-01-01

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

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

    Science.gov (United States)

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

    2018-05-01

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

  9. Polaron effects on nonlinear optical rectification in asymmetrical Gaussian potential quantum wells with applied electric fields

    International Nuclear Information System (INIS)

    Wu, Jinghe; Guo, Kangxian; Liu, Guanghui

    2014-01-01

    Polaron effects on nonlinear optical rectification in asymmetrical Gaussian potential quantum wells are studied by the effective mass approximation and the perturbation theory. The numerical results show that nonlinear optical rectification coefficients are strongly dependent on the barrier hight V 0 of the Gaussian potential quantum wells, the range L of the confinement potential and the electric field F. Besides, the numerical results show that no matter how V 0 , L and F change, taking into consideration polaron effects, the optical rectification coefficients χ 0 (2) get greatly enhanced.

  10. 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......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 Ag...

  11. 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.

  12. 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.

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

    Science.gov (United States)

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

    2017-02-01

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

  14. 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.

  15. Electromagnetic-field dependence of the internal excited state of the polaron and the qubit in quantum dot with thickness

    Science.gov (United States)

    Bai, Xu-Fang; Xin, Wei; Yin, Hong-Wu; Eerdunchaolu

    2017-06-01

    The electromagnetic-field dependence of the ground and the first excited-state (GFES) energy eigenvalues and eigenfunctions of the strong-coupling polaron in a quantum dot (QD) was studied for various QD thicknesses by using the variational method of the Pekar type (VMPT). On this basis, we construct a qubit in the quantum dot (QQD) by taking a two-level structure of the polaron as the carrier. The results of numerical calculations indicate that the oscillation period of the qubit, {itT}{in0}, increases with increasing the thickness of the quantum dot (TQD) {itL}, but decreases with increasing the cyclotron frequency of the magnetic field (CFMF) ω{in{itc}}, electric-field strength {itF}, and electron-phonon coupling strength (EPCS) α. The probability density of the qubit |Ψ({itρ}, {itz}, {itt})|{su2} presents a normal distribution of the electronic transverse coordinate ρ, significantly influenced by the TQD and effective radius of the quantum dot (ERQD) {itR}{in0}, and shows a periodic oscillation with variations in the electronic longitudinal coordinate {itz}, polar angle φ and time {itt}. The decoherence time τ and the quality factor {itQ} of the free rotation increase with increasing the CFMF ω{in{itc}}, dispersion coefficient η, and EPCS α, but decrease with increasing the electric-field strength {itF}, TQD {itL}, and ERQD {itR}{in0}. The TQD is an important parameter of the qubit. Theoretically, the target, which is to regulate the oscillation period, decoherence time and quality factor of the free rotation of the qubit, can be achieved by designing different TQDs and regulating the strength of the electromagnetic field.

  16. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-11-30

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

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

    Science.gov (United States)

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

    1981-08-01

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

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

    NARCIS (Netherlands)

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

    2012-01-01

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

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

    International Nuclear Information System (INIS)

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

    1985-08-01

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

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

    Science.gov (United States)

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

    2011-08-01

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

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

    International Nuclear Information System (INIS)

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

    1983-01-01

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

  3. 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

  4. 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.)

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

    KAUST Repository

    Steyrleuthner, Robert; Zhang, Yuexing; Zhang, Lei; Kraffert, Felix; Cherniawski, Benjamin P.; Bittl, Robert; Briseno, Alejandro L.; Bredas, Jean-Luc; Behrends, Jan

    2016-01-01

    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

  6. 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- ...

  7. A new polaronic order-disorder phase transition in magnetite as observed through μSR

    International Nuclear Information System (INIS)

    Boekema, C.; Lichti, R.L.; Denison, A.B.; Brabers, V.A.M.; Cooke, D.W.; Heffner, R.H.; Hutson, R.L.; Schillaci, M.E.

    1986-01-01

    Recent μSr measurements on the Mott-Wigner glass magnetite, as a function of temperature and external magnetic field have shown the existence of two inequivalent magnetic sites below T A = 247 K. These data are being interpreted in terms of the onset or destruction of local order manifested as local atomic correlations (molecular polarons). (orig.)

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2010-10-01

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

  10. 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

  11. 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

  12. 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...

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

    Science.gov (United States)

    Huang, Y; Ackers, G K

    1996-01-23

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

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

    International Nuclear Information System (INIS)

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

    1981-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Guangxin Wang

    2013-01-01

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

  16. 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.

  17. 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)

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

    OpenAIRE

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

    2009-01-01

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

  19. 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

  20. 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

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

    International Nuclear Information System (INIS)

    Osman, A.; Ramadan, S.

    1986-01-01

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

  2. 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)

  3. 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)

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

    Science.gov (United States)

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

    2018-06-01

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

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

    International Nuclear Information System (INIS)

    Hakimifard, A.

    2010-01-01

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

  6. 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.

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2018-03-01

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

  9. Effects of system-bath coupling on a photosynthetic heat engine: A polaron master-equation approach

    Science.gov (United States)

    Qin, M.; Shen, H. Z.; Zhao, X. L.; Yi, X. X.

    2017-07-01

    Stimulated by suggestions of quantum effects in energy transport in photosynthesis, the fundamental principles responsible for the near-unit efficiency of the conversion of solar to chemical energy became active again in recent years. Under natural conditions, the formation of stable charge-separation states in bacteria and plant reaction centers is strongly affected by the coupling of electronic degrees of freedom to a wide range of vibrational motions. These inspire and motivate us to explore the effects of the environment on the operation of such complexes. In this paper, we apply the polaron master equation, which offers the possibilities to interpolate between weak and strong system-bath coupling, to study how system-bath couplings affect the exciton-transfer processes in the Photosystem II reaction center described by a quantum heat engine (QHE) model over a wide parameter range. The effects of bath correlation and temperature, together with the combined effects of these factors are also discussed in detail. We interpret these results in terms of noise-assisted transport effect and dynamical localization, which correspond to two mechanisms underpinning the transfer process in photosynthetic complexes: One is resonance energy transfer and the other is the dynamical localization effect captured by the polaron master equation. The effects of system-bath coupling and bath correlation are incorporated in the effective system-bath coupling strength determining whether noise-assisted transport effect or dynamical localization dominates the dynamics and temperature modulates the balance of the two mechanisms. Furthermore, these two mechanisms can be attributed to one physical origin: bath-induced fluctuations. The two mechanisms are manifestations of the dual role played by bath-induced fluctuations depending on the range of parameters. The origin and role of coherence are also discussed. It is the constructive interplay between noise and coherent dynamics, rather

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

    Science.gov (United States)

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

    2018-04-01

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

  11. 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.

  12. Effect of thermodynamic fluctuations of magnetization on the bound magnetic polaron state in ferromagnetic semiconductors

    International Nuclear Information System (INIS)

    Bednarski, Henryk; Spałek, Józef

    2014-01-01

    We extend the theory of the bound magnetic polaron (BMP) in diluted paramagnetic semiconductors to the situation with a ferromagnetic phase transition. This is achieved by including the classical Gaussian fluctuations of magnetization from the quartic (non-Gaussian) term in the effective Ginzburg–Landau Hamiltonian for the spins. Within this approach, we find a ferromagnetically ordered state within the BMP in the temperature range well above the Curie temperature for the host magnetic semiconductor. Numerical results are compared directly with the recently available experimental data for the ferromagnetic semiconductor GdN. The agreement is excellent, given the simplicity of our model, and is because the polaron size (≃1.4 nm) encompasses a relatively large but finite number (N≈400) of quasiclassical spins S=7/2 coming from Gd 3+ ions. The presence of BMP invalidates the notion of critical temperature and thus makes the incorporation of classical Gaussian fluctuations sufficient to realistically describe the situation. (paper)

  13. 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.

  14. 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

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

    DEFF Research Database (Denmark)

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

    1999-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-03-15

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

  18. Generalized formula for electron emission taking account of the polaron effect

    Science.gov (United States)

    Barengolts, Yu A.; Beril, S. I.; Barengolts, S. A.

    2018-01-01

    A generalized formula is derived for the electron emission current as a function of temperature, field, and electron work function in a metal-dielectric system that takes account of the quantum nature of the image forces. In deriving the formula, the Fermi-Dirac distribution for electrons in a metal and the quantum potential of the image obtained in the context of electron polaron theory are used.

  19. 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

  20. Quantum fluctuations of D5d polarons on C60 molecules

    International Nuclear Information System (INIS)

    Wang Chui-Lin; Wang Wenzheng; Liu Yuliang; Su Zhaobin; Yu Lu.

    1994-06-01

    The dynamic Jahn-Teller splitting of the six equivalent D 5d polarons due to quantum fluctuations is studied in the framework of the Bogoliubov-de Gennes formalism. The tunneling induced level splittings are determined to be 2 T 1u + 2 T 2u and 1 A g + 1 H g for C 1- 60 and C -2 60 , respectively, which should give rise to observable effects in experiments. (author). 17 refs, 2 tabs

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

    Science.gov (United States)

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

    2017-08-01

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

  2. 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.

  3. 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

  4. Holstein polaron in a valley-degenerate two-dimensional semiconductor.

    Science.gov (United States)

    Kang, Mingu; Jung, Sung Won; Shin, Woo Jong; Sohn, Yeongsup; Ryu, Sae Hee; Kim, Timur K; Hoesch, Moritz; Kim, Keun Su

    2018-05-28

    Two-dimensional (2D) crystals have emerged as a class of materials with tunable carrier density 1 . Carrier doping to 2D semiconductors can be used to modulate many-body interactions 2 and to explore novel composite particles. The Holstein polaron is a small composite particle of an electron that carries a cloud of self-induced lattice deformation (or phonons) 3-5 , which has been proposed to play a key role in high-temperature superconductivity 6 and carrier mobility in devices 7 . Here we report the discovery of Holstein polarons in a surface-doped layered semiconductor, MoS 2 , in which a puzzling 2D superconducting dome with the critical temperature of 12 K was found recently 8-11 . Using a high-resolution band mapping of charge carriers, we found strong band renormalizations collectively identified as a hitherto unobserved spectral function of Holstein polarons 12-18 . The short-range nature of electron-phonon (e-ph) coupling in MoS 2 can be explained by its valley degeneracy, which enables strong intervalley coupling mediated by acoustic phonons. The coupling strength is found to increase gradually along the superconducting dome up to the intermediate regime, which suggests a bipolaronic pairing in the 2D superconductivity.

  5. DFT +U Modeling of Hole Polarons in Organic Lead Halide Perovskites

    Science.gov (United States)

    Welch, Eric; Erhart, Paul; Scolfaro, Luisa; Zakhidov, Alex

    Due to the ever present drive towards improved efficiencies in solar cell technology, new and improved materials are emerging rapidly. Organic halide perovskites are a promising prospect, yet a fundamental understanding of the organic perovskite structure and electronic properties is missing. Particularly, explanations of certain physical phenomena, specifically a low recombination rate and high mobility of charge carriers still remain controversial. We theoretically investigate possible formation of hole polarons adopting methodology used for oxide perovskites. The perovskite studied here is the ABX3structure, with A being an organic cation, B lead and C a halogen; the combinations studied allow for A1,xA2 , 1 - xBX1,xX2 , 3 - xwhere the alloy convention is used to show mixtures of the organic cations and/or the halogens. Two organic cations, methylammonium and formamidinium, and three halogens, iodine, chlorine and bromine are studied. Electronic structures and polaron behavior is studied through first principle density functional theory (DFT) calculations using the Vienna Ab Initio Simulation Package (VASP). Local density approximation (LDA) pseudopotentials are used and a +U Hubbard correction of 8 eV is added; this method was shown to work with oxide perovskites. It is shown that a localized state is realized with the Hubbard correction in systems with an electron removed, residing in the band gap of each different structure. Thus, hole polarons are expected to be seen in these perovskites.

  6. Influence of quasi-particle density over polaron mobility in armchair graphene nanoribbons.

    Science.gov (United States)

    Silva, Gesiel Gomes; da Cunha, Wiliam Ferreira; de Sousa Junior, Rafael Timóteo; Almeida Fonseca, Antonio Luciano; Ribeiro Júnior, Luiz Antônio; E Silva, Geraldo Magela

    2018-06-20

    An important aspect concerning the performance of armchair graphene nanoribbons (AGNRs) as materials for conceiving electronic devices is related to the mobility of charge carriers in these systems. When several polarons are considered in the system, a quasi-particle wave function can be affected by that of its neighbor provided the two are close enough. As the overlap may affect the transport of the carrier, the question concerning how the density of polarons affect its mobility arises. In this work, we investigate such dependence for semiconducting AGNRs in the scope of nonadiabatic molecular dynamics. Our results unambiguously show an impact of the density on both the stability and average velocity of the quasi-particles. We have found a phase transition between regimes where increasing density stops inhibiting and starts promoting mobility; densities higher than 7 polarons per 45 Å present increasing mean velocity with increasing density. We have also established three different regions relating electric field and average velocity. For the lowest electric field regime, surpassing the aforementioned threshold results in overcoming the 0.3 Å fs-1 limit, thus representing a transition between subsonic and supersonic regimes. For the highest of the electric fields, density effects alone are responsible for a stunning difference of 1.5 Å fs-1 in the mean carrier velocity.

  7. Finite temperature dynamics of a Holstein polaron: The thermo-field dynamics approach

    Science.gov (United States)

    Chen, Lipeng; Zhao, Yang

    2017-12-01

    Combining the multiple Davydov D2 Ansatz with the method of thermo-field dynamics, we study finite temperature dynamics of a Holstein polaron on a lattice. It has been demonstrated, using the hierarchy equations of motion method as a benchmark, that our approach provides an efficient, robust description of finite temperature dynamics of the Holstein polaron in the simultaneous presence of diagonal and off-diagonal exciton-phonon coupling. The method of thermo-field dynamics handles temperature effects in the Hilbert space with key numerical advantages over other treatments of finite-temperature dynamics based on quantum master equations in the Liouville space or wave function propagation with Monte Carlo importance sampling. While for weak to moderate diagonal coupling temperature increases inhibit polaron mobility, it is found that off-diagonal coupling induces phonon-assisted transport that dominates at high temperatures. Results on the mean square displacements show that band-like transport features dominate the diagonal coupling cases, and there exists a crossover from band-like to hopping transport with increasing temperature when including off-diagonal coupling. As a proof of concept, our theory provides a unified treatment of coherent and incoherent transport in molecular crystals and is applicable to any temperature.

  8. Structural correlations in the generation of polaron pairs in low-bandgap polymers for photovoltaics

    Science.gov (United States)

    Tautz, Raphael; da Como, Enrico; Limmer, Thomas; Feldmann, Jochen; Egelhaaf, Hans-Joachim; von Hauff, Elizabeth; Lemaur, Vincent; Beljonne, David; Yilmaz, Seyfullah; Dumsch, Ines; Allard, Sybille; Scherf, Ullrich

    2012-07-01

    Polymeric semiconductors are materials where unique optical and electronic properties often originate from a tailored chemical structure. This allows for synthesizing conjugated macromolecules with ad hoc functionalities for organic electronics. In photovoltaics, donor-acceptor co-polymers, with moieties of different electron affinity alternating on the chain, have attracted considerable interest. The low bandgap offers optimal light-harvesting characteristics and has inspired work towards record power conversion efficiencies. Here we show for the first time how the chemical structure of donor and acceptor moieties controls the photogeneration of polaron pairs. We show that co-polymers with strong acceptors show large yields of polaron pair formation up to 24% of the initial photoexcitations as compared with a homopolymer (η=8%). π-conjugated spacers, separating the donor and acceptor centre of masses, have the beneficial role of increasing the recombination time. The results provide useful input into the understanding of polaron pair photogeneration in low-bandgap co-polymers for photovoltaics.

  9. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-04-14

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

  11. Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis.

    Science.gov (United States)

    Wang, Qiantao; Edupuganti, Ramakrishna; Tavares, Clint D J; Dalby, Kevin N; Ren, Pengyu

    2015-01-01

    A-484954 is a known eEF2K inhibitor with submicromolar IC50 potency. However, the binding mechanism and the crystal structure of the kinase remains unknown. Here, we employ a homology eEF2K model, docking and alchemical free energy simulations to probe the binding mechanism of eEF2K, and in turn, guide the optimization of potential lead compounds. The inhibitor was docked into the ATP-binding site of a homology model first. Three different binding poses, hypothesis 1, 2, and 3, were obtained and subsequently applied to molecular dynamics (MD) based alchemical free energy simulations. The calculated relative binding free energy of the analogs of A-484954 using the binding pose of hypothesis 1 show a good correlation with the experimental IC50 values, yielding an r (2) coefficient of 0.96 after removing an outlier (compound 5). Calculations using another two poses show little correlation with experimental data, (r (2) of less than 0.5 with or without removing any outliers). Based on hypothesis 1, the calculated relative free energy suggests that bigger cyclic groups, at R1 e.g., cyclobutyl and cyclopentyl promote more favorable binding than smaller groups, such as cyclopropyl and hydrogen. Moreover, this study also demonstrates the ability of the alchemical free energy approach in combination with docking and homology modeling to prioritize compound synthesis. This can be an effective means of facilitating structure-based drug design when crystal structures are not available.

  12. 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.

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

    International Nuclear Information System (INIS)

    Tangarife, E.; Duque, C.A.

    2010-01-01

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

  14. 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.)

  15. 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.)

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

    International Nuclear Information System (INIS)

    Grange, P.; Lejeune, A.

    1979-01-01

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

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

    International Nuclear Information System (INIS)

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

    1991-01-01

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

  18. 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

  19. 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.

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

    International Nuclear Information System (INIS)

    Tangarife, E.; Duque, C.A.

    2011-01-01

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

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

    Science.gov (United States)

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

    2017-07-01

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

  2. Kinetic Monte Carlo Study of Ambipolar Lithium Ion and Electron-Polaron Diffusion into Nanostructured TiO2

    International Nuclear Information System (INIS)

    Yu, Jianguo; Sushko, Maria L.; Kerisit, Sebastien N.; Rosso, Kevin M.; Liu, Jun

    2012-01-01

    Nanostructured titania (TiO2) polymorphs have proved to be promising electrode materials for next generation lithium-ion batteries. However, there is still a lack of understanding of the fundamental microscopic processes that control charge transport in these materials. Here we present microscopic simulations of the collective dynamics of lithium-ion (Li+) and charge compensating electron polarons (e-) in rutile TiO2 nanoparticles in contact with idealized conductive matrix and electrolyte. Kinetic Monte Carlo simulations are used, parameterized by molecular dynamics-based predictions of activation energy barriers for Li+ and e- diffusion. Simulations reveal the central role of electrostatic coupling between Li+ and e- on their collective drift diffusion at the nanoscale. They also demonstrate that high contact area between conductive matrix and rutile nanoparticles leads to undesirable coupling-induced surface saturation effects during Li+ insertion, which limits the overall capacity and conductivity of the material. These results help provide guidelines for design of nanostructured electrode materials with improved electrochemical performance.

  3. 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...

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

    Directory of Open Access Journals (Sweden)

    Luigi Capoferri

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

  5. Interface phonon effect on optical spectra of quantum nanostructures

    International Nuclear Information System (INIS)

    Maslov, Alexander Yu.; Proshina, Olga V.; Rusina, Anastasia N.

    2009-01-01

    This paper deals with theory of large radius polaron effect in quantum wells, wires and dots. The interaction of charge particles and excitons with both bulk and interface optical phonons is taken into consideration. The analytical expression for polaron binding energy is obtained for different types of nanostructures. It is shown that the contribution of interface phonons to the polaron binding energy may exceed the bulk phonon part. The manifestation of polaron effects in optical spectra of quantum nanostructures is discussed.

  6. Crossover from Polaronic to Magnetically Phase-Separated Behavior in La1-xSrxCoO3

    Science.gov (United States)

    Phelan, D.; El Khatib, S.; Wang, S.; Barker, J.; Zhao, J.; Zheng, H.; Mitchell, J. F.; Leighton, C.

    2013-03-01

    Dilute hole-doping in La1-xSrxCoO3 leads to the formation of ``spin-state polarons'' where a non-zero spin-state is stabilized on the nearest Co3+ ions surrounding a hole. Here, we discuss the development of electronic/magnetic properties of this system from non-magnetic x=0, through the regime of spin-state polarons, and into the region where longer-range spin correlations and phase separation develop. We present magnetometry, transport, heat capacity, and small-angle neutron scattering (SANS) on single crystals. Magnetometry indicates a crossover with x from Langevin-like behavior (polaronic) to a state with a freezing temperature and finite coercivity. Fascinating correlations with this behavior are seen in transport measurements, the evolution from polaronic to clustered states being accompanied by a crossover from Mott variable range hopping to intercluster hopping. SANS data shows Lorentzian scattering from short-range ferromagnetic clusters first emerging around x = 0.03 with correlation lengths of order two unit cells. We argue that this system provides a unique opportunity to understand in detail the crossover from polaronic to truly phase-separated states.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  8. 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 )

  9. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-10-15

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

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

    Science.gov (United States)

    2014-01-01

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

  12. 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.

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

    International Nuclear Information System (INIS)

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

    1985-01-01

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

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

    KAUST Repository

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

    2010-01-01

    Despite exhaustive chemical and crystal structure studies, the mechanistic details of how FoF1-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations

  15. 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

  16. 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)

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

    Energy Technology Data Exchange (ETDEWEB)

    Chung, T. C. Mike

    2018-04-19

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

  18. Vibronic effects and destruction of exciton coherence in optical spectra of J-aggregates: A variational polaron transformation approach

    Energy Technology Data Exchange (ETDEWEB)

    Bloemsma, E.A.; Silvis, M.H.; Stradomska, A.; Knoester, J., E-mail: j.knoester@rug.nl

    2016-12-20

    Using a symmetry adapted polaron transformation of the Holstein Hamiltonian, we study the interplay of electronic excitation-vibration couplings, resonance excitation transfer interactions, and temperature in the linear absorption spectra of molecular J-aggregates. Semi-analytical expressions for the spectra are derived and compared with results obtained from direct numerical diagonalization of the Hamiltonian in the two-particle basis set representation. At zero temperature, we show that our polaron transformation reproduces both the collective (exciton) and single-molecule (vibrational) optical response associated with the appropriate standard perturbation limits. Specifically, for the molecular dimer excellent agreement with the spectra from the two-particle approach for the entire range of model parameters is obtained. This is in marked contrast to commonly used polaron transformations. Upon increasing the temperature, the spectra show a transition from the collective to the individual molecular features, which results from the thermal destruction of the exciton coherence.

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

    International Nuclear Information System (INIS)

    Henke, Paul S.; Mak, Chi H.

    2014-01-01

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

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

    Science.gov (United States)

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

    1993-09-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-08-14

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

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

    Science.gov (United States)

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

    2009-09-01

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

  3. Polaron Hopping in Nano-scale Poly(dA–Poly(dT DNA

    Directory of Open Access Journals (Sweden)

    Singh Mahi

    2010-01-01

    Full Text Available Abstract We investigate the current–voltage relationship and the temperature-dependent conductance of nano-scale samples of poly(dA–poly(dT DNA molecules. A polaron hopping model has been used to calculate the I–V characteristic of nano-scale samples of DNA. This model agrees with the data for current versus voltage at temperatures greater than 100 K. The quantities G 0 , i 0 , and T 1d are determined empirically, and the conductivity is estimated for samples of poly(dA–poly(dT.

  4. Polaron Self-localization in White-light Emitting Hybrid Perovskites

    OpenAIRE

    Cortecchia, Daniele; Yin, Jun; Bruno, Annalisa; Lo, Shu-Zee Alencious; Gurzadyan, Gagik G.; Mhaisalkar, Subodh; Brédas, Jean-Luc; Soci, Cesare

    2016-01-01

    Two-dimensional (2D) perovskites with general formula $APbX_4$ 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 color centers; however, the nature and dynamics of the emissive species have remained elusive. Here we show that the broadband photoluminescence of the 2D perovskites $(EDBE)PbCl_4$ and $(EDBE)PbBr_4$ stems from the localization of small polaron...

  5. 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

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

    International Nuclear Information System (INIS)

    Asghari, M.

    2004-01-01

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

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

    Science.gov (United States)

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

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

  8. 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

  9. Feature of polaronic charge carriers in polysilanes: Experimental and theoretical approach

    Czech Academy of Sciences Publication Activity Database

    Nešpůrek, Stanislav; Kochalska, Anna; Nožár, Juraj; Kadashchuk, A.; Fishchuk, I. I.; Sworakowski, J.; Kajzar, F.

    2010-01-01

    Roč. 521, - (2010), s. 72-83 ISSN 1542-1406. [International Conference on Frontiers of Polymers and Advanced Materials /10./. Santiago, 27.09.2009-02.10.2009] R&D Projects: GA AV ČR IAA100100622; GA AV ČR KAN400720701 Institutional research plan: CEZ:AV0Z40500505 Keywords : binding energy * charge mobility * hopping transport Subject RIV: CD - Macromolecular Chemistry Impact factor: 0.543, year: 2010

  10. 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.

  11. 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.

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

    International Nuclear Information System (INIS)

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

    1987-01-01

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

  13. 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

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

    International Nuclear Information System (INIS)

    Northby, J.A.; Xie, J.

    1989-01-01

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

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

    International Nuclear Information System (INIS)

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

    1986-10-01

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

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  17. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-11-21

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

  19. Non-relativistic Limit of a Dirac Polaron in Relativistic Quantum Electrodynamics

    CERN Document Server

    Arai, A

    2006-01-01

    A quantum system of a Dirac particle interacting with the quantum radiation field is considered in the case where no external potentials exist. Then the total momentum of the system is conserved and the total Hamiltonian is unitarily equivalent to the direct integral $\\int_{{\\bf R}^3}^\\oplus\\overline{H({\\bf p})}d{\\bf p}$ of a family of self-adjoint operators $\\overline{H({\\bf p})}$ acting in the Hilbert space $\\oplus^4{\\cal F}_{\\rm rad}$, where ${\\cal F}_{\\rm rad}$ is the Hilbert space of the quantum radiation field. The fibre operator $\\overline{H({\\bf p})}$ is called the Hamiltonian of the Dirac polaron with total momentum ${\\bf p} \\in {\\bf R}^3$. The main result of this paper is concerned with the non-relativistic (scaling) limit of $\\overline{H({\\bf p})}$. It is proven that the non-relativistic limit of $\\overline{H({\\bf p})}$ yields a self-adjoint extension of a Hamiltonian of a polaron with spin $1/2$ in non-relativistic quantum electrodynamics.

  20. 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)

  1. 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)

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

    Science.gov (United States)

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

    2009-04-14

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

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

    International Nuclear Information System (INIS)

    Campi, X.; Flocard, H.

    1975-01-01

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

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

    Science.gov (United States)

    2017-01-01

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

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

    Science.gov (United States)

    Robergs, Robert Andrew

    2017-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Robert Andrew Robergs

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

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

    Science.gov (United States)

    Stewart, James J P

    2016-11-01

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

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

    International Nuclear Information System (INIS)

    Kouki, Tuomo.

    1975-10-01

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

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

    International Nuclear Information System (INIS)

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

    1996-01-01

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

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

    Science.gov (United States)

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

    2008-01-01

    We revisit the reactivity of trapped pure gold (Au(n)+, n cations (Ag(m)Au(n)+, m + n carbon monoxide as studied in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The experimental results are discussed in terms of ab initio computations which provide a comprehensive picture of the chemical binding behaviour (like binding energy, adsorption sites, associated vibrational frequencies) of CO to the noble metal as a function of cluster size and composition. Starting from results for pure gold cluster cations for which an overall decrease of CO binding energy with increasing cluster size was experimentally observed--from about 1.09 +/- 0.1 eV (for n = 6) to below 0.65 +/- 0.1 eV (for n > 26) we demonstrate that metal--CO bond energies correlate with the total electron density and with the energy of the lowest unoccupied molecular orbital (LUMO) on the bare metal cluster cation as obtained by density functional theory (DFT) computations. This is a consequence of the predominantly sigma-donating character of the CO-M bond. Further support for this concept is found by contrasting the predictions of binding energies to the experimental results for small alloy cluster cations (Ag(m)Au(n)+, 4 < m + n < 7) as a function of composition. Here, binding energy drops with increasing silver content, while CO still binds always in a head-on fashion to a gold atom. Finally we show how the CO stretch frequency of Ag(m)Au(n)CO+ may be used to identify possible adsorption sites and pre-screen favorable isomers.

  12. 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.

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

    Science.gov (United States)

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

    2015-02-01

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

  14. Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations

    Science.gov (United States)

    Selwa, Edithe; Elisée, Eddy; Zavala, Agustin; Iorga, Bogdan I.

    2018-01-01

    Our participation to the D3R Grand Challenge 2 involved a protocol in two steps, with an initial analysis of the available structural data from the PDB allowing the selection of the most appropriate combination of docking software and scoring function. Subsequent docking calculations showed that the pose prediction can be carried out with a certain precision, but this is dependent on the specific nature of the ligands. The correct ranking of docking poses is still a problem and cannot be successful in the absence of good pose predictions. Our free energy calculations on two different subsets provided contrasted results, which might have the origin in non-optimal force field parameters associated with the sulfonamide chemical moiety.

  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. Many-polaron theory for superconductivity and charge-density waves in a strongly coupled electron-phonon system with quasi-two-dimensionality: An interpolation between the adiabatic limit and the inverse-adiabatic limit

    International Nuclear Information System (INIS)

    Nasu, K.

    1987-01-01

    The phase diagram of a two-dimensional N-site N-electron system (N>>1) with site-diagonal electron-phonon (e-ph) coupling is studied in the context of polaron theory, so as to clarify the competition between the superconducting (SC) state and the charge-density wave (CDW) state. The Fermi surface of noninteracting electrons is assumed to be a complete circle with no nesting-type instability in the case of weak e-ph coupling, so as to focus on such a strong coupling that even the standard ''strong-coupling theory'' for superconductivity breaks down. Phonon clouds moving with electrons as well as a frozen phonon are taken into account by a variational method, combined with a mean-field theory. It covers the whole region of three basic parameters characterizing the system: the intersite transfer energy of electron T, the e-ph coupling energy S, and the phonon energy ω. The resultant phase diagram is given in a triangular coordinate space spanned by T, S, and ω. In the adiabatic region ω >(T,S) near the ω vertex of the triangle, on the other hand, each electron becomes a small polaron, and the SC state is always more stable than the CDW state, because the retardation effect is absent

  17. The Bi{sup 3+} 6s and 6p electron binding energies in relation to the chemical environment of inorganic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Awater, Roy H.P., E-mail: R.H.P.Awater@tudelft.nl; Dorenbos, Pieter

    2017-04-15

    This paper provides an overview and interpretation of the spectroscopic data of the Bi{sup 3+} activator ion in 117 different inorganic compounds. The energies of the metal-to-metal charge transfer and the interconfigurational transitions of Bi{sup 3+} were collected from the archival literature. Using these energies, in combination with the electron binding energies in the host conduction and valence band, the binding energies in the 6s ground state and 6p excited state were determined relative to the vacuum level. The locations of the Bi{sup 3+} energy levels within the forbidden gap of the host compound provides valuable insight in the physical properties of the Bi{sup 3+} activator ion in different compounds.

  18. Direct observation of anisotropic small-hole polarons in an orthorhombic structure of BiV O4 films

    Science.gov (United States)

    Chaudhuri, A.; Mandal, L.; Chi, X.; Yang, M.; Scott, M. C.; Motapothula, M.; Yu, X. J.; Yang, P.; Shao-Horn, Y.; Venkatesan, T.; Wee, A. T. S.; Rusydi, A.

    2018-05-01

    Here, we report an anisotropic small-hole polaron in an orthorhombic structure of BiV O4 films grown by pulsed-laser deposition on yttrium-doped zirconium oxide substrate. The polaronic state and electronic structure of BiV O4 films are revealed using a combination of polarization-dependent x-ray absorption spectroscopy at V L3 ,2 edges, spectroscopic ellipsometry, x-ray photoemission spectroscopies, and high-resolution x-ray diffraction with the support of first-principles calculations. We find that in the orthorhombic phase, which is slightly different from the conventional pucherite structure, the unoccupied V 3d orbitals and charge inhomogeneities lead to an anisotropic small-hole polaron state. Our result shows the importance of the interplay of charge and lattice for the formation of a hole polaronic state, which has a significant impact in the electrical conductivity of BiV O4 , hence its potential use as a photoanode for water splitting.

  19. 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 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...

  20. Shallow trapping vs. deep polarons in a hybrid lead halide perovskite, CH3NH3PbI3.

    Science.gov (United States)

    Kang, Byungkyun; Biswas, Koushik

    2017-10-18

    There has been considerable speculation over the nature of charge carriers in organic-inorganic hybrid perovskites, i.e., whether they are free and band-like, or they are prone to self-trapping via short range deformation potentials. Unusually long minority-carrier diffusion lengths and moderate-to-low mobilities, together with relatively few deep defects add to their intrigue. Here we implement density functional methods to investigate the room-temperature, tetragonal phase of CH 3 NH 3 PbI 3 . We compare charge localization behavior at shallow levels and associated lattice relaxation versus those at deep polaronic states. The shallow level originates from screened Coulomb interaction between the perturbed host and an excited electron or hole. The host lattice has a tendency towards forming these shallow traps where the electron or hole is localized not too far from the band edge. In contrast, there is a considerable potential barrier that must be overcome in order to initiate polaronic hole trapping. The formation of a hole polaron (I 2 - center) involves strong lattice relaxation, including large off-center displacement of the organic cation, CH 3 NH 3 + . This type of deep polaron is energetically unfavorable, and active shallow traps are expected to shape the carrier dynamics in this material.

  1. 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

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

    KAUST Repository

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

    2018-01-01

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

  3. 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.

  4. 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.

  5. 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.

  6. The effect of higher order different meson exchange nucleon-nucleon interactions on the three-nucleon binding energy coupling problem

    International Nuclear Information System (INIS)

    Osman, A.; Ramadan, S.

    1989-01-01

    Faddeev equations of bound three-nucleon system are presented as a set of integral equations. To solve them, a sutable form of the nucleon-nucleon interactions is used: with the exchange of a scalar meson, a pseudoscalar meson and a massless vector meson. Higher orders of these different meson exchanges in the nucleon-nucleon interactions have been taken into account. With these nuclear forces and nucleon-nucleon interactions, the three-nucleon binding energy is calculated by solving the Faddeev integral equations. The obtained value of the three-nucleon binding energy is 8.441 MeV. The inclusion of the higher order terms of the different meson exchange in the nuclear nucleon-nucleon interaction is found to affect the three-nucleon binding by about 3.92%. 3 figs., 16 refs

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

    Directory of Open Access Journals (Sweden)

    Yuzhen Niu

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

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

    International Nuclear Information System (INIS)

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

    2009-01-01

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

  9. Formation of spin-polarons in the ferromagnetic Kondo lattice model away from half-filling

    International Nuclear Information System (INIS)

    Arredondo, Y; Navarro, O; Vallejo, E; Avignon, M

    2012-01-01

    Even though realistic one-dimensional experiments in the field of half-metallic semiconductors are not at hand yet, we are interested in the underlying fundamental physics. In this regard we study a one-dimensional ferromagnetic Kondo lattice model, a model in which a conduction band is coupled ferromagnetically to a background of localized d moments with coupling constant J H , and investigate the T = 0 phase diagram as a function of the antiferromagnetic interaction J between the localized moments and the band-filling n, since it has been observed that doping of the compounds has led to formation of magnetic domains. We explore the spin-polaron formation by looking at the nearest-neighbour correlation functions in the spin and charge regimes for which we use the density matrix renormalization group method, which is a highly efficient method to investigate quasi-one-dimensional strongly correlated systems. (paper)

  10. 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.

  11. An experimental and theoretical investigation of the valence orbital momentum distributions and binding energy spectra of nitrogen

    International Nuclear Information System (INIS)

    Cook, J.P.D.; Pascual, R.; Weigold, E.

    1989-05-01

    A detailed electron momentum spectrosocpy (EMS) and a manybody theoretical study of the complete valence region of N 2 was carried out. The 1500eV EMS momentum distributions show that they provide a sensitive test for orbital wavefunctions of SCF calculations, and of correlation effects. The outermost 3σ g orbital is more sharply peaked at the origin than predicted by the orbital wavefunction. The inner valence 2σ g orbital is severely split, with spectroscopic strength ranging from 34eV to over 60eV in binding energy. The results of the present extended basis 1p Green's function calculations, as well as those of several previous manybody calculations, are only in semiquantitative agreement with this. There is a 2σ u pole at 25eV with a pole strength of approximately 0.067 in agreement with the results of manybody calculations. There is significant 2σ u and or 1π u strength and little 2σ g strength in the region 26-34eV. Poles observed at 29 and 32eV, previously attributed to the 2σ g orbital, are shown to be largely 2σ u in character. The manybody calculations predict too much 2σ g strength in the region 26-34eV. 29 refs., 1 tab., 16 figs

  12. 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.

  13. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yang; Tu, Xingchen; Wang, Hao; Hou, Shimin, E-mail: smhou@pku.edu.cn [Centre for Nanoscale Science and Technology, Key Laboratory for the Physics and Chemistry of Nanodevices, Department of Electronics, Peking University, Beijing 100871 (China); Sanvito, Stefano [School of Physics, AMBER and CRANN Institute, Trinity College, Dublin 2 (Ireland)

    2015-04-28

    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.

  15. 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; Tu, Xingchen; Wang, Hao; Sanvito, Stefano; Hou, Shimin

    2015-01-01

    © 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.

  16. Effects of an Intense Laser Field and Hydrostatic Pressure on the Intersubband Transitions and Binding Energy of Shallow Donor Impurities in a Quantum Well

    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)

  17. Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series.

    Science.gov (United States)

    Güssregen, Stefan; Matter, Hans; Hessler, Gerhard; Lionta, Evanthia; Heil, Jochen; Kast, Stefan M

    2017-07-24

    Water molecules play an essential role for mediating interactions between ligands and protein binding sites. Displacement of specific water molecules can favorably modulate the free energy of binding of protein-ligand complexes. Here, the nature of water interactions in protein binding sites is investigated by 3D RISM (three-dimensional reference interaction site model) integral equation theory to understand and exploit local thermodynamic features of water molecules by ranking their possible displacement in structure-based design. Unlike molecular dynamics-based approaches, 3D RISM theory allows for fast and noise-free calculations using the same detailed level of solute-solvent interaction description. Here we correlate molecular water entities instead of mere site density maxima with local contributions to the solvation free energy using novel algorithms. Distinct water molecules and hydration sites are investigated in multiple protein-ligand X-ray structures, namely streptavidin, factor Xa, and factor VIIa, based on 3D RISM-derived free energy density fields. Our approach allows the semiquantitative assessment of whether a given structural water molecule can potentially be targeted for replacement in structure-based design. Finally, PLS-based regression models from free energy density fields used within a 3D-QSAR approach (CARMa - comparative analysis of 3D RISM Maps) are shown to be able to extract relevant information for the interpretation of structure-activity relationship (SAR) trends, as demonstrated for a series of serine protease inhibitors.

  18. Photoelectron spectrum of valence anions of uracil and first-principles calculations of excess electron binding energies.

    Science.gov (United States)

    Bachorz, Rafał A; Klopper, Wim; Gutowski, Maciej; Li, Xiang; Bowen, Kit H

    2008-08-07

    The photoelectron spectrum (PES) of the uracil anion is reported and discussed from the perspective of quantum chemical calculations of the vertical detachment energies (VDEs) of the anions of various tautomers of uracil. The PES peak maximum is found at an electron binding energy of 2.4 eV, and the width of the main feature suggests that the parent anions are in a valence rather than a dipole-bound state. The canonical tautomer as well as four tautomers that result from proton transfer from an NH group to a C atom were investigated computationally. At the Hartree-Fock and second-order Moller-Plesset perturbation theory levels, the adiabatic electron affinity (AEA) and the VDE have been converged to the limit of a complete basis set to within +/-1 meV. Post-MP2 electron-correlation effects have been determined at the coupled-cluster level of theory including single, double, and noniterative triple excitations. The quantum chemical calculations suggest that the most stable valence anion of uracil is the anion of a tautomer that results from a proton transfer from N1H to C5. It is characterized by an AEA of 135 meV and a VDE of 1.38 eV. The peak maximum is as much as 1 eV larger, however, and the photoelectron intensity is only very weak at 1.38 eV. The PES does not lend support either to the valence anion of the canonical tautomer, which is the second most stable anion, and whose VDE is computed at about 0.60 eV. Agreement between the peak maximum and the computed VDE is only found for the third most stable tautomer, which shows an AEA of approximately -0.1 eV and a VDE of 2.58 eV. This tautomer results from a proton transfer from N3H to C5. The results illustrate that the characteristics of biomolecular anions are highly dependent on their tautomeric form. If indeed the third most stable anion is observed in the experiment, then it remains an open question why and how this species is formed under the given conditions.

  19. Correlation between excited d-orbital electron lifetime in polaron dynamics and coloration of WO3 upon ultraviolet exposure

    Science.gov (United States)

    Lee, Young-Ahn; Han, Seung-Ik; Rhee, Hanju; Seo, Hyungtak

    2018-05-01

    Polarons have been suggested to explain the mechanism of the coloration of WO3 induced by UV light. However, despite the many experimental results that support small polarons as a key mechanism, direct observation of the carrier dynamics of polarons have yet to be reported. Here, we investigate the correlation between the electronic structure and the coloration of WO3 upon exposure to UV light in 5% H2/N2 gas and, more importantly, reveal photon-induced excited d-electron generation/relaxation via the W5+ oxidation state. The WO3 is fabricated by radio-frequency magnetron sputtering. X-ray diffraction patterns show that prepared WO3 is amorphous. Optical bandgap of 3.1 eV is measured by UV-vis before and after UV light. The results of Fourier transform infrared and Raman exhibit pristine WO3 is formed with surface H2O. The colored WO3 shows reduced state of W5+ state (34.3 eV) by using X-ray photoelectron spectroscopy. The valence band maximum of WO3 after UV light in H2 is shifted from mid gap to shallow donor by using ultraviolet photoelectron spectroscopy. During the exploration of the carrier dynamics, pump (700 nm)-probe (1000 nm) spectroscopy at the femtosecond scale was used. The results indicated that electron-phonon relaxation of UV-irradiated WO3, which is the origin of the polaron-induced local surface plasmonic effect, is dominant, resulting in slow decay (within a few picoseconds); in contrast, pristine WO3 shows fast decay (less than a picosecond). Accordingly, the long photoinduced carrier relaxation is ascribed to the prolonged hot-carrier lifetime in reduced oxides resulting in a greater number of free d-electrons and, therefore, more interactions with the W5+ sub-gap states.

  20. 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.)

  1. 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.

  2. 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.

  3. Observation of core-level binding energy shifts between (100) surface and bulk atoms of epitaxial CuInSe2

    International Nuclear Information System (INIS)

    Nelson, A.J.; Berry, G.; Rockett, A.

    1997-01-01

    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 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

  4. 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

  5. Molecular dynamics simulation and binding free energy studies of novel leads belonging to the benzofuran class inhibitors of Mycobacterium tuberculosis Polyketide Synthase 13.

    Science.gov (United States)

    Cruz, Jorddy N; Costa, José F S; Khayat, André S; Kuca, Kamil; Barros, Carlos A L; Neto, A M J C

    2018-05-04

    In this work, the binding mechanism of new Polyketide Synthase 13 (Pks13) inhibitors has been studied through molecular dynamics simulation and free energy calculations. The drug Tam1 and its analogs, belonging to the benzofuran class, were submitted to 100 ns simulations, and according to the results obtained for root mean square deviation, all the simulations converged from approximately 30 ns. For the analysis of backbone flotation, the root mean square fluctuations were plotted for the Cα atoms; analysis revealed that the greatest fluctuation occurred in the residues that are part of the protein lid domain. The binding free energy value (ΔG bind ) obtained for the Tam16 lead molecule was of -51.43 kcal/mol. When comparing this result with the ΔG bind values for the remaining analogs, the drug Tam16 was found to be the highest ranked: this result is in agreement with the experimental results obtained by Aggarwal and collaborators, where it was verified that the IC 50 for Tam16 is the smallest necessary to inhibit the Pks13 (IC 50  = 0.19 μM). The energy decomposition analysis suggested that the residues which most interact with inhibitors are: Ser1636, Tyr1637, Asn1640, Ala1667, Phe1670, and Tyr1674, from which the greatest energy contribution to Phe1670 was particularly notable. For the lead molecule Tam16, a hydrogen bond with the hydroxyl of the phenol not observed in the other analogs induced a more stable molecular structure. Aggarwal and colleagues reported this hydrogen bonding as being responsible for the stability of the molecule, optimizing its physic-chemical, toxicological, and pharmacokinetic properties.

  6. THEORETICAL-ANALYSIS OF THE O(1S) BINDING-ENERGY SHIFTS IN ALKALINE-EARTH OXIDES - CHEMICAL OR ELECTROSTATIC CONTRIBUTIONS

    NARCIS (Netherlands)

    PACCHIONI, G; BAGUS, PS

    1994-01-01

    We report results from ab initio cluster-model calculations on the O(1s) binding energy (BE) in the alkaline-earth oxides, MgO, CaO, SrO, and BaO; all these oxides have a cubic lattice structure. We have obtained values for both the initial- and final-state BE's. A simple point-charge model, where

  7. Effect of structural modulation and thickness of a graphene overlayer on the binding energy of the Rashba-type surface state of Ir(111)

    International Nuclear Information System (INIS)

    Sánchez-Barriga, J; Marchenko, D; Rader, O; Varykhalov, A; Bihlmayer, G; Wortmann, D

    2013-01-01

    The Ir(111) surface is known to host a surface state with a giant spin–orbit splitting due to the Rashba effect. This surface state is stable even in air when Ir is protected with an epitaxial graphene overlayer. In the present paper, we reveal an effect allowing one to tune the binding energy of this spin-split surface state up and down and demonstrate the practical application of this effect by two different approaches. The first approach is related to a decoration of the moiré pattern of single-layer graphene on Ir(111) by self-assembled nanoclusters of different compositions. The clusters locally pin graphene to the Ir substrate and enhance the amplitude of its structural corrugation, which, in turn, leads to an increase in the surface state binding energy. The second approach is related to the synthesis of few-layer graphene on Ir(111) by segregation of carbon. Additional graphene layers induce a shift of the Ir surface state towards lower binding energies and bring it almost to the Fermi level. Based on density functional calculations performed for the graphene/Ir(111) system, we show that in both cases the effect causing the binding energy shifts is intimately related to the distance between graphene and the Ir surface, which is subject to change due to deposition of clusters or by increasing the amount of graphene overlayers. In contrast, the observed spin–orbit splitting of the Ir(111) surface state remains remarkably robust and constant in all cases. Our theoretical analysis reveals that such stability can be explained by the localization properties of the Ir surface state that is a deep surface resonance. (paper)

  8. 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

  9. Benchmark CCSD(T) and DFT study of binding energies in Be7 - 12: in search of reliable DFT functional for beryllium clusters

    Science.gov (United States)

    Labanc, Daniel; Šulka, Martin; Pitoňák, Michal; Černušák, Ivan; Urban, Miroslav; Neogrády, Pavel

    2018-05-01

    We present a computational study of the stability of small homonuclear beryllium clusters Be7 - 12 in singlet electronic states. Our predictions are based on highly correlated CCSD(T) coupled cluster calculations. Basis set convergence towards the complete basis set limit as well as the role of the 1s core electron correlation are carefully examined. Our CCSD(T) data for binding energies of Be7 - 12 clusters serve as a benchmark for performance assessment of several density functional theory (DFT) methods frequently used in beryllium cluster chemistry. We observe that, from Be10 clusters on, the deviation from CCSD(T) benchmarks is stable with respect to size, and fluctuating within 0.02 eV error bar for most examined functionals. This opens up the possibility of scaling the DFT binding energies for large Be clusters using CCSD(T) benchmark values for smaller clusters. We also tried to find analogies between the performance of DFT functionals for Be clusters and for the valence-isoelectronic Mg clusters investigated recently in Truhlar's group. We conclude that it is difficult to find DFT functionals that perform reasonably well for both beryllium and magnesium clusters. Out of 12 functionals examined, only the M06-2X functional gives reasonably accurate and balanced binding energies for both Be and Mg clusters.

  10. 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

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

    International Nuclear Information System (INIS)

    Ortakaya, Sami; Kirak, Muharrem

    2016-01-01

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

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-10-01

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  15. 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.

  16. 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.

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

    KAUST Repository

    Li, Yang

    2015-04-28

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

  18. 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.

  19. Polaronic transport and thermoelectricity in Fe1 -xCoxSb2S4 (x =0 , 0.1, and 0.2)

    Science.gov (United States)

    Liu, Yu; Kang, Chang-Jong; Stavitski, Eli; Du, Qianheng; Attenkofer, Klaus; Kotliar, G.; Petrovic, C.

    2018-04-01

    We report a study of Co-doped berthierite Fe1 -xCoxSb2S4 (x =0 , 0.1, and 0.2). The alloy series of Fe1 -xCoxSb2S4 crystallize in an orthorhombic structure with the Pnma space group, similar to FeSb2, and show semiconducting behavior. The large discrepancy between activation energy for conductivity, Eρ (146 ˜270 meV ), and thermopower, ES (47 ˜108 meV ), indicates the polaronic transport mechanism. Bulk magnetization and heat-capacity measurements of pure FeSb2S4 (x =0 ) exhibit a broad antiferromagnetic transition (TN=46 K ) followed by an additional weak transition (T*=50 K ). Transition temperatures (TN and T*) slightly decrease with increasing Co content x . This is also reflected in the thermal conductivity measurement, indicating strong spin-lattice coupling. Fe1 -xCoxSb2S4 shows relatively high value of thermopower (up to ˜624 μ V K-1 at 300 K) and thermal conductivity much lower when compared to FeSb2, a feature desired for potential applications based on FeSb2 materials.

  20. Propagation effect on photoluminescence of spin-aligned high-density exciton magnetic polarons in Cd{sub 0.8}Mn{sub 0.2}Te

    Energy Technology Data Exchange (ETDEWEB)

    Nagata, M.; Hirase, T.; Miyajima, K., E-mail: miyajima@rs.tus.ac.jp

    2017-04-15

    Characteristics of photoluminescence (PL) originating from high-density exciton magnetic polarons (HD-EMPs) for Cd{sub 0.8}Mn{sub 0.2}Te were investigated. The PL appeared only under selective excitation of the localized excitons, and the intensity increased superlinearly with the excitation density. Directivity of the PL was revealed. Therefore, it is concluded that the superlinear increase in the PL intensity resulted from a light amplification process owing to the stimulated emission. In addition, the existence of birefringence that originates from a uniaxial gradation of the Mn ion concentrations was revealed. The degree of circular polarization (DOCP) of the PL is important to obtain the spin alignment state of the HD-EMPs. The initial DOCPs of the PL were examined by removing a variation of the polarization during propagation inside the sample. As a result, it was found that the initial DOCPs of the PL were almost constant for the photon energy. The obtained initial DOCPs exhibited different values for right- and left-circularly polarized excitations, which resulted from different mechanisms of the spin alignment of the HD-EMPs.