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Sample records for residual two-body interaction

  1. Pseudopotential treatment of two body interactions

    NASA Astrophysics Data System (ADS)

    Kanjilal, Krittika

    Ultracold atomic gases have been of great theoretical and experimental interest in the last two decades. In these systems, the de Broglie wavelength of the particles is much greater than the two body van der Waals length. As a result, the details of the two body interaction potential are irrelevant for a large number of applications and the realistic two body interaction potential can be replaced by a simple finite range or zero range model potential that reproduces the scattering quantities of the full interaction potential. This thesis develops zero range pseudopotentials and applies them to trapped two-particle systems. Ultracold gases loaded into optical lattices can be used to realize two particle systems under approximately harmonic confinement. We use pseudopotentials to obtain the eigenspectrum of two particles under external harmonic confinement semi-analytically. Advancements in trapping technology have resulted in the realization of low-dimensional systems. We develop pseudopotentials to treat two body interactions in one and two dimensions. We also elaborate on the physics that is unique to one and two dimensional systems. Feshbach resonances allow for the tunability of the effective two body interaction strength in the presence of a magnetic field. To model Feshbach resonances in two and three dimensions we develop coupled two channel zero range potentials. Dipole-dipole interactions in Chromium and polar molecules have been the subject of a lot of recent research. Unlike the interactions between two alkali atoms, these interactions are long range and anisotropic. We explore the scattering properties of two aligned dipoles using a simple shape dependent model potential. To understand a system two aligned dipoles under confinement, we develop a pseudopotential treatment for cylindrically symmetric interaction potentials under cylindrically symmetric harmonic confinement. This pseudopotential can be used to model any cylindrically symmetric interaction

  2. Separable approximations of two-body interactions

    NASA Astrophysics Data System (ADS)

    Haidenbauer, J.; Plessas, W.

    1983-01-01

    We perform a critical discussion of the efficiency of the Ernst-Shakin-Thaler method for a separable approximation of arbitrary two-body interactions by a careful examination of separable 3S1-3D1 N-N potentials that were constructed via this method by Pieper. Not only the on-shell properties of these potentials are considered, but also a comparison is made of their off-shell characteristics relative to the Reid soft-core potential. We point out a peculiarity in Pieper's application of the Ernst-Shakin-Thaler method, which leads to a resonant-like behavior of his potential 3SD1D. It is indicated where care has to be taken in order to circumvent drawbacks inherent in the Ernst-Shakin-Thaler separable approximation scheme. NUCLEAR REACTIONS Critical discussion of the Ernst-Shakin-Thaler separable approximation method. Pieper's separable N-N potentials examined on shell and off shell.

  3. Multinucleon Ejection Model for Two Body Current Neutrino Interactions

    SciTech Connect

    Sobczyk, Jan T.; /Fermilab

    2012-06-01

    A model is proposed to describe nucleons ejected from a nucleus as a result of two-body-current neutrino interactions. The model can be easily implemented in Monte Carlo neutrino event generators. Various possibilities to measure the two-body-current contribution are discussed. The model can help identify genuine charge current quasielastic events and allow for a better determination of the systematic error on neutrino energy reconstruction in neutrino oscillation experiments.

  4. Unsteady Aerodynamic Interaction between Two Bodies at Hypersonic Speed

    NASA Astrophysics Data System (ADS)

    Ozawa, Hiroshi; Kitamura, Keiichi; Hanai, Katsuhisa; Mori, Koichi; Nakamura, Yoshiaki

    This paper presents experimental results of unsteady aerodynamic interactions including Shock/Shock Interaction (SSI) and Shock/Boundary Layer Interaction (SBLI) between two bodies at hypersonic speed. These interactions can be seen in space vehicles consisting of multi-bodies, such as a TSTO, or at a scramjet engine inlet. The present study considers the effect of a flat plate below the SSI where a boundary-layer is developed on the plate surface. More specifically, the interacted flow for a combination of a flat plate (FP) and a hemi-circular cylinder (HCC) is examined at a hypersonic speed (M∞=8.1) the distributions of surface pressure and heat transfer rate are measured. To obtain various SSI patterns, the clearance between two bodies (FP and HCC) is changed. Results show that unsteadiness at the SSI point causes a feedback loop between the two bodies; a jet flow impinges on the FP, the effect of which propagates upstream where the jet impinges on the FP, and the aerodynamic and aerothermodynamic loads reach their maxima. Finally, we found that the feedback loop can be destroyed by installing a fence on the FP to reduce unsteadiness of flow field.

  5. Two body and multibody interaction in a cold Rydberg gas

    NASA Astrophysics Data System (ADS)

    Han, Jianing; Gallagher, Tom

    2009-05-01

    Cold Rydberg atoms trapped in a Magneto Optical Trap (MOT) are not isolated and they tend to bond through dipole-dipole and multiple-multiple interactions between Rydberg atoms. The dipole-dipole interaction and van der Waals interaction between two atoms have been intensively studied. However, the fact that the dipole-dipole interaction and van der Waals interaction show the same size of broadening, studied by Raithel's group, and there is transition between two molecular states, studied by Farooqi and Overstreet, can not be explained by the two atom picture. The purpose of this paper is to show the multibody nature of a dense cold Rydberg gas by studying the molecular state microwave spectrum. Specifically, single body, two body and three body interaction regions are separated. Moreover, the multibody energy levels for selected geometries are calculated. In addition, multibody blockade will be discussed. [3pt] [1] A. Reinhard, K. C. Younge, T. Cubel Liebisch, B. Knuffman, P. R. Berman, and G. Raithel, Phys. Rev. Lett. 100, 233201 (2008).[0pt] [2] S.M. Farooqi, D. Tong, S. Krishnan, J. Stanojevic,Y.P. Zhang, J.R. Ensher, A.S. Estrin, C. Boisseau, R. Cote, E.E. Eyler, and P.L. Gould, Phys. Rev. Lett. 91, 183002 (2003).[0pt] [3] K. Richard Overstreet, Arne Schwettmann, Jonathan Tallant, and James P. Shaffer, Phys. Rev. A 76, 011403 (2007).

  6. Implicit Theories of Static Interactions between Two Bodies

    ERIC Educational Resources Information Center

    Montanero, M.; Suero, M. I.; Perez, A. L.; Pardo, P. J.

    2002-01-01

    There are many spontaneous conceptions related to the principle of action and reaction for two bodies in static contact. A study of a broad sample of students showed Newton's third law to be a great unknown for most of them. The conceptions were found to be consistent, forming authentic minitheories (implicit theories) with general laws governing…

  7. Proton-neutron interacting boson model under random two-body interactions

    SciTech Connect

    Yoshida, N.; Zhao, Y. M.; Arima, A.

    2009-12-15

    The low-lying states of sd-boson systems in the presence of random two-body interactions are studied in the proton-neutron interacting boson model (IBM-2). The predominance of spin-zero ground states is confirmed, and a very prominent maximum F-spin dominance in ground states is found. It turns out that the requirement of random interactions with F-spin conservation intensifies the above predominance. Collective motion in the low-lying states is discussed.

  8. Relationships between three-body and two-body interactions in fluids and solids.

    PubMed

    Wang, Liping; Sadus, Richard J

    2006-10-14

    Molecular dynamics data are reported for two-body and three-body interactions in noble gases at densities covering the gas, liquid, and solid phases. The data indicate that simple relationships exist between three- and two-body interactions in both fluid and solid phases. The relationship for liquids has a simple density dependence with only one external parameter. In contrast, the solid phase relationship depends both on density and on the square of density and requires the evaluation of two parameters. The relationships are tested for both system-size and temperature dependences. The values of the relationship parameters are only sensitive to system size when a small number of atoms are involved. For 500 or more atoms, they remain nearly constant. The relationships are valid for both subcritical and slightly supercritical temperatures. A practical benefit of the relationships is that they enable the use of two-body intermolecular potentials for the prediction of the properties of real systems without the computational expense of three-body calculations. PMID:17042611

  9. Statistical mechanics of nucleosome ordering by chromatin-structure-induced two-body interactions

    NASA Astrophysics Data System (ADS)

    Chereji, Răzvan V.; Tolkunov, Denis; Locke, George; Morozov, Alexandre V.

    2011-05-01

    One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to 10-11 base pair (bp) discretization of linker lengths caused by the smaller free energy cost of packaging nucleosomes into regular chromatin fibers if their rotational setting (defined by the DNA helical twist) is conserved. We describe nucleosome positions along the fiber using a thermodynamic model of finite-size particles with both intrinsic histone-DNA interactions and an effective two-body potential. We infer one- and two-body energies directly from high-throughput maps of nucleosome positions. We show that higher-order chromatin structure helps explains in vitro and in vivo nucleosome ordering in transcribed regions, and plays a leading role in establishing well-known 10-11 bp genome-wide periodicity of nucleosome positions.

  10. Collectivity of low-lying states under random two-body interactions

    SciTech Connect

    Zhao, Y. M.; Ping, J. L.; Arima, A.

    2007-11-15

    In this article we study the behavior of collectivity under random two-body interactions in the framework of the fermion dynamical symmetry model (FDSM). We found that a Hamiltonian with the SO(8) symmetry of the FDSM does not give vibrational and rotational modes under random interactions while a Hamiltonian with the SP(6) symmetry does. It is suggested that collective motions such as vibration and rotation are closely related not only to the quadruple-quadruple correlation in the Hamiltonian but also to the dynamical symmetries of the Hamiltonian.

  11. New puzzle for many-body systems with random two-body interactions

    SciTech Connect

    Johnson, Calvin W.; Nam, Hai Ah

    2007-04-15

    We continue a series of numerical experiments on many-body systems with random two-body interactions, by examining correlations in ratios in excitation energies of yrast J=0,2,4,6,8 states. Previous studies, limited only to J=0,2,4 states, had shown strong correlations in boson systems but not fermion systems. By including J{>=}6 states and considering different scatter plots, strong correlations between ratios of yrast excitation energies appear in both boson and fermion systems. Such correlations agree with real nuclear data and include the well-known limits of seniority, vibrations, and rotations.

  12. Renormalization group analysis of ultracold Fermi gases with two-body attractive interaction

    NASA Astrophysics Data System (ADS)

    Guo, Xiaoyong; Chi, Zimeng; Zheng, Qiang; Wang, Zaijun

    2016-01-01

    We propose a new functional renormalization group (RG) strategy to investigate the many-body physics of interacting ultracold Fermi gases. By mapping the Ginzburg-Landau (GL) action of Fermi gases onto a complex φ4-model, we can obtain the closed flow equation in the one-loop approximation. An analysis of the emerging RG flow gives the ground state behavior. The Hamiltonian of a Fermi gas with a two-body attractive interaction is used as a demonstration to clarify our treatment. The fixed point structure reveals not only the condensation phase transition, but also the Bardeen-Cooper-Schrieffer (BCS) to Bose-Einstein condensation (BEC) crossover. The effect of the imaginary time renormalization is also discussed. It is shown that for the dynamical field configuration our RG procedure can reproduce the well known theoretical results of BCS-BEC crossover, while under a static approximation the phase transition takes place at a higher critical temperature.

  13. One-Dimensional Traps, Two-Body Interactions, Few-Body Symmetries. II. N Particles

    NASA Astrophysics Data System (ADS)

    Harshman, N. L.

    2016-01-01

    This is the second in a pair of articles that classify the configuration space and kinematic symmetry groups for N identical particles in one-dimensional traps experiencing Galilean-invariant two-body interactions. These symmetries explain degeneracies in the few-body spectrum and demonstrate how tuning the trap shape and the particle interactions can manipulate these degeneracies. The additional symmetries that emerge in the non-interacting limit and in the unitary limit of an infinitely strong contact interaction are sufficient to algebraically solve for the spectrum and degeneracy in terms of the one-particle observables. Symmetry also determines the degree to which the algebraic expressions for energy level shifts by weak interactions or nearly-unitary interactions are universal, i.e. independent of trap shape and details of the interaction. Identical fermions and bosons with and without spin are considered. This article analyzes the symmetries of N particles in asymmetric, symmetric, and harmonic traps; the prequel article treats the one, two and three particle cases.

  14. The role of two body interaction on the broadening of a Förster resonance

    NASA Astrophysics Data System (ADS)

    Kondo, Jorge; Goncalves, Luis; Tallant, Jonathan; Booth, Donald; Shaffer, James; Marcassa, Luis

    2015-05-01

    Since the early days of ultracold Rydberg atom physics, many-body effects in ultracold trapped alkali gases has been of central interest. The first experiments in this field involved the study of Förster resonances as a function of atomic density. We present a study of a dc electric field tuned Förster resonance involving 37D state Rb atoms in a high density atomic sample held in an optical dipole trap. Our results show that as the atomic density increases, the resonance linewidth increases until the resonance peaks merge. Simultaneously, we measure the 39P state population which is produced through interactions between 37D atoms. It is shown that the 39P population depends quadratically on the total Rydberg 37D atomic population. A theoretical model that takes into account the multilevel character of the interaction and Rydberg atom blockade process using only pair interactions was implemented to explain the results. The comparison between the experimental data and the model is very good, suggesting that the Föster resonance process is dominate by two-body interaction. This work was supported by Fapesp, NSF and INCT-IQ.

  15. The two-body interaction potential in the STF tensor formalism: an application to binary asteroids

    NASA Astrophysics Data System (ADS)

    Compère, A.; Lemaître, A.

    2014-08-01

    The symmetric trace free (STF) tensor formalism, developed by Hartmann et al. (Celest Mech Dyn Astron 60:139-159. doi: 10.1007/BF00693097, 1994), is a nice tool, not much used in Celestial Mechanics. It is fully equivalent to the usual spherical harmonics but permits more elegant and compact formulations. The coupling between the gravitational fields of extended bodies with this formalism has been used in Mathis and Le Poncin-Lafitte (Astron Astrophys 497:889-910. doi: 10.1051/0004-6361/20079054, 2009) for binary stars or planetary systems, but not yet applied to binary asteroids. However, binary asteroids are common in the Solar System and usually their study requires a full two rigid body approach. The formulation of the two-body interaction potential in the STF formalism in the full two rigid body problem is detailed and completed in this article. An application to the binary asteroid (66391) 1999 KW4 is presented with a comparison of our results with other results of the literature for validation.

  16. Periodic orbit quantization of a weakly interacting two-body system using perturbed symmetry-broken trace formulas

    SciTech Connect

    Sakhr, Jamal; Whelan, Niall D.; Dumont, Randall S.

    2006-11-15

    The semiclassical limit of the quantum few-body problem has not been studied in general terms from the point of view of periodic orbit theory. In a previous paper, we studied noninteracting two-body systems [Phys. Rev. A 62, 042109 (2000)] and discussed the fact that the periodic orbits occur in continuous families. Interactions destroy the periodic orbit families leaving a discrete set of isolated periodic orbits. In this paper, we consider the effect of weak two-body interactions, which can be thought of as symmetry-breaking perturbations and can thus be analyzed using a theory developed by Creagh [Ann. Phys. (N.Y.) 248, 1 (1996)]. The Poeschl-Teller two-body system confined in a square well is analyzed to illustrate the use of the formalism. It is shown that the effect of the interaction can be evaluated for all two-particle periodic orbits, and that the coarse-grained quantum density of states can be fully reproduced from simply summing the perturbed contributions of each periodic orbit family. Good numerical estimates of the quantum singlet energies can actually be obtained, but it is found that that perturbed trace formulas cannot reproduce the multiplet splittings predicted from quantum mechanics. Several interesting properties are observed depending on the range of the interaction and on whether the interaction is attractive or repulsive.

  17. Cornell interaction in the two-body semi-relativistic framework: The Lie algebraic approach

    NASA Astrophysics Data System (ADS)

    Panahi, H.; Zarrinkamar, S.; Baradaran, M.

    2016-02-01

    We consider an approximation to the two-body spinless Salpeter equation which is valid for the case of heavy quarks with the Cornell potential. We then replace the square of kinetic term with its nonrelativistic equivalent and obtain an equation which can be alternatively viewed as the generalization of the Schrödinger equation into the relativistic regime. In the calculations, we use the Lie algebraic approach within the framework of quasi-exact solvability. With the help of the representation theory of sl(2) , the ( n+1 -dimensional matrix equation of the problem is constructed in a quite detailed manner and thereby the quasi-exact expressions for the energy eigenvalues and the corresponding wave functions as well as the allowed values of the potential parameters are obtained.

  18. Fluid-structure interaction of two bodies in an inviscid fluid

    NASA Astrophysics Data System (ADS)

    Tchieu, A. A.; Crowdy, D.; Leonard, A.

    2010-10-01

    The interaction of two arbitrary bodies immersed in a two-dimensional inviscid fluid is investigated. Given the linear and angular velocities of the bodies, the solution of the potential flow problem with zero circulation around both bodies is reduced to the determination of a suitable Laurent series in a conformally mapped domain that satisfies the boundary conditions. The potential flow solution is then used to determine the force and moment acting on each body by using generalized Blasius formulas. The current formulation is applied to two examples. First, the case of two rigid circular cylinders interacting in an unbounded domain is investigated. The forces on two cylinders with prescribed motion (forced-forced) is determined and compared to previous results for validation purposes. We then study the response of a single "free" cylinder due to the prescribed motion of the other cylinder (forced-free). This forced-free situation is used to justify the hydrodynamic benefits of drafting in aquatic locomotion. In the case of two neutrally buoyant circular cylinders, the aft cylinder is capable of attaining a substantial propulsive force that is the same order of magnitude of its inertial forces. Additionally, the coupled interaction of two cylinders given an arbitrary initial condition (free-free) is studied to show the differences of perfect collisions with and without the presence of an inviscid fluid. For a certain range of collision parameters, the fluid acts to deflect the cylinder paths just enough before the collision to drastically affect the long time trajectories of the bodies. In the second example, the flapping of two plates is explored. It is seen that the interactions between each plate can cause a net force and torque at certain instants in time, but for idealized sinusoidal motions in irrotational potential flow, there is no net force and torque acting at the system center.

  19. Interacting quantum walkers: two-body bosonic and fermionic bound states

    NASA Astrophysics Data System (ADS)

    Krapivsky, P. L.; Luck, J. M.; Mallick, K.

    2015-11-01

    We investigate the dynamics of bound states of two interacting particles, either bosons or fermions, performing a continuous-time quantum walk on a one-dimensional lattice. We consider the situation where the distance between both particles has a hard bound, and the richer situation where the particles are bound by a smooth confining potential. The main emphasis is on the velocity characterizing the ballistic spreading of these bound states, and on the structure of the asymptotic distribution profile of their center-of-mass coordinate. The latter profile generically exhibits many internal fronts.

  20. Solution of two-body relativistic bound state equations with confining plus Coulomb interactions

    NASA Technical Reports Server (NTRS)

    Maung, Khin Maung; Kahana, David E.; Norbury, John W.

    1992-01-01

    Studies of meson spectroscopy have often employed a nonrelativistic Coulomb plus Linear Confining potential in position space. However, because the quarks in mesons move at an appreciable fraction of the speed of light, it is necessary to use a relativistic treatment of the bound state problem. Such a treatment is most easily carried out in momentum space. However, the position space Linear and Coulomb potentials lead to singular kernels in momentum space. Using a subtraction procedure we show how to remove these singularities exactly and thereby solve the Schroedinger equation in momentum space for all partial waves. Furthermore, we generalize the Linear and Coulomb potentials to relativistic kernels in four dimensional momentum space. Again we use a subtraction procedure to remove the relativistic singularities exactly for all partial waves. This enables us to solve three dimensional reductions of the Bethe-Salpeter equation. We solve six such equations for Coulomb plus Confining interactions for all partial waves.

  1. One-Dimensional Traps, Two-Body Interactions, Few-Body Symmetries: I. One, Two, and Three Particles

    NASA Astrophysics Data System (ADS)

    Harshman, N. L.

    2016-01-01

    This is the first in a pair of articles that classify the configuration space and kinematic symmetry groups for N identical particles in one-dimensional traps experiencing Galilean-invariant two-body interactions. These symmetries explain degeneracies in the few-body spectrum and demonstrate how tuning the trap shape and the particle interactions can manipulate these degeneracies. The additional symmetries that emerge in the non-interacting limit and in the unitary limit of an infinitely strong contact interaction are sufficient to algebraically solve for the spectrum and degeneracy in terms of the one-particle observables. Symmetry also determines the degree to which the algebraic expressions for energy level shifts by weak interactions or nearly-unitary interactions are universal, i.e. independent of trap shape and details of the interaction. Identical fermions and bosons with and without spin are considered. This article sequentially analyzes the symmetries of one, two and three particles in asymmetric, symmetric, and harmonic traps; the sequel article treats the N particle case.

  2. Repulsive bound-atom pairs in an optical lattice with two-body interaction of nearest neighbors

    SciTech Connect

    Wang, Y.-M.; Liang, J.-Q.

    2010-04-15

    Repulsively interacting particles in a periodic potential can form bound composite objects with long lifetimes, as has been observed experimentally [Winkler et al., Nature (London) 441, 853 (2006)]. In this paper, a complete two-particle solution of one-dimensional periodical potential was derived in a strong interaction regime, where the on-site approximation of a two-body interaction in the Bose-Hubbard model (BHM) is extended to include the interaction of nearest neighbors, which results in atom-pair hopping. The energy spectrum of the bound pair is drastically reshaped due to the pair-hopping term, and complex eigenenergy corresponding to metastable states is also found that has not been discovered in the usual BHM. When the absolute value of a center-of-mass quasimomentum wave vector is greater than a critical value (|K|>K{sub c}), two bound-pair solutions are found. Furthermore, the spatial and momentum distributions of the bound pair displays a crossover from dark to bright soliton-like solutions in the extended BHM. Our results reduce to that of the usual BHM in the weak interaction case.

  3. Effects of the two-body and three-body hyperon-nucleon interactions in Λ hypernuclei

    NASA Astrophysics Data System (ADS)

    Lonardoni, D.; Gandolfi, S.; Pederiva, F.

    2013-04-01

    Background: The calculation of the hyperon binding energy in hypernuclei is crucial to understanding the interaction between hyperons and nucleons.Purpose: We assess the relative importance of two- and three-body hyperon-nucleon force by studying the effect of the hyperon-nucleon-nucleon interaction in closed shell Λ hypernuclei from A = 5 to 91.Methods: The Λ binding energy has been calculated using the auxiliary field diffusion Monte Carlo method for the first time, to study light and heavy hypernuclei within the same model.Results: Our results show that including a three-body component in the hyperon-nucleon interaction leads to a saturation of the Λ binding energy remarkably close to the experimental data. In contrast, the two-body force alone gives an unphysical limit for the binding energy.Conclusions: The repulsive contribution of the three-body hyperon-nucleon-nucleon force is essential to reproduce, even qualitatively, the binding energy of hypernuclei in the mass range considered.

  4. Topological quantum-phase coherence in full counting statistics of transport electrons with two-body interaction

    NASA Astrophysics Data System (ADS)

    Guo, Xiao-Fang; Xue, Hai-Bin; Liang, Jiu-Qing

    2014-08-01

    The full counting statistics of electron transport through two parallel quantum dots with antiparallel magnetic fluxes is investigated as a probe to detect the topological quantum-phase coherence (TQPC), which results in the characteristic oscillation of the zero-frequency cumulants including the shot noise and skewness. We show explicitly the phase transition of cumulant spectrum-patterns induced by the topology change of electron path-loops while the pattern period, which depends only on the topology (or Chern number), is robust against the variation of Coulomb interaction and interdot coupling strengths. Most importantly we report for the first time on a new type of TQPC, which is generated by the two-particle interaction and does not exist in the single-particle wave function interference. Moreover, the accurately quantized peaks of Fano-factor spectrum, which characterize the super- and sub-Poissonian shot noises, are of fundamental importance in technical applications similar to the superconducting quantum interference device.

  5. Gravitational self-force corrections to two-body tidal interactions and the effective one-body formalism

    NASA Astrophysics Data System (ADS)

    Bini, Donato; Damour, Thibault

    2014-12-01

    Tidal interactions have a significant influence on the late dynamics of compact binary systems, which constitute the prime targets of the upcoming network of gravitational-wave detectors. We refine the theoretical description of tidal interactions (hitherto known only to the second post-Newtonian level) by extending our recently developed analytic self-force formalism, for extreme-mass-ratio binary systems, to the computation of several tidal invariants. Specifically, we compute, to linear order in the mass ratio and to the 7.5th post-Newtonian order, the following tidal invariants: the square and the cube of the gravitoelectric quadrupolar tidal tensor, the square of the gravitomagnetic quadrupolar tidal tensor, and the square of the gravitoelectric octupolar tidal tensor. Our high-accuracy analytic results are compared to recent numerical self-force tidal data by Dolan et al. [arXiv:1406.4890 [Phys. Rev. D (to be published)] ], and, notably, provide an analytic understanding of the light ring asymptotic behavior found by them. We transcribe our kinematical tidal-invariant results in the more dynamically significant effective one-body description of the tidal interaction energy. By combining, in a synergetic manner, analytical and numerical results, we provide simple, accurate analytic representations of the global, strong-field behavior of the gravitoelectric quadrupolar tidal factor. A striking finding is that the linear-in-mass-ratio piece in the latter tidal factor changes sign in the strong-field domain, to become negative (while its previously known second post-Newtonian approximant was always positive). We, however, argue that this will be more than compensated by a probable fast growth, in the strong-field domain, of the nonlinear-in-mass-ratio contributions in the tidal factor.

  6. Analytic determination of the eight-and-a-half post-Newtonian self-force contributions to the two-body gravitational interaction potential

    NASA Astrophysics Data System (ADS)

    Bini, Donato; Damour, Thibault

    2014-05-01

    We analytically compute, to the eight-and-a-half post-Newtonian order, and to linear order in the mass ratio, the radial potential describing (within the effective one-body formalism) the gravitational interaction of two bodies, thereby extending previous analytic results. These results are obtained by applying analytical gravitational self-force theory (for a particle in circular orbit around a Schwarzschild black hole) to Detweiler's gauge-invariant redshift variable. We emphasize the increase in "transcendentality" of the numbers entering the post-Newtonian expansion coefficients as the order increases, in particular we note the appearance of ζ(3) (as well as the square of Euler's constant γ) starting at the seventh post-Newtonian order. We study the convergence of the post-Newtonian expansion as the expansion parameter u =GM/(c2r) leaves the weak-field domain u ≪1 to enter the strong field domain u=O(1).

  7. Effect of the band structure in a rigorous two-body model with long-range interactions in 1D optical lattices

    NASA Astrophysics Data System (ADS)

    Kristensen, Tom; Simoni, Andrea; Launay, Jean-Michel

    2016-05-01

    We compute scattering and bound state properties for two ultracold molecules in a pure 1D optical lattice. We introduce reference functions with complex quasi-momentum that naturally account for the effect of excited energy bands. Our exact results for a short-range interaction are first compared with the simplest version of the standard Bose-Hubbard (BH) model. Such comparison allows us to highlight the effect of the excited bands, of the non-on-site interaction and of tunneling with distant neighbor, that are not taken into account in the BH model. The effective interaction can depend strongly on the particle quasi-momenta and can present a resonant behavior even in a deep lattice. As a second step, we study scattering of two polar particles in the optical lattice. Peculiar Wigner threshold laws stem from the interplay of the long range dipolar interaction and the presence of the energy bands. We finally assess the validity of an extended Bose-Hubbard model for dipolar gases based on our exact two-body calculations. This work was supported by the Agence Nationale de la Recherche (Contract No. ANR-12-BS04-0020-01).

  8. Are distance-dependent statistical potentials considering three interacting bodies superior to two-body statistical potentials for protein structure prediction?

    PubMed

    Ghomi, Hamed Tabatabaei; Thompson, Jared J; Lill, Markus A

    2014-10-01

    Distance-based statistical potentials have long been used to model condensed matter systems, e.g. as scoring functions in differentiating native-like protein structures from decoys. These scoring functions are based on the assumption that the total free energy of the protein can be calculated as the sum of pairwise free energy contributions derived from a statistical analysis of pair-distribution functions. However, this fundamental assumption has been challenged theoretically. In fact the free energy of a system with N particles is only exactly related to the N-body distribution function. Based on this argument coarse-grained multi-body statistical potentials have been developed to capture higher-order interactions. Having a coarse representation of the protein and using geometric contacts instead of pairwise interaction distances renders these models insufficient in modeling details of multi-body effects. In this study, we investigated if extending distance-dependent pairwise atomistic statistical potentials to corresponding interaction functions that are conditional on a third interacting body, defined as quasi-three-body statistical potentials, could model details of three-body interactions. We also tested if this approach could improve the predictive capabilities of statistical scoring functions for protein structure prediction. We analyzed the statistical dependency between two simultaneous pairwise interactions and showed that there is surprisingly little if any dependency of a third interacting site on pairwise atomistic statistical potentials. Also the protein structure prediction performance of these quasi-three-body potentials is comparable with their corresponding two-body counterparts. The scoring functions developed in this study showed better or comparable performances compared to some widely used scoring functions for protein structure prediction. PMID:25212727

  9. Energy and structural properties of N -boson clusters attached to three-body Efimov states: Two-body zero-range interactions and the role of the three-body regulator

    NASA Astrophysics Data System (ADS)

    Yan, Yangqian; Blume, D.

    2015-09-01

    The low-energy spectrum of N -boson clusters with pairwise zero-range interactions is believed to be governed by a three-body parameter. We study the ground state of N -boson clusters with infinite two-body s -wave scattering length by performing ab initio Monte Carlo simulations. To prevent Thomas collapse, different finite-range three-body regulators are used. The energy and structural properties for the three-body Hamiltonian with two-body zero-range interactions and three-body regulator are in much better agreement with the "ideal zero-range Efimov theory" results than those for Hamiltonian with two-body finite-range interactions. For larger clusters we find that the ground-state energy and structural properties of the Hamiltonian with two-body zero-range interactions and finite-range three-body regulators are not universally determined by the three-body parameter, i.e., dependencies on the specific form of the three-body regulator are observed. For comparison, we consider Hamiltonian with two-body van der Waals interactions and no three-body regulator. For the interactions considered, the ground-state energy of the N -body clusters is—if scaled by the three-body ground-state energy—fairly universal, i.e., the dependence on the short-range details of the two-body van der Waals potentials is small. Our results are compared with those in the literature.

  10. Two-Body Scattering in (1 + 1) Dimensions by a Semi-relativistic Formalism and a Hulthén Interaction Potential

    NASA Astrophysics Data System (ADS)

    Hassanabadi, S.; Ghominejad, M.; Thylwe, K.-E.

    2015-04-01

    Scattering solutions of two-body Spinless Salpeter Equation (SSE) are investigated in the center of mass frame with a repulsive, symmetric Hulthén potential in one spatial dimension. Transmission and reflection coefficients are calculated and discussed.

  11. Two- and quasi-two-body strange particle final state production in. pi. /sup +/p interactions at low to intermediate energies

    SciTech Connect

    Hanson, P.

    1982-10-01

    The two and quasi-two body final states ..sigma../sup +/K/sup +/, ..sigma../sup +/K* (892)/sup +/, ..sigma..*(1385)/sup +/K/sup +/, ..sigma..(1385)/sup +/K*(892)/sup +/ produced by neutral strangeness exchange in ..pi../sup +/p interactions are studied using our own 1-3 GeV/c data, comprising the 14 incident momenta of a two million picture bubble chamber experiment, in combination with the world data on the same and related channels. Because low energy resonance formation is not strongly coupled to the ..sigma..,..sigma..* production channels, at very modest incident momenta their dominant features are seen to be understandable in terms of high energy hypercharge exchange phenomenology. We find that Regge models fitted to data in the 10 to 20 GeV/c range adequately describe the ..sigma.. and ..sigma..* channels down to within a few hundred MeV/c of threshold and out to large center of mass scattering angles, and that over the range of the available world data weak exchange degeneracy expectations for these reactions are at least qualitatively successful. We observe that the SU(2), SU(3) flavor symmetries successfully describe these hypercharge exchange processes and relate them to charge exchange via sum rules and equalities expressing flavor independence of the strong interaction; in particular, we derive and test on the available world data a mass broken SU(3) sum rule for ..pi../sup +/p ..-->.. K/sup +/..sigma../sup +/, ..pi../sup -/p ..-->.. K/sup 0/..lambda.., K/sup -/p ..-->.. anti K/sup 0/n and test over a wider range of momenta than before an earlier expression relating ..sigma..* and ..delta.. production. We also find at least qualitative agreement between quark model predictions for forward hypercharge exchange and the data, and we find that 90/sup 0/ hypercharge exchange cross sections also conform to the expectations of the quark constituent picture for hadrons.

  12. Applications of two-body Dirac equations to the meson spectrum with three versus two covariant interactions, SU(3) mixing, and comparison to a quasipotential approach

    SciTech Connect

    Crater, Horace W.; Schiermeyer, James

    2010-11-01

    In a previous paper, Crater and Van Alstine applied the two-body Dirac equations of constraint dynamics to quark-antiquark bound states using a relativistic extention of the Adler-Piran potential and compared their spectral results to those from other approaches which also considered meson spectroscopy as a whole and not in parts. In this paper, we explore in more detail the differences and similarities in an important subset of those approaches, the quasipotential approach. In the earlier paper, the transformation properties of the quark-antiquark potentials were limited to a scalar and an electromagnetic-like four-vector, with the former accounting for the confining aspects of the overall potential, and the latter the short range portion. The static Adler-Piran potential was first given an invariant form and then apportioned between those two different types of potentials. Here, we make a change in this apportionment that leads to a substantial improvement in the resultant spectroscopy by including a timelike confining vector potential over and above the scalar confining one and the electromagnetic-like vector potential. Our fit includes 19 more mesons than the earlier results and we modify the scalar portion of the potential in such a way that allows this formalism to account for the isoscalar mesons {eta} and {eta}{sup '} not included in the previous work. Continuing the comparisons of formalisms and spectral results made in the previous paper with other approaches to meson spectroscopy, we examine in this paper the quasipotential approach of Ebert, Faustov, and Galkin.

  13. Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions

    NASA Astrophysics Data System (ADS)

    Wang, Yimin; Bowman, Joel M.; Kamarchik, Eugene

    2016-03-01

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na+H2O, F-H2O, and Cl-H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20 000 coupled cluster CCSD(T) energies (awCVTZ basis for Na+ and aVTZ basis for Cl- and F-), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

  14. Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions.

    PubMed

    Wang, Yimin; Bowman, Joel M; Kamarchik, Eugene

    2016-03-21

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na(+)H2O, F(-)H2O, and Cl(-)H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20,000 coupled cluster CCSD(T) energies (awCVTZ basis for Na(+) and aVTZ basis for Cl(-) and F(-)), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs. PMID:27004880

  15. Orbits of Two-Body Problem From the Lenz Vector

    ERIC Educational Resources Information Center

    Caplan, S.; And Others

    1978-01-01

    Obtains the orbits with reference to the center of mass of two bodies under mutual universe square law interaction by use of the eccentricity vector which is equivalent to the Lenz vector within a numerical factor. (Author/SL)

  16. Towards a two-body neuroscience.

    PubMed

    Dumas, Guillaume

    2011-05-01

    Recent work from our interdisciplinary research group has revealed the emergence of inter-brain synchronization across multiple frequency bands during social interaction.1 Our findings result from the close collaboration between experts who study neural dynamics and developmental psychology. The initial aim of the collaboration was to combine knowledge from these two fields in order to move from a classical one-brain neuroscience towards a novel two-body approach. A new technique called hyperscanning has made it possible to study the neural activity of two individuals simultaneously. However, this advanced methodology was not sufficient in itself. What remained to be found was a way to promote real-time reciprocal social interaction between two individuals during brain recording and analyze the neural and behavioral phenomenon from an inter-individual perspective. Approaches used in infancy research to study nonverbal communication and coordination, between a mother and her child for example, have so far been poorly applied to neuroimaging experiments. We thus adapted an ecological two-body experiment inspired by the use of spontaneous imitation in preverbal infants. Numerous methodological and theoretical problems had to be overcome, ranging from the choice of a common time-unit for behavioral and brain recordings to the creation of algorithms for data processing between distant brain regions in different brains. This article will discuss the underlying issues and perspectives involved in elucidating the pathway from individual to social theories of cognition. PMID:21980578

  17. Towards a two-body neuroscience

    PubMed Central

    2011-01-01

    Recent work from our interdisciplinary research group has revealed the emergence of inter-brain synchronization across multiple frequency bands during social interaction.1 Our findings result from the close collaboration between experts who study neural dynamics and developmental psychology. The initial aim of the collaboration was to combine knowledge from these two fields in order to move from a classical one-brain neuroscience towards a novel two-body approach. A new technique called hyperscanning has made it possible to study the neural activity of two individuals simultaneously. However, this advanced methodology was not sufficient in itself. What remained to be found was a way to promote real-time reciprocal social interaction between two individuals during brain recording and analyze the neural and behavioral phenomenon from an inter-individual perspective. Approaches used in infancy research to study nonverbal communication and coordination, between a mother and her child for example, have so far been poorly applied to neuroimaging experiments. We thus adapted an ecological two-body experiment inspired by the use of spontaneous imitation in preverbal infants. Numerous methodological and theoretical problems had to be overcome, ranging from the choice of a common time-unit for behavioral and brain recordings to the creation of algorithms for data processing between distant brain regions in different brains. This article will discuss the underlying issues and perspectives involved in elucidating the pathway from individual to social theories of cognition. PMID:21980578

  18. Optimization of therapeutic proteins to delete T-cell epitopes while maintaining beneficial residue interactions.

    PubMed

    Parker, Andrew S; Griswold, Karl E; Bailey-Kellogg, Chris

    2011-04-01

    Exogenous enzymes, signaling peptides, and other classes of nonhuman proteins represent a potentially massive but largely untapped pool of biotherapeutic agents. Adapting a foreign protein for therapeutic use poses numerous design challenges. We focus here on one significant problem: modifying the protein to mitigate the immune response mounted against "non-self" proteins, while not adversely affecting the protein's stability or therapeutic activity. In order to propose such variants suitable for experimental evaluation, this paper develops a computational method to select sets of mutations predicted to delete immunogenic T-cell epitopes, as evaluated by a 9-mer potential, while simultaneously maintaining important residues and residue interactions, as evaluated by one- and two-body potentials. While this design problem is NP-hard, we develop an integer programming approach that works very well in practice. We demonstrate the effectiveness of our approach by developing plans for biotherapeutic proteins that, in previous studies, have been partially deimmunized via extensive experimental characterization and modification of limited segments. In contrast, our global optimization technique considers an entire protein and accounts for all residues, residue interactions, and epitopes in proposing candidates worth subjecting to experimental evaluation. PMID:21523929

  19. Two-body problem in graphene

    NASA Astrophysics Data System (ADS)

    Kezerashvili, Roman Ya.; Berman, Oleg L.; Ziegler, Klaus

    2013-04-01

    The description of excitons in graphene as a bound electron and hole using two dimensional Dirac equation is presented. We introduce a transformation to decouple the center-of-mass motion and the relative motion and analyze the two body problem with action-at-a-distance inter-particle Coulomb potential in a gapped graphene sheet. Then turn to a problem of two Dirac particles in two-layer graphene sheets separated by a dielectric, assuming that exciton in this system is formed by the electron located in the one graphene sheet and the hole located in the other. Assuming that interaction potential and both relative and center-of-mass kinetic energies are small compared to the gap energy, the analytical solution for the wave functions and energy spectrum of the exciton are found. The advantage of the consideration of exciton formed by an electron and a hole from two different graphene layers, separated by an insulating slab, is that the dielectric slab creates the barrier for the electron-hole recombination which increases the life-time of the exciton compared to the exciton formed by an electron and a hole in a single graphene layer.

  20. Two-body nonleptonic decays of D mesons

    NASA Astrophysics Data System (ADS)

    Buccella, F.; Lusignoli, M.; Miele, G.; Pugliese, A.

    1992-06-01

    The amplitudes for two-body Cabibbo allowed nonleptonic decays of D mesons are evaluated within the factorization approximation from the effective Hamiltonian including short distance QCD corrections to next-to-leading order. Annihilation and W-exchange contributions as well as final state interaction effects have been included and are in fact crucial to obtain agreement with the experimental data.

  1. Bioinformatic prediction and in vivo validation of residue-residue interactions in human proteins

    NASA Astrophysics Data System (ADS)

    Jordan, Daniel; Davis, Erica; Katsanis, Nicholas; Sunyaev, Shamil

    2014-03-01

    Identifying residue-residue interactions in protein molecules is important for understanding both protein structure and function in the context of evolutionary dynamics and medical genetics. Such interactions can be difficult to predict using existing empirical or physical potentials, especially when residues are far from each other in sequence space. Using a multiple sequence alignment of 46 diverse vertebrate species we explore the space of allowed sequences for orthologous protein families. Amino acid changes that are known to damage protein function allow us to identify specific changes that are likely to have interacting partners. We fit the parameters of the continuous-time Markov process used in the alignment to conclude that these interactions are primarily pairwise, rather than higher order. Candidates for sites under pairwise epistasis are predicted, which can then be tested by experiment. We report the results of an initial round of in vivo experiments in a zebrafish model that verify the presence of multiple pairwise interactions predicted by our model. These experimentally validated interactions are novel, distant in sequence, and are not readily explained by known biochemical or biophysical features.

  2. Computational learning on specificity-determining residue-nucleotide interactions

    PubMed Central

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Moses, Alan M.; Zhang, Zhaolei

    2015-01-01

    The protein–DNA interactions between transcription factors and transcription factor binding sites are essential activities in gene regulation. To decipher the binding codes, it is a long-standing challenge to understand the binding mechanism across different transcription factor DNA binding families. Past computational learning studies usually focus on learning and predicting the DNA binding residues on protein side. Taking into account both sides (protein and DNA), we propose and describe a computational study for learning the specificity-determining residue-nucleotide interactions of different known DNA-binding domain families. The proposed learning models are compared to state-of-the-art models comprehensively, demonstrating its competitive learning performance. In addition, we describe and propose two applications which demonstrate how the learnt models can provide meaningful insights into protein–DNA interactions across different DNA binding families. PMID:26527718

  3. The Nature of Intermolecular Interactions Between Aromatic Amino Acid Residues

    SciTech Connect

    Gervasio, Francesco; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo

    2002-05-01

    The nature of intermolecular interactions between aromatic amino acid residues has been investigated by a combination of molecular dynamics and ab initio methods. The potential energy surface of various interacting pairs, including tryptophan, phenilalanine, and tyrosine, was scanned for determining all the relevant local minima by a combined molecular dynamics and conjugate gradient methodology with the AMBER force field. For each of these minima, single-point correlated ab initio calculations of the binding energy were performed. The agreement between empirical force field and ab initio binding energies of the minimum energy structures is excellent. Aromatic-aromatic interactions can be rationalized on the basis of electrostatic and van der Waals interactions, whereas charge transfer or polarization phenomena are small for all intermolecular complexes and, particularly, for stacked structures.

  4. Terminal residue hydrophobicity modulates transmembrane helix-helix interactions.

    PubMed

    Ng, Derek P; Deber, Charles M

    2014-06-17

    Central to the formation of tertiary structure in membrane protein folding is the presence of amino acid sequence motifs (such as "small-XXX-small" segments) in the TM segments that promote interaction-compatible surfaces through which the TM α-helices interact. Here, we sought to elucidate additional factors that may work in tandem to dictate the ultimate interaction fate of TM-embedded segments. In this context, we used proteolipid protein (PLP), the major protein from central nervous system myelin for which mutant-dependent non-native oligomerization has been implicated in neurological disorders, to explore the specific effects of TM boundary residues (the membrane entry and exit points), keying on the secondary structure and self-association of peptides corresponding to the PLP TM2 α-helix (wild-type sequence ⁶⁶AFQYVIYGTASFFFLYGALLLAEGF⁹⁰). Using gel electrophoresis, circular dichroism, and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate (SDS), we found that mutation of F90 to residues such as A, I, L, or V maintains the onset of TM2-TM2 dimerization, whereas mutation to E, G, Q, N, S, or T abrogates dimer formation. We attribute this sensitivity to changes in local hydrophobicity, viz., a decrease in hydrophobicity reduces local lipid-peptide interactions, which in turn disrupts peptide α-helicity and hence the effectiveness of an incipient interaction-compatible surface. Our results show that the secondary structure and oligomeric state of PLP TM2 Lys-tagged peptides are significantly modulated by the specific nature of their C-terminal boundary residue, thus providing insight as to how point mutations, particularly where they produce disease states, can compromise the folding process. PMID:24857611

  5. Two-body nonleptonic decays of D mesons

    NASA Astrophysics Data System (ADS)

    Buccella, F.; Lusignoli, M.; Miele, G.; Pugliese, A.

    1992-01-01

    The amplitudes for two body Cabibbo allowed nonleptonic decays of D mesons are evaluated. The factorization approximation from the effective hamiltonian including short distance corrections to next to leading order are considered. Annihilation and W exchange contributions as well as final state interaction effects are crucial to obtain agreement with the experimental data. The decay amplitudes in the factorized approximation are given. The matrix elements of currents for c decay and annihilation terms are discussed. The model used to introduce final state interaction effects is described. The results and conclusions are presented. A discussion of decays to VV final states is given.

  6. Controller-structure interaction compensation using adaptive residual mode filters

    NASA Technical Reports Server (NTRS)

    Davidson, Roger A.; Balas, Mark J.

    1990-01-01

    It is not feasible to construct controllers for large space structures or large scale systems (LSS's) which are of the same order as the structures. The complexity of the dynamics of these systems is such that full knowledge of its behavior cannot by processed by today's controller design methods. The controller for system performance of such a system is therefore based on a much smaller reduced-order model (ROM). Unfortunately, the interaction between the LSS and the ROM-based controller can produce instabilities in the closed-loop system due to the unmodeled dynamics of the LSS. Residual mode filters (RMF's) allow the systematic removal of these instabilities in a matter which does not require a redesign of the controller. In addition RMF's have a strong theoretical basis. As simple first- or second-order filters, the RMF CSI compensation technique is at once modular, simple and highly effective. RMF compensation requires knowledge of the dynamics of the system modes which resulted in the previous closed-loop instabilities (the residual modes), but this information is sometimes known imperfectly. An adaptive, self-tuning RMF design, which compensates for uncertainty in the frequency of the residual mode, has been simulated using continuous-time and discrete-time models of a flexible robot manipulator. Work has also been completed on the discrete-time experimental implementation on the Martin Marietta flexible robot manipulator experiment. This paper will present the results of that work on adaptive, self-tuning RMF's, and will clearly show the advantage of this adaptive compensation technique for controller-structure interaction (CSI) instabilities in actively-controlled LSS's.

  7. Two-body bound states & the Bethe-Salpeter equation

    SciTech Connect

    Pichowsky, M.; Kennedy, M.; Strickland, M.

    1995-01-18

    The Bethe-Salpeter formalism is used to study two-body bound states within a scalar theory: two scalar fields interacting via the exchange of a third massless scalar field. The Schwinger-Dyson equation is derived using functional and diagrammatic techniques, and the Bethe-Salpeter equation is obtained in an analogous way, showing it to be a two-particle generalization of the Schwinger-Dyson equation. The authors also present a numerical method for solving the Bethe-Salpeter equation without three-dimensional reduction. The ground and first excited state masses and wavefunctions are computed within the ladder approximation and space-like form factors are calculated.

  8. Loschmidt echoes in two-body random matrix ensembles

    NASA Astrophysics Data System (ADS)

    Pižorn, Iztok; Prosen, Tomaž; Seligman, Thomas H.

    2007-07-01

    Fidelity decay is studied for quantum many-body systems with a dominant independent particle Hamiltonian resulting, e.g., from a mean field theory with a weak two-body interaction. The diagonal terms of the interaction are included in the unperturbed Hamiltonian, while the off-diagonal terms constitute the perturbation that distorts the echo. We give the linear response solution for this problem in a random matrix framework. While the ensemble average shows no surprising behavior, we find that the typical ensemble member as represented by the median displays a very slow fidelity decay known as “freeze.” Numerical calculations confirm this result and show that the ground state even on average displays the freeze. This may contribute to explanation of the “unreasonable” success of mean field theories.

  9. Mutation analysis of the Pip interaction domain reveals critical residues for protein–protein interactions

    PubMed Central

    Ortiz, Maria Antonia; Light, James; Maki, Richard A.; Assa-Munt, Nuria

    1999-01-01

    The PU.1 interaction partner (Pip) is a member of the interferon regulatory factor family that regulates gene expression through heterodimerization with the ETS transcription factor PU.1. Binding of Pip alone to DNA is weak, and usually it is recruited by phosphorylated PU.1 to form a strong ternary complex with specific DNA sequences. An approach combining sequence homology analysis, secondary structure predictions, and a precise mutational strategy has been used to determine critical residues within the Pip heterodimerization domain that contribute to ternary complex formation. We have delimited the Pip interaction domain to residues 245–422 by using deletion analysis. Site-directed mutagenesis of conserved polar amino acids within two predicted α-helices contained in this region, and which are highly conserved in the IRF family, confirmed the importance of these residues for Pip–PU.1 interaction with DNA as well as for trans-activation activity. Our results suggest the existence of a functional epitope essential for heterodimerization between Pip and PU.1 and possibly, in general, between interferon regulatory factor family members and their partners. PMID:10077581

  10. Interactions between the transmembrane domains of CD39: identification of interacting residues by yeast selection

    PubMed Central

    Paavilainen, Sari; Guidotti, Guido

    2015-01-01

    Rat CD39, a membrane-bound ectonucleoside triphosphate diphosphohydrolase that hydrolyzes extracellular nucleoside tri- and diphosphates, is anchored to the membrane by two transmembrane domains at the two ends of the molecule. The transmembrane domains are important for enzymatic activity, as mutants lacking one or both of these domains have a fraction of the enzymatic activity of the wild-type CD39. We investigated the interactions between the transmembrane domains by using a strain of yeast that requires surface expression of CD39 for growth. Random mutagenesis of selected amino acid residues in the N-terminal transmembrane domain revealed that the presence of charged amino acids at these positions prevents expression of functional protein. Rescue of the growth of these mutants by complementary mutations on selected residues of the C-terminal transmembrane domain indicates that there is contact between particular faces of the transmembrane domains. PMID:26258004

  11. Ultralow field magnetization reversal of two-body magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Li, Fei; Lu, Jincheng; Lu, Xiaofeng; Tang, Rujun; Sun, Z. Z.

    2016-08-01

    Field induced magnetization reversal was investigated in a system of two magnetic nanoparticles with uniaxial anisotropies and magnetostatic interaction. By using the micromagnetic simulation, ultralow switching field strength was found when the separation distance between the two particles reaches a critical small value (on nanometer scale) in the perpendicular configuration where the anisotropic axes of the two particles are perpendicular to the separation line. The switching field increases sharply when the separation is away from the critical distance. The ultralow field switching phenomenon was missed in the parallel configuration where both the anisotropic axes are aligned along the separation line of the two particles. The micromagnetic results are consistent with the previous theoretical prediction [J. Appl. Phys. 109, 104303 (2011)] where dipolar interaction between two single-domain magnetic particles was considered. Our present simulations offered further proofs and possibilities for the low-power applications of information storage as the two-body magnetic nanoparticles might be implemented as a composite information bit.

  12. The study of the role of the two-body force in determining level densities

    NASA Astrophysics Data System (ADS)

    Huang, Po-Lin

    The study of the role of the two-body force in determining level densities explored the characteristics of the two-body force and their impact on nuclear level densities. Two different theoretical approaches, the statistical mechanical model and moment expansion method, were used for the determining the impact of the two-body force on level densities. Discrete levels in the lower excitation region were compiled to provide information about level density systematics. A shell model calculation for a number of light nuclei allowed a test of the input parameters including single particle energies and two-body matrix elements. Generally good agreement was found between the calculated and observed energies of low-lying states. A comparison of the results obtained with three widely used interactions for nuclei with mass numbers 18 and 20 allowed some insight into the two-body interaction and the possibilities for improving it. For the level density calculations twenty four nuclei with mass numbers between 20 and 41 were used. Both the values from tabulations of low-lying levels and the results from previous studies of level densities at 7 Mev and at 20 Mev were included. It was found that the parameters derived from the higher energy measurements gave poor results at energies below 5 Mev. The discrepancies appeared to be related to problems in determining one of the two parameters involved. Two approaches were used in an effort to improve the precision of this parameter. Both were reasonably successful. Calculations of the level of density using a super conducting model within a statistical mechanical framework and a full two-body interaction utilizing a moment method approach were completed. Both gave a reasonably good representation of the data. An examination of the significance of the analysis for future study of the two body force and of nuclear level densities is presented.

  13. Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data

    PubMed Central

    Ahmad, Shandar; Mizuguchi, Kenji

    2011-01-01

    Computational prediction of residues that participate in protein-protein interactions is a difficult task, and state of the art methods have shown only limited success in this arena. One possible problem with these methods is that they try to predict interacting residues without incorporating information about the partner protein, although it is unclear how much partner information could enhance prediction performance. To address this issue, the two following comparisons are of crucial significance: (a) comparison between the predictability of inter-protein residue pairs, i.e., predicting exactly which residue pairs interact with each other given two protein sequences; this can be achieved by either combining conventional single-protein predictions or making predictions using a new model trained directly on the residue pairs, and the performance of these two approaches may be compared: (b) comparison between the predictability of the interacting residues in a single protein (irrespective of the partner residue or protein) from conventional methods and predictions converted from the pair-wise trained model. Using these two streams of training and validation procedures and employing similar two-stage neural networks, we showed that the models trained on pair-wise contacts outperformed the partner-unaware models in predicting both interacting pairs and interacting single-protein residues. Prediction performance decreased with the size of the conformational change upon complex formation; this trend is similar to docking, even though no structural information was used in our prediction. An example application that predicts two partner-specific interfaces of a protein was shown to be effective, highlighting the potential of the proposed approach. Finally, a preliminary attempt was made to score docking decoy poses using prediction of interacting residue pairs; this analysis produced an encouraging result. PMID:22194998

  14. Description and evaluation of nuclear masses based on residual proton-neutron interactions

    SciTech Connect

    Fu, G. J.; Lei, Y.; Jiang, H.; Zhao, Y. M.; Sun, B.; Arima, A.

    2011-09-15

    In this paper we study the residual proton-neutron interactions and make use of the systematics of these interactions to describe experimental data of nuclear masses and to predict some of the unknown masses. The odd-even effect staggering of the residual proton-neutron interaction between the last proton and the last neutron is found and argued in terms of pairing interactions. Two local mass relations, which work very accurately for masses of four neighboring nuclei, are discovered. The accuracy of our predicted masses for medium and heavy nuclei is competitive with that of the AME2003 extrapolations, with the virtue of simplicity.

  15. The Sharma-Parthasarathy stochastic two-body problem

    SciTech Connect

    Cresson, J.

    2015-03-15

    We study the Sharma-Parthasarathy stochastic two-body problem introduced by Sharma and Parthasarathy in [“Dynamics of a stochastically perturbed two-body problem,” Proc. R. Soc. A 463, 979-1003 (2007)]. In particular, we focus on the preservation of some fundamental features of the classical two-body problem like the Hamiltonian structure and first integrals in the stochastic case. Numerical simulations are performed which illustrate the dynamical behaviour of the osculating elements as the semi-major axis, the eccentricity, and the pericenter. We also derive a stochastic version of Gauss’s equations in the planar case.

  16. Exactness of wave functions from two-body exponential transformations in many-body quantum theory

    SciTech Connect

    Mazziotti, David A.

    2004-01-01

    Recent studies have considered the possibility that the exact ground-state wavefunction from any Hamiltonian with two-particle interactions may be generated from a single finite two-body exponential transformation acting on an arbitrary Slater determinant [Piecuch et al., Phys. Rev. Lett. 90, 113001 (2003)]. Using the Campbell-Baker-Hausdorff relation, we show that it is difficult for the variational minimum of this trial wave function to satisfy the contracted Schroedinger equation which is a necessary and sufficient condition for the wave function to satisfy the Schroedinger equation. A counterexample is presented through the Lipkin quasispin model with 4-50 fermions. When the number of fermions exceeds four, the wave function from a finite two-body exponential transformation is shown to be inexact. If the trial wave function ansatz is extended to include products of finite two-body exponential transformations acting on an arbitrary Slater-determinant reference, then we show that the ansatz includes the exact ground-state wave function from any Hamiltonian with only two-particle interactions. Connections between the two-body exponential transformation of the wave function and recent research on two-body exponential similarity transformations of the Hamiltonian [S.R. White, J. Chem. Phys. 117, 7472 (2002)] are discussed.

  17. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

    PubMed

    Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

    2014-12-12

    Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations. PMID:25311860

  18. Two-component Bose gases with one-body and two-body couplings

    NASA Astrophysics Data System (ADS)

    Lellouch, Samuel; Dao, Tung-Lam; Koffel, Thomas; Sanchez-Palencia, Laurent

    2013-12-01

    We study the competition between one-body and two-body couplings in weakly interacting two-component Bose gases, in particular as regards field correlations. We derive the mean-field theory for both ground-state and low-energy pair excitations in the general case where both one-body and two-body couplings are position dependent and the fluid is subjected to a state-dependent trapping potential. General formulas for phase and density correlations are also derived. Focusing on the case of homogeneous systems, we discuss the pair-excitation spectrum and the corresponding excitation modes, and use them to calculate correlation functions, including both quantum and thermal fluctuation terms. We show that the relative phase of the two components is imposed by that of the one-body coupling, while its fluctuations are determined by the modulus of the one-body coupling and by the two-body coupling. One-body coupling and repulsive two-body coupling cooperate to suppress relative-phase fluctuations, while attractive two-body coupling tends to enhance them. Further applications of the formalism presented here and extensions of our work are also discussed.

  19. Identification of Critical Paraoxonase 1 Residues Involved in High Density Lipoprotein Interaction.

    PubMed

    Gu, Xiaodong; Huang, Ying; Levison, Bruce S; Gerstenecker, Gary; DiDonato, Anthony J; Hazen, Leah B; Lee, Joonsue; Gogonea, Valentin; DiDonato, Joseph A; Hazen, Stanley L

    2016-01-22

    Paraoxonase 1 (PON1) is a high density lipoprotein (HDL)-associated protein with atherosclerosis-protective and systemic anti-oxidant functions. We recently showed that PON1, myeloperoxidase, and HDL bind to one another in vivo forming a functional ternary complex (Huang, Y., Wu, Z., Riwanto, M., Gao, S., Levison, B. S., Gu, X., Fu, X., Wagner, M. A., Besler, C., Gerstenecker, G., Zhang, R., Li, X. M., Didonato, A. J., Gogonea, V., Tang, W. H., et al. (2013) J. Clin. Invest. 123, 3815-3828). However, specific residues on PON1 involved in the HDL-PON1 interaction remain unclear. Unambiguous identification of protein residues involved in docking interactions to lipid surfaces poses considerable methodological challenges. Here we describe a new strategy that uses a novel synthetic photoactivatable and click chemistry-taggable phospholipid probe, which, when incorporated into HDL, was used to identify amino acid residues on PON1 that directly interact with the lipoprotein phospholipid surface. Several specific PON1 residues (Leu-9, Tyr-185, and Tyr-293) were identified through covalent cross-links with the lipid probes using affinity isolation coupled to liquid chromatography with on-line tandem mass spectrometry. Based upon the crystal structure for PON1, the identified residues are all localized in relatively close proximity on the surface of PON1, defining a domain that binds to the HDL lipid surface. Site-specific mutagenesis of the identified PON1 residues (Leu-9, Tyr-185, and Tyr-293), coupled with functional studies, reveals their importance in PON1 binding to HDL and both PON1 catalytic activity and stability. Specifically, the residues identified on PON1 provide important structural insights into the PON1-HDL interaction. More generally, the new photoactivatable and affinity-tagged lipid probe developed herein should prove to be a valuable tool for identifying contact sites supporting protein interactions with lipid interfaces such as found on cell membranes

  20. Two-body wear resistance of some indirect composite resins.

    PubMed

    Savabi, Omid; Nejatidanesh, Farahnaz; Shabanian, Mitra; Anbari, Zahra

    2011-06-01

    The aim of this study was to evaluate two-body wear of five indirect composites and compare them with enamel. Signum, belleGlass HP, SR Adoro, Dialog, GC Gradia and enamel were formed into cylinders (n = 10). Two-body abrasive wear rates were determined using a porcelain disk and a pin on disk apparatus. The height and weight loss of the specimens were measured by stereomicroscope and digital scale. The data were subjected to analysis of variance and Tukey HSD tests to determine significant differences (alpha = 0.05). GC Gradia showed significantly less wear resistance than the other materials. Enamel was more resistant than any of the tested composites. Within the limitations of this study it can be concluded that the type of resin, filler size and method of polymerization could have affect the two-body abrasion resistance of indirect composites. PMID:21780731

  1. Canine distemper virus envelope protein interactions modulated by hydrophobic residues in the fusion protein globular head.

    PubMed

    Avila, Mislay; Khosravi, Mojtaba; Alves, Lisa; Ader-Ebert, Nadine; Bringolf, Fanny; Zurbriggen, Andreas; Plemper, Richard K; Plattet, Philippe

    2015-01-15

    Membrane fusion for morbillivirus cell entry relies on critical interactions between the viral fusion (F) and attachment (H) envelope glycoproteins. Through extensive mutagenesis of an F cavity recently proposed to contribute to F's interaction with the H protein, we identified two neighboring hydrophobic residues responsible for severe F-to-H binding and fusion-triggering deficiencies when they were mutated in combination. Since both residues reside on one side of the F cavity, the data suggest that H binds the F globular head domain sideways. PMID:25355896

  2. Constraints on two-body lepton flavor violating decay processes

    SciTech Connect

    Nussinov, S.; Peccei, R. D.; Zhang, X. M.

    2001-01-01

    Simple ''unitarity inspired'' relations between two- and three-body lepton flavor violating decays are noted and discussed. In the absence of cancellations, the existing strong bounds on {mu}{yields}3e and {mu}{yields}e{gamma}{gamma} severely constrain two-body lepton flavor violating decays.

  3. Two-Body and Three-Body Atomic Recombination Reactions.

    ERIC Educational Resources Information Center

    Alvarino, Jose M.; Martinez, E.

    1983-01-01

    Discusses how, in some circumstances, a two-body reaction (association in absence of a third body) is the only possible association, and how reactions proceed in this case. Taking competition between two/three-body reactions into account, considers relative importance of such combinations and conditions under which the former can be competitive.…

  4. A transformation of the two-body problem

    NASA Technical Reports Server (NTRS)

    Bond, V. R.

    1985-01-01

    A transformation of the differential equations of motion of the two-body problem in the spherical coordinates to oscillator form is derived. It is shown that the independent variable transformation dt/ds = r squared is a transformation which makes the oscillator form possible.

  5. RANS Simulation of the Heave Response of a Two-Body Floating Point Wave Absorber: Preprint

    SciTech Connect

    Yu, Y.; Li, Y.

    2011-03-01

    A preliminary study on a two-body floating wave absorbers is presented in this paper. A Reynolds-Averaged Navier-Stokes computational method is applied for analyzing the hydrodynamic heave response of the absorber in operational wave conditions. The two-body floating wave absorber contains a float section and a submerged reaction section. For validation purposes, our model is first assumed to be locked. The two sections are forced to move together with each other. The locked single body model is used in a heave decay test, where the RANS result is validated with the experimental measurement. For the two-body floating point absorber simulation, the two sections are connected through a mass-spring-damper system, which is applied to simulate the power take-off mechanism under design wave conditions. Overall, the details of the flow around the absorber and its nonlinear interaction with waves are investigated, and the power absorption efficiency of the two-body floating wave absorber in waves with a constant value spring-damper system is examined.

  6. Contributions of conserved serine residues to the interactions of ligands with dopamine D2 receptors.

    PubMed

    Cox, B A; Henningsen, R A; Spanoyannis, A; Neve, R L; Neve, K A

    1992-08-01

    Four dopamine D2 receptor mutants were constructed, in each of which an alanine residue was substituted for one of four conserved serine residues, i.e., Ser-193, Ser-194, Ser-197, and Ser-391. Wild-type and mutant receptors were expressed transiently in COS-7 cells and stably in C6 glioma cells for analysis of ligand-receptor interactions. In radioligand binding assays, the affinity of D2 receptors for dopamine was decreased 50-fold by substitution of alanine for Ser-193, implicating this residue in the binding of dopamine. Each mutant had smaller decreases in affinity for one or more of the ligands tested, with no apparent relationship between the class of ligand and the pattern of mutation-induced changes in affinity, except that the potency of agonists was decreased by substitution for Ser-193. The potency of dopamine for inhibition of adenylyl cyclase was reduced substantially by substitution of alanine for Ser-193 or Ser-197. Mutation of Ser-194 led to a complete loss of efficacy for dopamine and p-tyramine, which would be consistent with an interaction between Ser-194 and the p-hydroxyl substituent of dopamine that is necessary for activation of the receptors to occur. Because mutation of the corresponding residues of beta 2-adrenergic receptors has very different consequences, we conclude that although the position of these serine residues is highly conserved among catecholamine receptors, and the residues as a group are important in ligand binding and activation of receptors by agonists, the function of each of the residues considered separately varies among catecholamine receptors. PMID:1321233

  7. Alterations of Nonconserved Residues Affect Protein Stability and Folding Dynamics through Charge-Charge Interactions.

    PubMed

    Tripathi, Swarnendu; Garcìa, Angel E; Makhatadze, George I

    2015-10-15

    Charge-charge interactions play an important role in thermal stability of proteins. We employed an all-atom, native-topology-based model with non-native electrostatics to explore the interplay between folding dynamics and stability of TNfn3 (the third fibronectin type III domain from tenascin-C). Our study elucidates the role of charge-charge interactions in modulating the folding energy landscape. In particular, we found that incorporation of explicit charge-charge interactions in the WT TNfn3 induces energetic frustration due to the presence of residual structure in the unfolded state. Moreover, optimization of the surface charge-charge interactions by altering the evolutionarily nonconserved residues not only increases the thermal stability (in agreement with previous experimental study) but also reduces the formation of residual structure and hence minimizes the energetic frustration along the folding route. We concluded that charge-charge interaction in the rationally designed TNfn3 plays an important role not only in enhancing the stability but also in assisting folding. PMID:26413861

  8. Solitary solutions to a relativistic two-body problem

    NASA Astrophysics Data System (ADS)

    Marcinkevicius, R.; Navickas, Z.; Ragulskis, M.; Telksnys, T.

    2016-06-01

    Necessary and sufficient conditions for the existence of solitary solutions to a generalized model of a two-body problem perturbed by small post-Newtonian relativistic term are derived in this paper. It is demonstrated that kink, bright and dark solitary solutions exist in the model, when the relativistic effects are treated as higher order perturbations. Numerical experiments are used to verify theoretical results.

  9. Atlas2bgeneral: Two-body resonance calculator

    NASA Astrophysics Data System (ADS)

    Gallardo, Tabaré

    2016-07-01

    For a massless test particle and given a planetary system, Atlas2bgeneral calculates all resonances in a given range of semimajor axes with all the planets taken one by one. Planets are assumed in fixed circular and coplanar orbits and the test particle with arbitrary orbit. A sample input data file to calculate the two-body resonances is available for use with the Fortran77 source code.

  10. Computational studies of protein-peptide interactions with systematic mutation of residues

    NASA Astrophysics Data System (ADS)

    Clare, Dominic F.; Clary, David C.

    2004-01-01

    The interactions between proteins and peptides in aqueous solution have been simulated using a molecular dynamics procedure with the systematic mutation of residues. An implicit solvent model has been used in post-processing to calculate the free energy of each of the complex, protein and peptide in solution and, subsequently, the binding free energy. Entropic contributions to the binding free energy have been estimated using classical ideal gas thermodynamics. A program has also been developed that systematically mutates each residue of the interacting peptide to alanine and determines the effect on the binding free energy. The interaction between the oncoprotein Mdm2 and the tumour suppressor peptide p53 has been used to test the method and reasonable agreement has been found with experiment and previous theoretical studies. The method has been extended to investigate the interaction between D10-p1, a mirror image D-peptide and potential Human Immunodeficiency Virus HIV-1 inhibitor, and IQN17, a model protein representing a potential drug target in the HIV-1 cell-cell fusion process. The key residues involved in the binding in each protein-peptide system have been identified and quantitative information on the significant factors in their importance have been obtained and compared with available experimental data.

  11. Interaction between dimer interface residues of native and mutated SOD1 protein: a theoretical study.

    PubMed

    Keerthana, S P; Kolandaivel, P

    2015-04-01

    Cu-Zn superoxide dismutase 1 (SOD1) is a highly conserved bimetallic protein enzyme, used for the scavenging the superoxide radicals (O2 (-)) produced due to aerobic metabolism in the mitochondrial respiratory chain. Over 100 mutations have been identified and found to be in the homodimeric structure of SOD1. The enzyme has to be maintained in its dimeric state for the structural stability and enzymatic activity. From our investigation, we found that the mutations apart from the dimer interface residues are found to affect the dimer stability of protein and hence enhancing the aggregation and misfolding tendency of mutated protein. The homodimeric state of SOD1 is found to be held together by the non-covalent interactions. The molecular dynamics simulation has been used to study the hydrogen bond interactions between the dimer interface residues of the monomers in native and mutated forms of SOD1 in apo- and holo-states. The results obtained by this analysis reveal the fact that the loss of hydrogen bond interactions between the monomers of the dimer is responsible for the reduced stability of the apo- and holo-mutant forms of SOD1. The conformers with dimer interface residues in native and mutated protein obtained by the molecular dynamics simulation is subjected to quantum mechanical study using M052X/6-31G(d) level of theory. The charge transfer between N-H···O interactions in the dimer interface residues were studied. The weak interaction between the monomers of the dimer accounts for the reduced dimerization and enhanced deformation energy in the mutated SOD1 protein. PMID:25578810

  12. Sulphur Atoms from Methionines Interacting with Aromatic Residues Are Less Prone to Oxidation.

    PubMed

    Aledo, Juan C; Cantón, Francisco R; Veredas, Francisco J

    2015-01-01

    Methionine residues exhibit different degrees of susceptibility to oxidation. Although solvent accessibility is a relevant factor, oxidation at particular sites cannot be unequivocally explained by accessibility alone. To explore other possible structural determinants, we assembled different sets of oxidation-sensitive and oxidation-resistant methionines contained in human proteins. Comparisons of the proteins containing oxidized methionines with all proteins in the human proteome led to the conclusion that the former exhibit a significantly higher mean value of methionine content than the latter. Within a given protein, an examination of the sequence surrounding the non-oxidized methionine revealed a preference for neighbouring tyrosine and tryptophan residues, but not for phenylalanine residues. However, because the interaction between sulphur atoms and aromatic residues has been reported to be important for the stabilization of protein structure, we carried out an analysis of the spatial interatomic distances between methionines and aromatic residues, including phenylalanine. The results of these analyses uncovered a new determinant for methionine oxidation: the S-aromatic motif, which decreases the reactivity of the involved sulphur towards oxidants. PMID:26597773

  13. Sulphur Atoms from Methionines Interacting with Aromatic Residues Are Less Prone to Oxidation

    PubMed Central

    Aledo, Juan C.; Cantón, Francisco R.; Veredas, Francisco J.

    2015-01-01

    Methionine residues exhibit different degrees of susceptibility to oxidation. Although solvent accessibility is a relevant factor, oxidation at particular sites cannot be unequivocally explained by accessibility alone. To explore other possible structural determinants, we assembled different sets of oxidation-sensitive and oxidation-resistant methionines contained in human proteins. Comparisons of the proteins containing oxidized methionines with all proteins in the human proteome led to the conclusion that the former exhibit a significantly higher mean value of methionine content than the latter. Within a given protein, an examination of the sequence surrounding the non-oxidized methionine revealed a preference for neighbouring tyrosine and tryptophan residues, but not for phenylalanine residues. However, because the interaction between sulphur atoms and aromatic residues has been reported to be important for the stabilization of protein structure, we carried out an analysis of the spatial interatomic distances between methionines and aromatic residues, including phenylalanine. The results of these analyses uncovered a new determinant for methionine oxidation: the S-aromatic motif, which decreases the reactivity of the involved sulphur towards oxidants. PMID:26597773

  14. Sulphur Atoms from Methionines Interacting with Aromatic Residues Are Less Prone to Oxidation

    NASA Astrophysics Data System (ADS)

    Aledo, Juan C.; Cantón, Francisco R.; Veredas, Francisco J.

    2015-11-01

    Methionine residues exhibit different degrees of susceptibility to oxidation. Although solvent accessibility is a relevant factor, oxidation at particular sites cannot be unequivocally explained by accessibility alone. To explore other possible structural determinants, we assembled different sets of oxidation-sensitive and oxidation-resistant methionines contained in human proteins. Comparisons of the proteins containing oxidized methionines with all proteins in the human proteome led to the conclusion that the former exhibit a significantly higher mean value of methionine content than the latter. Within a given protein, an examination of the sequence surrounding the non-oxidized methionine revealed a preference for neighbouring tyrosine and tryptophan residues, but not for phenylalanine residues. However, because the interaction between sulphur atoms and aromatic residues has been reported to be important for the stabilization of protein structure, we carried out an analysis of the spatial interatomic distances between methionines and aromatic residues, including phenylalanine. The results of these analyses uncovered a new determinant for methionine oxidation: the S-aromatic motif, which decreases the reactivity of the involved sulphur towards oxidants.

  15. A residue level protein-protein interaction model in electrolyte solutions

    NASA Astrophysics Data System (ADS)

    Song, Xueyu

    2014-03-01

    The osmotic second virial coefficients B2 are directly related to the solubility of protein molecules in electrolyte solutions and can be useful to narrow down the search parameter space of protein crystallization conditions. Using a residue level model of protein-protein interaction in electrolyte solutions B2 of bovine pancreatic trypsin inhibitor and lysozyme in various solution conditions such as salt concentration, pH and temperature are calculated using an extended Fast Multipole Methods in combination with the boundary element formulation. Overall, the calculated B2 are well correlated with the experimental observations for various solution conditions. In combination with our previous work on the binding affinity calculations of protein complexes it is demonstrated that our residue level model can be used as a reliable model to describe protein-protein interaction in solutions.

  16. Infinity Manifold in Popovici's Photogravitational Two-Body Problem

    NASA Astrophysics Data System (ADS)

    Mioc, Vasile

    The two-body problem associated to the modified photogravitational law proposed by the Romanian astronomer Constantin Popovici is being resumed. After studying the equilibria and the collision manifold (Mioc and Blaga 2001) via the powerful tools of the qualitative analysis, here we tackle the escape/capture orbits. We start from the equations of motion established in the quoted paper, then we apply a mixed sequence of McGehee-type transformations of the first and second kind, obtaining new regular motion equations. In this way the infinity singularity is replaced by the infinity manifold, pasted on the phase space. The flow on this manifold is entirely described, pointing out special features.

  17. Heuristic judgment of mass ratio in two-body collisions.

    PubMed

    Gilden, D L; Proffitt, D R

    1994-12-01

    The logic of judging relative mass from a two-body collision is developed from data presented by Runeson and Vedeler (1993). Data from two experiments are analyzed on a point-by-point basis, and strong support for the theory that mass-ratio judgments are mediated by separate speed and angle heuristics is shown. This analysis is accomplished by reducing the collision event to two elementary features: the presence of ricochet and the ratio of exit speeds. The heuristics that both ricochet and greater exit speed specify relative lightness are shown to explain the basic patterns of data presented by Runeson and Vedeler. PMID:7816541

  18. Two-body problem of core-region coupled magnetic vortex stacks

    NASA Astrophysics Data System (ADS)

    Hänze, Max; Adolff, Christian F.; Velten, Sven; Weigand, Markus; Meier, Guido

    2016-02-01

    The dynamics of all four combinations of possible polarity and circularity states in a stack of two vortices is investigated by time-resolved scanning transmission x-ray microscopy. The vortex stacks are excited by unidirectional magnetic fields leading to a collective oscillation. Four different modes are observed that depend on the relative polarizations and circularities of the stacks. They are excited to a driven oscillation. We observe a repulsive and attractive interaction of the vortex cores depending on their relative polarizations. The nonlinearity of this core interaction results in different trajectories that describe a two-body problem.

  19. The RING 2.0 web server for high quality residue interaction networks.

    PubMed

    Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

    2016-07-01

    Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. PMID:27198219

  20. The RING 2.0 web server for high quality residue interaction networks

    PubMed Central

    Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C.E.

    2016-01-01

    Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico–chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain–domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π–π stacking and π–cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. PMID:27198219

  1. Conserved Residues of the Human Mitochondrial Holocytochrome c Synthase Mediate Interactions with Heme

    PubMed Central

    2015-01-01

    C-type cytochromes are distinguished by the covalent attachment of a heme cofactor, a modification that is typically required for its subsequent folding, stability, and function. Heme attachment takes place in the mitochondrial intermembrane space and, in most eukaryotes, is mediated by holocytochrome c synthase (HCCS). HCCS is the primary component of the eukaryotic cytochrome c biogenesis pathway, known as System III. The catalytic function of HCCS depends on its ability to coordinate interactions between its substrates: heme and cytochrome c. Recent advancements in the recombinant expression and purification of HCCS have facilitated comprehensive analyses of the roles of conserved residues in HCCS, as demonstrated in this study. Previously, we proposed a four-step model describing HCCS-mediated cytochrome c assembly, identifying a conserved histidine residue (His154) as an axial ligand to the heme iron. In this study, we performed a systematic mutational analysis of 17 conserved residues in HCCS, and we provide evidence that the enzyme contains two heme-binding domains. Our data indicate that heme contacts mediated by residues within these domains modulate the dynamics of heme binding and contribute to the stability of the HCCS–heme–cytochrome c steady state ternary complex. While some residues are essential for initial heme binding (step 1), others impact the subsequent release of the holocytochrome c product (step 4). Certain HCCS mutants that were defective in heme binding were corrected for function by exogenous aminolevulinic acid (ALA, the precursor to heme). This chemical “correction” supports the proposed role of heme binding for the corresponding residues. PMID:25054239

  2. Simple ``invariance'' of two-body decay kinematics

    NASA Astrophysics Data System (ADS)

    Agashe, Kaustubh; Franceschini, Roberto; Kim, Doojin

    2013-09-01

    We study the two-body decay of a mother particle into a massless daughter. We further assume that the mother particle is unpolarized and has a generic boost distribution in the laboratory frame. In this case, we show analytically that the laboratory frame energy distribution of the massless decay product has a peak, whose location is identical to the (fixed) energy of that particle in the rest frame of the corresponding mother particle. Given its simplicity and “invariance” under changes in the boost distribution of the mother particle, our finding should be useful for the determination of masses of mother particles. In particular, we anticipate that such a procedure will then not require a full reconstruction of this two-body decay chain (or, for that matter, information about the rest of the event). With this eventual goal in mind, we make a proposal for extracting the peak position by fitting the data to a well-motivated analytic function describing the shape of such an energy distribution. This fitting function is then tested on the theoretical prediction for top quark pair production and its decay, and it is found to be quite successful in this regard. As a proof of principle of the usefulness of our observation, we apply it for measuring the mass of the top quark at the LHC, using simulated data and including experimental effects.

  3. Institutional Solutions to the ``Two-Body Problem"

    NASA Astrophysics Data System (ADS)

    Knezek, P.

    2005-05-01

    The Committee on the Status of Women (CSWA), in conjunction with the Employment Committee (EC), will hold a special session that will focus on institutional approaches to solving the ``two-body problem". In step with the national employment trend, for the majority of astronomers with partners, those partners work outside the home. This is particularly true for female astronomers, who generally are married to professionals (and often to other astronomers). Academic and professional institutions that employ the majority of astronomers are now beginning to recognize the importance of addressing what has come to be known as the ``two-body" problem in order to attract and retain the best scientists. A few of those institutions are making pioneering efforts to create pro-active approaches to the issue of dual-career couples. The special session will feature two or three speakers involved with the administration at institutions with pro-active policies. This special session will be coupled with the normal afternoon CSWA session, which will focus on the other side of the issue - how dual-career couples have successfully approached the issue at institutions that do NOT have proactive policies.

  4. Empirical residual neutron-proton interaction in odd-odd nuclei

    NASA Astrophysics Data System (ADS)

    Wu, Zheying; Changizi, S. A.; Qi, Chong

    2016-03-01

    Two types of average neutron-proton interaction formulas are compared: In the first type, neutron-proton interactions for even-even and odd-A nuclei extracted from experimental binding energies show a smooth behavior as a function of mass number A and are dominated by the contribution from the symmetry energy. Whereas in the second type large systematic staggering is seen between even-A and odd-A nuclei. This deviation is understood in terms of the additional neutron-proton interaction in odd-odd nuclei relative to the neighboring even-even and odd-A systems. We explore three possible ways to extract this additional interaction from the binding energy difference of neighboring nuclei. The extracted interactions are positive in nearly all cases and show weak dependence on the mass number. The empirical interactions are also compared with theoretical values extracted from recent nuclear mass models where large unexpected fluctuations are seen in certain nuclei. The reproduction of the residual neutron-proton interaction and the correction of those irregular fluctuations can be a good criterion for the refinement of those mass models.

  5. Visualized kinematics code for two-body nuclear reactions

    NASA Astrophysics Data System (ADS)

    Lee, E. J.; Chae, K. Y.

    2016-05-01

    The one or few nucleon transfer reaction has been a great tool for investigating the single-particle properties of a nucleus. Both stable and exotic beams are utilized to study transfer reactions in normal and inverse kinematics, respectively. Because many energy levels of the heavy recoil from the two-body nuclear reaction can be populated by using a single beam energy, identifying each populated state, which is not often trivial owing to high level-density of the nucleus, is essential. For identification of the energy levels, a visualized kinematics code called VISKIN has been developed by utilizing the Java programming language. The development procedure, usage, and application of the VISKIN is reported.

  6. The role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational study.

    PubMed

    Bonet, Jaume; Caltabiano, Gianluigi; Khan, Abdul Kareem; Johnston, Michael A; Corbí, Carles; Gómez, Alex; Rovira, Xavier; Teyra, Joan; Villà-Freixa, Jordi

    2006-04-01

    Finding why protein-protein interactions (PPIs) are so specific can provide a valuable tool in a variety of fields. Statistical surveys of so-called transient complexes (like those relevant for signal transduction mechanisms) have shown a tendency of polar residues to participate in the interaction region. Following this scheme, residues in the unbound partners have to compete between interacting with water or interacting with other residues of the protein. On the other hand, several works have shown that the notion of active site electrostatic preorganization can be used to interpret the high efficiency in enzyme reactions. This preorganization can be related to the instability of the residues important for catalysis. In some enzymes, in addition, conformational changes upon binding to other proteins lead to an increase in the activity of the enzymatic partner. In this article the linear response approximation version of the semimacroscopic protein dipoles Langevin dipoles (PDLD/S-LRA) model is used to evaluate the stability of several residues in two phosphate hydrolysis enzymes upon complexation with their activating partners. In particular, the residues relevant for PPI and for phosphate hydrolysis in the CDK2/Cyclin A and Ras/GAP complexes are analyzed. We find that the evaluation of the stability of residues in these systems can be used to identify not only active site regions but it can also be used as a guide to locate "hot spots" for PPIs. We also show that conformational changes play a major role in positioning interfacing residues in a proper "energetic" orientation, ready to interact with the residues in the partner protein surface. Thus, we extend the preorganization theory to PPIs, extrapolating the results we obtained from the above-mentioned complexes to a more general case. We conclude that the correlation between stability of a residue in the surface and the likelihood that it participates in the interaction can be a general fact for transient

  7. A detailed study of nonperturbative solutions of two-body Dirac equations

    SciTech Connect

    Crater, H.W.; Becker, R.L.; Wong, C.Y.; Van Alstine, P.

    1992-12-01

    In quark model calculations of the meson spectrums fully covariant two-body Dirac equations dictated by Dirac's relativistic constraint mechanics gave a good fit to the entire meson mass spectrum for light quark mesons as well as heavy quark mesons with constituent world scalar and vector potentials depending on just one or two parameters. In this paper, we investigate the properties of these equations that made them work so well by solving them numerically for quantum electrodynamics (QED) and related field theories. The constraint formalism generates a relativistic quantum mechanics defined by two coupled Dirac equations on a sixteen component wave function which contain Lorentz covariant constituent potentials that are initially undetermined. An exact Pauli reduction leads to a second order relativistic Schroedinger-like equation for a reduced eight component wave function determined by an effective interaction -- the quasipotential. We first determine perturbatively to lowest order the relativistic quasipotential for the Schroedinger-like equation by comparing that form with one derived from the Bethe-Salpeter equation. Insertion of this perturbative information into the minimal interaction structures of the two-body Dirac equations then completely determines their interaction structures. Then we give a procedure for constructing the full sixteen component solution to our coupled first-order Dirac equations from a solution of the second order equation for the reduced wave function. Next, we show that a perturbative treatment of these equations yields the standard spectral results for QED and related interactions.

  8. A detailed study of nonperturbative solutions of two-body Dirac equations

    SciTech Connect

    Crater, H.W.; Becker, R.L.; Wong, C.Y.; Van Alstine, P.

    1992-12-01

    In quark model calculations of the meson spectrums fully covariant two-body Dirac equations dictated by Dirac`s relativistic constraint mechanics gave a good fit to the entire meson mass spectrum for light quark mesons as well as heavy quark mesons with constituent world scalar and vector potentials depending on just one or two parameters. In this paper, we investigate the properties of these equations that made them work so well by solving them numerically for quantum electrodynamics (QED) and related field theories. The constraint formalism generates a relativistic quantum mechanics defined by two coupled Dirac equations on a sixteen component wave function which contain Lorentz covariant constituent potentials that are initially undetermined. An exact Pauli reduction leads to a second order relativistic Schroedinger-like equation for a reduced eight component wave function determined by an effective interaction -- the quasipotential. We first determine perturbatively to lowest order the relativistic quasipotential for the Schroedinger-like equation by comparing that form with one derived from the Bethe-Salpeter equation. Insertion of this perturbative information into the minimal interaction structures of the two-body Dirac equations then completely determines their interaction structures. Then we give a procedure for constructing the full sixteen component solution to our coupled first-order Dirac equations from a solution of the second order equation for the reduced wave function. Next, we show that a perturbative treatment of these equations yields the standard spectral results for QED and related interactions.

  9. Non multa, sed multum: Future lessons from two-prong, two-body decays of beauty

    SciTech Connect

    Bigi, I.I.; Stech, B.

    1987-12-01

    There are four two-body, two-prong decays modes of B mesons and two for beauty baryons and they are quite rare, i.e., their branching ratios are not expected to exceed the script O(10/sup -4/) level. Yet a detailed study of their relative rates with a sensitivity level of 10/sup -5/ can yield unique and important information on strong interactions. If the evolution of these reactions in proper time can be traced then, under favorable conditions, one can analyze B/sup 0/ - anti B/sup 0/ mixing and CP invariance in a detailed way. 4 refs.

  10. Structural Evolution in Atomic Nuclei: Residual Interactions, Quantum Phase Transitions and the Emergence of Collectivity

    SciTech Connect

    Casten, R. F.

    2007-10-26

    A synoptic view of the evolution of structure with Z and N in nuclei is beginning to emerge from the confiuence of new experimental results on phase transitional behavior, newly proposed many-body symmetries for critical point nuclei, a new generation of solvable collective models, powerful approaches to viewing the systematics of nuclear properties based on simple models of residual interactions, and advances in microscopic calculations of medium mass and heavy nuclei. A recent compilation of nuclear masses has contributed by permitting empirical extractions of new p-n interaction strengths of the last protons with the last neutrons in many nuclei across the nuclear chart. A number of these developments will be discussed with an eye to the opportunities and challenges they provide for the future, especially in the era of next-generation exotic beam facihties throughout the world.

  11. Modulating Transmembrane α-Helix Interactions through pH-Sensitive Boundary Residues.

    PubMed

    Ng, Derek P; Deber, Charles M

    2016-08-01

    Changes in pH can alter the structure and activity of proteins and may be used by the cell to control molecular function. This coupling can also be used in non-native applications through the design of pH-sensitive biomolecules. For example, the pH (low) insertion peptide (pHLIP) can spontaneously insert into a lipid bilayer when the pH decreases. We have previously shown that the α-helicity and helix-helix interactions of the TM2 α-helix of the proteolipid protein (PLP) are sensitive to the local hydrophobicity at its C-terminus. Given that there is an ionizable residue (Glu-88) at the C-terminus of this transmembrane (TM) segment, we hypothesized that changing the ionization state of this residue through pH may alter the local hydrophobicity of the peptide enough to affect both its secondary structure and helix-helix interactions. To examine this phenomenon, we synthesized peptide analogues of the PLP TM2 α-helix (wild-type sequence (66)AFQYVIYGTASFFFLYGALLLAEGF(90)). Using circular dichroism and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate, we found that a decrease in pH increases both peptide α-helicity and the extent of self-association. This pH-dependent effect is due specifically to the presence of Glu-88 at the C-terminus. Additional experiments in which Phe-90 was mutated to residues of varying hydrophobicities indicated that the strength of this effect is dependent on the local hydrophobicity near Glu-88. Our results have implications for the design of TM peptide switches and improve our understanding of how membrane protein structure and activity can be regulated through local molecular environmental changes. PMID:27434090

  12. Orbit determination with the two-body integrals

    NASA Astrophysics Data System (ADS)

    Gronchi, G. F.; Dimare, L.; Milani, A.

    2010-07-01

    We investigate a method to compute a finite set of preliminary orbits for solar system bodies using the first integrals of the Kepler problem. This method is thought for the applications to the modern sets of astrometric observations, where often the information contained in the observations allows only to compute, by interpolation, two angular positions of the observed body and their time derivatives at a given epoch; we call this set of data attributable. Given two attributables of the same body at two different epochs we can use the energy and angular momentum integrals of the two-body problem to write a system of polynomial equations for the topocentric distance and the radial velocity at the two epochs. We define two different algorithms for the computation of the solutions, based on different ways to perform elimination of variables and obtain a univariate polynomial. Moreover we use the redundancy of the data to test the hypothesis that two attributables belong to the same body ( linkage problem). It is also possible to compute a covariance matrix, describing the uncertainty of the preliminary orbits which results from the observation error statistics. The performance of this method has been investigated by using a large set of simulated observations of the Pan-STARRS project.

  13. Material loss in two-body collisions during planet formation

    NASA Astrophysics Data System (ADS)

    Werner, J.; Schäfer, C.; Maindl, T. I.; Burger, C.; Speith, R.

    2016-02-01

    During the formation process of a terrestrial planet, a planetary embryo does not only accrete smaller dust particles but also suffers collisions with larger planetesimals. When simulating these collisions, most N-body codes treat them as perfect merging events, i.e. the resulting body's mass is the sum of the previous ones. In our work, we aim to determine whether this assumption is a justified simplification, specifically focusing on bodies containing volatile elements, such as water. To analyze this, we have developed a new Smooth Particle Hydrodynamics (SPH) code that includes elasto-plastic dynamics, a damage model for brittle materials and self gravity. It makes use of the Compute Unified Device Architecture (CUDA) and runs on modern GPU architectures which allows for higher resolution in less calculation time. This enables us to take a precise look at two-body collisions and determine the amount of both transferred and ejected mass according to specific parameters such as mass ratio of impactor and target, porosity, impact velocity, impact angle and water distribution.

  14. On the Mass Difference Between pi and rho Using a Relativistic Two-Body Model

    SciTech Connect

    Wong, Cheuk-Yin; Kim, Byeong-Noh; Crater, H. W.; Yoon, Jin-Hee

    2012-01-01

    The big mass difference between the pion(pi) and rho meson(rho) possibly originated from the spin-dependent nature of the interactions in the two states since these two states are similar except for spin. Both pi and rho are quark-antiquark systems which can be treated using the two-body Dirac equations (TBDE) of constraint dynamics. This relativistic approach for the two-body system has the advantage over the non-relativistic treatment in the sense that the spin-dependent nature is automatically coming out from the formalism. We employed Dirac's relativistic constraint dynamics to describe quark-antiquark systems. Within this formalism, the 16-component Dirac equation is reduced to the 4-component 2nd-order differential equation and the radial part of this equation is simply a Schroedinger-type equation with various terms calculated from the basic radial potential. We used a modified Richardson potential for quark-antiquark systems which satisfies the conditions of confinement and asymptotic freedom. We obtained the wave functions for these two mesons which are not singular at short distances. We also found that the cancellation between the Darwin and spin-spin interaction terms occurs in the pi mass but not in the rho mass, and this is the main source of the big difference in the two meson masses.

  15. One plus two-body random matrix ensembles with parity: Density of states and parity ratios

    SciTech Connect

    Vyas, Manan; Srivastava, P. C.; Kota, V. K. B.

    2011-06-15

    One plus two-body embedded Gaussian orthogonal ensemble of random matrices with parity [EGOE(1+2)-{pi}] generated by a random two-body interaction (modeled by GOE in two-particle spaces) in the presence of a mean field for spinless identical fermion systems is defined, generalizing the two-body ensemble with parity analyzed by Papenbrock and Weidenmueller [Phys. Rev. C 78, 054305 (2008)], in terms of two mixing parameters and a gap between the positive ({pi}=+) and negative ({pi}=-) parity single-particle (sp) states. Numerical calculations are used to demonstrate, using realistic values of the mixing parameters appropriate for some nuclei, that the EGOE(1+2)-{pi} ensemble generates Gaussian form (with corrections) for fixed parity eigenvalue densities (i.e., state densities). The random matrix model also generates many features in parity ratios of state densities that are similar to those predicted by a method based on the Fermi-gas model for nuclei. We have also obtained, by applying the formulation due to Chang et al. [Ann. Phys. (NY) 66, 137 (1971)], a simple formula for the spectral variances defined over fixed-(m{sub 1},m{sub 2}) spaces, where m{sub 1} is the number of fermions in the positive parity sp states and m{sub 2} is the number of fermions in the negative parity sp states. Similarly, using the binary correlation approximation, in the dilute limit, we have derived expressions for the lowest two-shape parameters. The smoothed densities generated by the sum of fixed-(m{sub 1},m{sub 2}) Gaussians with lowest two-shape corrections describe the numerical results in many situations. The model also generates preponderance of positive parity ground states for small values of the mixing parameters, and this is a feature seen in nuclear shell-model results.

  16. Possible chirality in the doubly-odd {sup 198}Tl nucleus: Residual interaction at play

    SciTech Connect

    Lawrie, E. A.; Lawrie, J. J.; Bark, R. A.; Mullins, S. M.; Murray, S. H. T.; Vymers, P. A.; Maliage, S. M.; Masiteng, P. L.; Ramashidzha, T. M.; Sharpey-Schafer, J. F.; Shirinda, O.; Vieu, Ch.; Schueck, C.; Lindsay, R.; Mabala, G. K.; Ragnarsson, I.

    2008-08-15

    A candidate for chiral bands was found in {sup 198}Tl for the first time in a mass region of oblate (or nonaxial with {gamma}{>=}30 deg.) deformed nuclei. Two bands show very similar quasiparticle alignments, moments of inertia, and B(M1)/B(E2) ratios. They have a relative excitation energy of about 500 keV and different patterns of energy staggering. Calculations using the two-quasiparticle-plus-triaxial-rotor model with residual proton-neutron interaction included show that a triaxial deformation with {gamma}{approx}44 deg. agrees very well with all the experimental observations. Furthermore, considerable energy staggering for both partner bands was calculated for this {pi}h{sub 9/2} x {nu}i{sub 13/2}{sup -1} configuration at {gamma}{approx}30 deg., suggesting that chiral bands may have substantial energy staggering.

  17. Ultralow field magnetization reversal of two-body Stoner particles system

    NASA Astrophysics Data System (ADS)

    Li, Fei; Lu, Xiaofeng; Tang, Rujun; Sun, Z. Z.

    Magnetic mechanism of nanoparticles has attracted explosive attention in the development of modern information industry. On the base of Landau-Lifshitz-Gilbert equation, we studied the magnetization reversal in a system of two Stoner particles with uniaxial anisotropies and static magnetic interaction. Using micromagnetic simulation, two typical geometrical configurations of perpendicular(PERP) and parallel(PARA) configuration where the diameter of each particle is 20nm are considered. We found that when the separation between two particles has 23nm in PERP configuration ultralow switching field strength, 17mT can be realized, which satisfies the zero-field condition in our previous works[J. Appl. Phys. 109, 104303(2011)] according to the chosen parameters of cobalt material. For other separation values the switching field are multiple of lowest field. However, in PARA configuration the switching field changes with the separation faintly. This two-body system considered in our work might be implement as a composite information bit and our results offer further possibilities for its applications in information storage and/or fast magnetic response. Ultralow field magnetization reversal of two-body Stoner particles system.

  18. A Failure to Communicate: MYOSIN RESIDUES INVOLVED IN HYPERTROPHIC CARDIOMYOPATHY AFFECT INTER-DOMAIN INTERACTION.

    PubMed

    Kronert, William A; Melkani, Girish C; Melkani, Anju; Bernstein, Sanford I

    2015-12-01

    Our molecular modeling studies suggest a charge-dependent interaction between residues Glu-497 in the relay domain and Arg-712 in the converter domain of human β-cardiac myosin. To test the significance of this putative interaction, we generated transgenic Drosophila expressing indirect flight muscle myosin with charge reversal mutations in the relay (E496R) or converter (R713E). Each mutation yielded dramatic reductions in myosin Ca-ATPase activity (~80%) as well as in basal (~67%) and actin-activated (~84%) Mg-ATPase activity. E496R myosin-induced in vitro actin-sliding velocity was reduced by 71% and R713E myosin permitted no actin motility. Indirect flight muscles of late pupae from each mutant displayed disrupted myofibril assembly, with adults having severely abnormal myofibrils and no flight ability. To understand the molecular basis of these defects, we constructed a putative compensatory mutant that expresses myosin with both E496R and R713E. Intriguingly, ATPase values were restored to ~73% of wild-type and actin-sliding velocity increased to 40%. The double mutation suppresses myofibril assembly defects in pupal indirect flight muscles and dramatically reduces myofibril disruption in young adults. Although sarcomere organization is not sustained in older flies and flight ability is not restored in homozygotes, young heterozygotes fly well. Our results indicate that this charge-dependent interaction between the myosin relay and converter domains is essential to the mechanochemical cycle and sarcomere assembly. Furthermore, the same inter-domain interaction is disrupted when modeling human β-cardiac myosin heavy chain cardiomyopathy mutations E497D or R712L, implying that abolishing this salt bridge is one cause of the human disease. PMID:26446785

  19. Is There a Preferential Interaction between Cholesterol and Tryptophan Residues in Membrane Proteins?†

    PubMed Central

    Holt, Andrea; de Almeida, Rodrigo F. M.; Nyholm, Thomas K. M.; Loura, Luís M. S.; Daily, Anna E.; Staffhorst, Rutger W. H. M.; Rijkers, Dirk T. S.; Koeppe, Roger E.; Prieto, Manuel; Killian, J. Antoinette

    2008-01-01

    Recently, several indications have been found that suggest a preferential interaction between cholesterol and tryptophan residues located near the membrane–water interface. The aim of this study was to investigate by direct methods how tryptophan and cholesterol interact with each other and what the possible consequences are for membrane organization. For this purpose, we used cholesterol-containing model membranes of dimyristoylphosphatidylcholine (DMPC) in which a transmembrane model peptide with flanking tryptophans [acetyl-GWW(LA)8LWWA-amide], called WALP23, was incorporated to mimic interfacial tryptophans of membrane proteins. These model systems were studied with two complementary methods. (1) Steady-state and time-resolved Förster resonance energy transfer (FRET) experiments employing the fluorescent cholesterol analogue dehydroergosterol (DHE) in combination with a competition experiment with cholesterol were used to obtain information about the distribution of cholesterol in the bilayer in the presence of WALP23. The results were consistent with a random distribution of cholesterol which indicates that cholesterol and interfacial tryptophans are not preferentially located next to each other in these bilayer systems. (2) Solid-state 2H NMR experiments employing either deuterated cholesterol or indole ring-deuterated WALP23 peptides were performed to study the orientation and dynamics of both molecules. The results showed that the quadrupolar splittings of labeled cholesterol were not affected by an interaction with tryptophan-flanked peptides and, vice versa, that the quadrupolar splittings of labeled indole rings in WALP23 are not significantly influenced by addition of cholesterol to the bilayer. Therefore, both NMR and fluorescence spectroscopy results independently show that, at least in the model systems studied here, there is no evidence for a preferential interaction between cholesterol and tryptophans located at the bilayer interface. PMID

  20. Polyunsaturated fatty acids inhibit Kv1.4 by interacting with positively charged extracellular pore residues.

    PubMed

    Farag, N E; Jeong, D; Claydon, T; Warwicker, J; Boyett, M R

    2016-08-01

    Polyunsaturated fatty acids (PUFAs) modulate voltage-gated K(+) channel inactivation by an unknown site and mechanism. The effects of ω-6 and ω-3 PUFAs were investigated on the heterologously expressed Kv1.4 channel. PUFAs inhibited wild-type Kv1.4 during repetitive pulsing as a result of slowing of recovery from inactivation. In a mutant Kv1.4 channel lacking N-type inactivation, PUFAs reversibly enhanced C-type inactivation (Kd, 15-43 μM). C-type inactivation was affected by extracellular H(+) and K(+) as well as PUFAs and there was an interaction among the three: the effect of PUFAs was reversed during acidosis and abolished on raising K(+) Replacement of two positively charged residues in the extracellular pore (H508 and K532) abolished the effects of the PUFAs (and extracellular H(+) and K(+)) on C-type inactivation but had no effect on the lipoelectric modulation of voltage sensor activation, suggesting two separable interaction sites/mechanisms of action of PUFAs. Charge calculations suggest that the acidic head group of the PUFAs raises the pKa of H508 and this reduces the K(+) occupancy of the selectivity filter, stabilizing the C-type inactivated state. PMID:27281482

  1. Accurate prediction of helix interactions and residue contacts in membrane proteins.

    PubMed

    Hönigschmid, Peter; Frishman, Dmitrij

    2016-04-01

    Accurate prediction of intra-molecular interactions from amino acid sequence is an important pre-requisite for obtaining high-quality protein models. Over the recent years, remarkable progress in this area has been achieved through the application of novel co-variation algorithms, which eliminate transitive evolutionary connections between residues. In this work we present a new contact prediction method for α-helical transmembrane proteins, MemConP, in which evolutionary couplings are combined with a machine learning approach. MemConP achieves a substantially improved accuracy (precision: 56.0%, recall: 17.5%, MCC: 0.288) compared to the use of either machine learning or co-evolution methods alone. The method also achieves 91.4% precision, 42.1% recall and a MCC of 0.490 in predicting helix-helix interactions based on predicted contacts. The approach was trained and rigorously benchmarked by cross-validation and independent testing on up-to-date non-redundant datasets of 90 and 30 experimental three dimensional structures, respectively. MemConP is a standalone tool that can be downloaded together with the associated training data from http://webclu.bio.wzw.tum.de/MemConP. PMID:26851352

  2. Study on fluorescence spectra of chlorothalonil residues and the interaction between chlorothalonil and Chinese herbal medicines.

    PubMed

    Ji, Ren-dong; Zhao, Zhi-min; Chen, Meng-lan; Wang, Le-xin; Zhu, Xing-yue

    2015-02-01

    The fluorescence spectrum was studied for the chlorothalonil (0.2928 mg x mL(-1)) using spectrofluorophotometer. The experiment results showed that the characteristic peaks (352 and 366 nm) are found in the spectrum of chlorothalonil standard solution when the excitation wavelength is 320 nm. And it was found that the shoulder peak gradually disappeared at 366 nm, while the fluorescence peak is stable at 352 nm with the decline of the solution concentration The exponential functional relationship between the concentration of chlorothalonil and fluorescence intensity at 352 nm was obtained, and its correlation coefficient is 0.999. The experimental results are consistent with the theoretical formula about fluorescence intensity and concentration The prediction model functions were also obtained through the liner fitting to the chlorothalonil solution of low concentration, and the correlation coefficient is 0. 995. The limit of detection (LOD) is 0.0188 microg x mL(-1), the limit of quantification (LOQ) is 0.0627 microg x mL(-1), and the linear range is 0.0627-28.45 microg x mL(-1). And fluorescence spectra were studied for the mixed system of astragalus, medlar and chlorothalonil. It was found that the fluorescence intensity of chlorothalonil solution is all declined with the addition of two kinds of Chinese Herbal Medicines, which indicates that there is an interaction between them. The decay rate of fluorescence intensity was obtained which is 88.5% and 99.7%, respectively. Then the model functions were established between fluorescence intensity and the volume of addition, and the correlation coefficient is 0.994 and 0.997, respectively. This study provides the experimental foundation for the detection of chlorothalonil residues using fluorescence spectrum. It is shown that it is possible to detect pesticide residues of chlorothalonil using fluorescence spectra directly, and the relevant parameter value satisfied the requirement of testing standard. Therefore

  3. Effect of Tensor Range in Nuclear Two-Body Problems

    DOE R&D Accomplishments Database

    Feshbach, H.; Schwinger, J.; Harr, J. A.

    1949-11-01

    The interaction between neutron and proton in the triplet state is investigated, a wide variation in the values of both central and tensor ranges are included; the per cent D state in the deuteron and the effective triplet range have been computed; the results are applied tot he discussion of the magnetic moment of the deuteron, the photoelectric disintegration of the deuteron, and neutron-proton scattering.

  4. Non-Collision Singularities in the Planar Two-Center-Two-Body Problem

    NASA Astrophysics Data System (ADS)

    Xue, Jinxin; Dolgopyat, Dmitry

    2016-08-01

    In this paper, we study a restricted four-body problem called the planar two-center-two-body problem. In the plane, we have two fixed centers Q 1 and Q 2 of masses 1, and two moving bodies Q 3 and Q 4 of masses {μ≪ 1}. They interact via Newtonian potential. Q 3 is captured by Q 2, and Q 4 travels back and forth between two centers. Based on a model of Gerver, we prove that there is a Cantor set of initial conditions that lead to solutions of the Hamiltonian system whose velocities are accelerated to infinity within finite time avoiding all earlier collisions. This problem is a simplified model for the planar four-body problem case of the Painlevé conjecture.

  5. Non-Collision Singularities in the Planar Two-Center-Two-Body Problem

    NASA Astrophysics Data System (ADS)

    Xue, Jinxin; Dolgopyat, Dmitry

    2016-06-01

    In this paper, we study a restricted four-body problem called the planar two-center-two-body problem. In the plane, we have two fixed centers Q 1 and Q 2 of masses 1, and two moving bodies Q 3 and Q 4 of masses {μ≪ 1} . They interact via Newtonian potential. Q 3 is captured by Q 2, and Q 4 travels back and forth between two centers. Based on a model of Gerver, we prove that there is a Cantor set of initial conditions that lead to solutions of the Hamiltonian system whose velocities are accelerated to infinity within finite time avoiding all earlier collisions. This problem is a simplified model for the planar four-body problem case of the Painlevé conjecture.

  6. The residual interaction of bound nucleons-two-nucleon matrix elements deduced from transfer experiments

    NASA Astrophysics Data System (ADS)

    Daehnick, W. W.

    1983-07-01

    Matrix elements for the effective two-nucleon interaction have been deduced from the population of multiplets near closed shells as observed in direct transfer reactions. In the evaluation, the limited purity of such multiples was taken into consideration, typically by weighting the observed fractions of the two-nucleon configurations by their spectroscopic strenghts and by using the resulting energy centroids. In a few cases, off-diagonal matrix elements are available from empirical wave funcitons. The systematic errors for particle-particle matrix elements extracted directly and those obtained from Pandya transformations were found to go in opposite directions. In some cases, this feautre of the empirical mehtod could be used to suggest upper and lower “bounds” for the extracted matrix elements. Diagonal matrix elements for the empirical residual interaction show a number of features suggestive of an underlying simplicity in the interaction of bound nucleons. Within experimental uncertainties (of about 10% for T=0 matrix elements) the monopole parts of the matrix elements are fit well with a simple A-0.75 dependence, and the data available to date do not reveal any significant monopole dependence on the quantum numbers of the interacting nucleons. The usefulness of scaling is suggested. Generally, diagonal matrix elements EJ( j1, j2) normalized by the extracted A-dependent monopole strength agree within expected experimental uncertainties whether derived from particle-particle or particle-hole multiples and whether extracted from the beginning or the end of a major shell. For values J≠0, the diagonal EJ( j2) matrix elements seem to follow two universal functions which depend on the semi-classical coupling angles θ 12, but are otherwise independent on j. For j1≠ j2 several “typical” functions ƒ(θ 12) can be constructed which fit subsets of the data and differ in a predictable way. The general features of the bound-nucleon interaction appear

  7. Interactions between allelochemicals and the microbial community affect weed suppresion following cover crop residue incorporation into soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study is to understand how soil microorganisms interact with cover crop-derived allelochemicals to suppress weed germination and growth following cover crop residue incorporation. We conducted a time series experiment by crossing sterilized and non-sterilized soil with four dif...

  8. Two-quasiparticle isomer, E1 hindrances and residual interactions in {sup 172}Tm

    SciTech Connect

    Hughes, R. O.; Lane, G. J.; Dracoulis, G. D.; Kibedi, T.; Nieminen, P.; Watanabe, H.

    2008-04-15

    The structure of the neutron-rich nucleus {sup 172}Tm has been studied using incomplete fusion of {sup 7}Li on an {sup 170}Er target at 30 MeV. A 190-{mu}s isomer at an excitation energy of 476 keV was identified using chopped beams and {gamma}-ray spectroscopy. The isomer decays with very inhibited E1 transitions to the rotational bands based on the parallel and antiparallel couplings of the {nu}5/2{sup -}[512] x {pi}1/2{sup +}[411] configuration, the latter (K{sup {pi}}=2{sup -}) being the ground state. The isomeric state has been assigned J{sup {pi}}=6{sup +}, arising from the energetically favored (parallel) coupling of the {nu}5/2{sup -}[512] x {pi}7/2{sup -}[523] configuration. The proton-neutron residual interaction was deduced for the configuration of the isomeric state and is found to agree with previous empirical studies.

  9. Residue Coulomb Interaction Among Isobars and Its Influence in Symmetry Energy of Neutron-Rich Fragment

    NASA Astrophysics Data System (ADS)

    Ma, Chun-Wang; Wang, Shan-Shan; Zhang, Yan-Li; Zhao, Yi-Long; Wei, Hui-Ling

    2015-09-01

    The residue Coulomb interaction (RCI), which affects the result of symmetry-energy coefficient of neutron-rich nucleus in isobaric yield ratio (IYR) method, is difficult to be determined. Four RCI approximations are investigated: (i) The M1-RCI adopting the ac/T (the ratio of Coulomb energy coefficient to temperature) determined from the IYR of mirror-nucleus fragments; (ii) The M2-RCI by fitting the difference between IYRs; (iii) The M3-RCI adopting the standard Coulomb energy at a temperature T = 2 MeV; and (iv) Neglecting the RCI among isobars. The M1-, M2- and M3-RCI are no larger than 0.4. In particular, the M2-RCI is very close to zero. The effects of RCI in asym/T of fragment are also studied. The M1- and M4-asym/T are found to be the lower and upper limitations of asym/T, respectively. The M2-asym/T overlaps the M4-asym/T, which indicates that the M2-RCI is negligible in the IYR method, and the RCI among the three isobars can be neglected. The relative consistent low values of M3-asym/T (7.5 ± 2.5) are found in very neutron-rich isobars. Supported by the Program for Science & Technology Innovation Talents in Universities of Henan Province (13HASTIT046), and Young Teacher Project in Henan Normal University (HNU), China

  10. On the question of current conservation for the two-body Dirac equations of constraint theory

    NASA Astrophysics Data System (ADS)

    Lienert, Matthias

    2015-08-01

    The two-body Dirac (2BD) equations of constraint theory are of special interest not only in view of applications for phenomenological calculations of mesonic spectra but also because they avoid no-go theorems about relativistic interactions. Furthermore, they provide a quantum mechanical description in a manifestly Lorentz invariant way using the concept of a multi-time wave function. In this paper, we place them into the context of the multi-time formalism of Dirac, Tomonaga and Schwinger for the first time. A general physical and mathematical framework is outlined and the mechanism which permits relativistic interaction is identified. The main requirement derived from the general framework is the existence of conserved tensor currents with a positive component which can play the role of a probability density. We analyze this question for a general class of 2BD equations thoroughly and comprehensively. While the free Dirac current is not conserved, it is possible to find replacements. Improving on previous research, we achieve definite conclusions whether restrictions of the function space or of the interaction terms can guarantee the positive definiteness of the currents—and whether such restrictions are physically adequate. The consequences of the results are drawn, with respect to both applied and foundational perspectives.

  11. Standardization of a Volumetric Displacement Measurement for Two-Body Abrasion Scratch Test Data Analysis

    NASA Technical Reports Server (NTRS)

    Street, K. W. Jr.; Kobrick, R. L.; Klaus, D. M.

    2011-01-01

    A limitation has been identified in the existing test standards used for making controlled, two-body abrasion scratch measurements based solely on the width of the resultant score on the surface of the material. A new, more robust method is proposed for analyzing a surface scratch that takes into account the full three-dimensional profile of the displaced material. To accomplish this, a set of four volume- displacement metrics was systematically defined by normalizing the overall surface profile to denote statistically the area of relevance, termed the Zone of Interaction. From this baseline, depth of the trough and height of the plowed material are factored into the overall deformation assessment. Proof-of-concept data were collected and analyzed to demonstrate the performance of this proposed methodology. This technique takes advantage of advanced imaging capabilities that allow resolution of the scratched surface to be quantified in greater detail than was previously achievable. When reviewing existing data analysis techniques for conducting two-body abrasive scratch tests, it was found that the ASTM International Standard G 171 specified a generic metric based only on visually determined scratch width as a way to compare abraded materials. A limitation to this method was identified in that the scratch width is based on optical surface measurements, manually defined by approximating the boundaries, but does not consider the three-dimensional volume of material that was displaced. With large, potentially irregular deformations occurring on softer materials, it becomes unclear where to systematically determine the scratch width. Specifically, surface scratches on different samples may look the same from a top view, resulting in an identical scratch width measurement, but may vary in actual penetration depth and/or plowing deformation. Therefore, two different scratch profiles would be measured as having identical abrasion properties, although they differ

  12. Interaction between soil mineralogy and the application of crop residues on aggregate stability and hydraulic conductivity of the soil

    NASA Astrophysics Data System (ADS)

    Lado, M.; Kiptoon, R.; Bar-Tal, A.; Wakindiki, I. I. C.; Ben-Hur, M.

    2012-04-01

    One of the main goals of modern agriculture is to achieve sustainability by maintaining crop productivity while avoiding soil degradation. Intensive cultivation could lead to a reduction in soil organic matter that could affect the structure stability and hydraulic conductivity of the soil. Moreover, crops extract nutrients from the soil that are taken away from the field when harvested, and as a consequence, the addition of fertilizers to the soil is necessary to maintain crop productivity. One way to deal with these problems is to incorporate crop residues into the soil after harvest. Crop residues are a source of organic matter that could improve soil physical properties, such as aggregate stability and soil hydraulic conductivity. However, this effect could vary according to other soil properties, such as clay content, clay mineralogy, and the presence of other cementing materials in the soil (mainly carbonates and aluminum and iron oxides). In the present work, the interaction between the addition of chickpea crop residues to the soil and clay mineralogy on aggregate stability and saturated hydraulic conductivity were studied. Chickpea plant residues were added at a rate of 0.5% (w/w) to smectitic, kaolinitic, illitic and non-phyllosilicate soils from different regions. The soils without (control) and with chickpea residues were incubated for 0, 3, 7 and 30 days, and the saturated hydraulic conductivity of the soils was measured in columns after each incubation time. The response of hydraulic conductivity to the addition of residues and incubation time was different in the soils with various mineralogies, although in general, the addition of chickpea residues increased the saturated hydraulic conductivity as compared with the control soils. This positive effect of crop residues on hydraulic conductivity was mainly a result of improved aggregate stability and resistance to slaking during wetting.

  13. Complete characterization of the ground-space structure of two-body frustration-free Hamiltonians for qubits

    SciTech Connect

    Ji Zhengfeng; Wei Zhaohui; Zeng Bei

    2011-10-15

    The problem of finding the ground state of a frustration-free Hamiltonian carrying only two-body interactions between qubits is known to be solvable in polynomial time. It is also shown recently that, for any such Hamiltonian, there is always a ground state that is a product of single- or two-qubit states. However, it remains unclear whether the whole ground space is of any succinct structure. Here, we give a complete characterization of the ground space of any two-body frustration-free Hamiltonian of qubits. Namely, it is a span of tree tensor network states of the same tree structure. This characterization allows us to show that the problem of determining the ground-state degeneracy is as hard as, but no harder than, its classical analog.

  14. Critical regions and residues for self-interaction of grapevine leafroll-associated virus 2 protein p24.

    PubMed

    Liu, Qing; Guo, Ran; Li, Mingjun; Feng, Ming; Wang, Xianyou; Wang, Qi; Cheng, Yuqin

    2016-07-15

    The 24-kDa protein (p24) encoded by grapevine leafroll-associated virus 2 (GLRaV-2) is an RNA-silencing suppressor. In this work, a yeast two-hybrid system (YTHS) and bimolecular fluorescence complementation analyses showed that GLRaV-2 p24 can interact with itself, and that this interaction occurs in the cytoplasm of Nicotiana benthamiana cells. To identify the functional region(s) and crucial amino acid residues required for p24 self-interaction, various truncated and substitution mutants were generated. YTHS assay showed that in both homologous pairing and pairing with the wild-type p24, the functional regions mapped to aa 10-180 or 1-170 which contain, respectively, all seven α-helices or the first six α-helices and the N-terminal end (aa 1-9) of the protein. When only the full-length p24 was an interaction partner, the functional region of aa 1-170 could be further mapped to aa 1-140 which contains four α-helices plus most of the fifth α-helix. Further analysis with substitution mutants demonstrated that hydrophobic residues I35/F38/V85/V89/W149 and V162/L169/L170, which may, respectively, mediate the inter-domain interaction of the same p24 monomer and the tail-to-tail association between two p24 counterparts, are crucial for homotypic p24-p24 interaction. In addition, substitution of two basic residues-R2 or R86-of p24, which may play important functional roles in RNA binding, did not seem to affect self-interaction of the mutants in yeast but had obvious effects in plant cells. Taken together, our results demonstrate the functional regions and crucial amino acids for p24 self-interaction. PMID:27084306

  15. Experimental Investigations on Fatigue Damage and Residual Properties of Interacting Notched Woven E-Glass/Epoxy Composite

    NASA Astrophysics Data System (ADS)

    Bhaskara Rao, Pathakokila; Rama Krishna, Avasarala; Ramji, Koona; Satya Devi, Ambadipudi

    2015-10-01

    The interacting notched laminates of plain weave E-glass fiber reinforced with epoxy were fatigued at predetermined frequency in tension-tension to investigate the fatigue damage and residual properties. The results from stress-life curves summarize that damage growing around the notches due to stress concentration is the underlying cause for the variation in fatigue strengths among the geometrically different specimens considered. The residual strength and modulus decay with respect to cycle number at 50 % of the ultimate tensile strength were investigated. It is evident from the experimental data that the residual strength decreases with cycle number and increases due to redistribution of stress around the notches. The detailed study of the damage development under cyclic loads also explains the causes of modulus reduction for all the laminate geometries.

  16. Three-body scattering hypervolume for ultracold atoms with a model two-body potential

    NASA Astrophysics Data System (ADS)

    Zhu, Shangguo; Tan, Shina

    2015-05-01

    It has been known that the three-boson low energy effective interaction influences the dynamic and the static properties of many bosons, including the ground state energies of dilute Bose-Einstein condensates. The three-body scattering hypervolume, which is a three-body analogue of the two-body scattering length, characterizes this effective interaction. Surprisingly, knowledge of this fundamental quantity has still been lacking, except for hard sphere bosons and bosons with large scattering length. For bosons with a soft-ball potential--the repulsive Gaussian potential, we determine the scattering hypervolume by solving the three-body Schrödinger equation numerically, and matching the solution with the asymptotic expansions for the wave function at large hyperradii. Our analyses of the three-body scattering hypervolume can be extended to the long-range Van der Waals potential. They will be necessary in the precise understanding of the energetics and dynamics of three, more, or many ultracold bosonic atoms.

  17. Standardization of a Volumetric Displacement Measurement for Two-Body Abrasion Scratch Test Data Analysis

    NASA Technical Reports Server (NTRS)

    Kobrick, Ryan L.; Klaus, David M.; Street, Kenneth W., Jr.

    2010-01-01

    A limitation has been identified in the existing test standards used for making controlled, two-body abrasion scratch measurements based solely on the width of the resultant score on the surface of the material. A new, more robust method is proposed for analyzing a surface scratch that takes into account the full three-dimensional profile of the displaced material. To accomplish this, a set of four volume displacement metrics are systematically defined by normalizing the overall surface profile to statistically denote the area of relevance, termed the Zone of Interaction (ZOI). From this baseline, depth of the trough and height of the ploughed material are factored into the overall deformation assessment. Proof of concept data were collected and analyzed to demonstrate the performance of this proposed methodology. This technique takes advantage of advanced imaging capabilities that now allow resolution of the scratched surface to be quantified in greater detail than was previously achievable. A quantified understanding of fundamental particle-material interaction is critical to anticipating how well components can withstand prolonged use in highly abrasive environments, specifically for our intended applications on the surface of the Moon and other planets or asteroids, as well as in similarly demanding, harsh terrestrial settings

  18. The Role of Putative Phosphatidylserine-Interactive Residues of Tissue Factor on Its Coagulant Activity at the Cell Surface

    PubMed Central

    Ansari, Shabbir A.; Pendurthi, Usha R.; Sen, Prosenjit; Rao, L. Vijaya Mohan

    2016-01-01

    Exposure of phosphatidylserine (PS) on the outer leaflet of the cell membrane is thought to play a critical role in tissue factor (TF) decryption. Recent molecular dynamics simulation studies suggested that the TF ectodomain may directly interact with PS. To investigate the potential role of TF direct interaction with the cell surface phospholipids on basal TF activity and the enhanced TF activity following the decryption, one or all of the putative PS-interactive residues in the TF ectodomain were mutated and tested for their coagulant activity in cell systems. Out of the 9 selected TF mutants, five of them -TFS160A, TFS161A, TFS162A, TFK165A, and TFD180A- exhibited a similar TF coagulant activity to that of the wild-type TF. The specific activity of three mutants, TFK159A, TFS163A, and TFK166A, was reduced substantially. Mutation of the glycine residue at the position 164 markedly abrogated the TF coagulant activity, resulting in ~90% inhibition. Mutation of all nine lipid binding residues together did not further decrease the activity of TF compared to TFG164A. A similar fold increase in TF activity was observed in wild-type TF and all TF mutants following the treatment of THP-1 cells with either calcium ionomycin or HgCl2, two agents that are commonly used to decrypt TF. Overall, our data show that a few select TF residues that are implicated in interacting with PS contribute to the TF coagulant activity at the cell surface. However, our data also indicate that TF regions outside of the putative lipid binding region may also contribute to PS-dependent decryption of TF. PMID:27348126

  19. The Role of Putative Phosphatidylserine-Interactive Residues of Tissue Factor on Its Coagulant Activity at the Cell Surface.

    PubMed

    Ansari, Shabbir A; Pendurthi, Usha R; Sen, Prosenjit; Rao, L Vijaya Mohan

    2016-01-01

    Exposure of phosphatidylserine (PS) on the outer leaflet of the cell membrane is thought to play a critical role in tissue factor (TF) decryption. Recent molecular dynamics simulation studies suggested that the TF ectodomain may directly interact with PS. To investigate the potential role of TF direct interaction with the cell surface phospholipids on basal TF activity and the enhanced TF activity following the decryption, one or all of the putative PS-interactive residues in the TF ectodomain were mutated and tested for their coagulant activity in cell systems. Out of the 9 selected TF mutants, five of them -TFS160A, TFS161A, TFS162A, TFK165A, and TFD180A- exhibited a similar TF coagulant activity to that of the wild-type TF. The specific activity of three mutants, TFK159A, TFS163A, and TFK166A, was reduced substantially. Mutation of the glycine residue at the position 164 markedly abrogated the TF coagulant activity, resulting in ~90% inhibition. Mutation of all nine lipid binding residues together did not further decrease the activity of TF compared to TFG164A. A similar fold increase in TF activity was observed in wild-type TF and all TF mutants following the treatment of THP-1 cells with either calcium ionomycin or HgCl2, two agents that are commonly used to decrypt TF. Overall, our data show that a few select TF residues that are implicated in interacting with PS contribute to the TF coagulant activity at the cell surface. However, our data also indicate that TF regions outside of the putative lipid binding region may also contribute to PS-dependent decryption of TF. PMID:27348126

  20. Identification of an 11-residue portion of CTP-phosphocholine cytidylyltransferase that is required for enzyme-membrane interactions.

    PubMed Central

    Yang, J; Wang, J; Tseu, I; Kuliszewski, M; Lee, W; Post, M

    1997-01-01

    CTP-phosphocholine cytidylyltransferase (CT) is a key regulatory enzyme in the biosynthesis of phosphatidylcholine (PC) in many cells. Enzyme-membrane interactions appear to play an important role in CT activation. A putative membrane-binding domain appears to be located between residues 236 and 293 from the N-terminus. To map the membrane-binding domain more precisely, glutathione S-transferase fusion proteins were prepared that contained deletions of various domains in this putative lipid-binding region. The fusion proteins were assessed for their binding of [3H]PC/oleic acid vesicles. Fusion proteins encompassing residues 267-277 bound to PC/oleic acid vesicles, whereas fragments lacking this region exhibited no specific binding to the lipid vesicles. The membrane-binding characteristics of the CT fusion proteins were also examined using intact lung microsomes. Only fragments encompassing residues 267-277 competed with full-length 125I-labelled CT, expressed in recombinant Sf9 insect cells, for microsomal membrane binding. To investigate the role of this region in PC biosynthesis, A549 and L2 cells were transfected with cDNA for CT mutants under the control of a glucocorticoid-inducible long terminal repeat (LTR) promoter. Induction of CT mutants containing residues 267-277 in transfectants resulted in reduced PC synthesis. The decrease in PC synthesis was accompanied by a shift in endogenous CT activity from the particulate to the soluble fraction. Expression of CT mutants lacking this region in A549 and L2 cells did not affect PC formation and subcellular distribution of CT activity. These results suggest that the CT region located between residues 267 and 277 from the N-terminus is required for the interaction of CT with membranes. PMID:9224626

  1. Residual meson-meson interaction from lattice gauge simulation in a simple QED{sub 2+1} model

    SciTech Connect

    J. Canosa; H. Fiebig

    1995-08-01

    The residual interaction for a meson-meson system is computed utilizing the cumulant, or cluster, expansion of the momentum-space time correlation matrix. The cumulant expansion serves to define asymptotic, or free, meson-meson operators. The definition of an effective interaction is then based on a comparison of the full (interacting) and the free (noninteracting) time correlation matrices. The proposed method, which may straight forwardly be transcribed to other hadron-hadron systems, here is applied to a simple 2+1 dimensional U(1) lattice gauge model tuned such that it is confining. Fermions are treated in the staggered scheme. The effective interaction exhibits a repulsive core and attraction at intermediate relative distances. These findings are consistent with an earlier study of the same model utilizing L{umlt u}scher's method where scattering phase shifts are obtained directly.

  2. Lorentz Boosted Potential for a Two-Body System with Unequal Masses

    NASA Astrophysics Data System (ADS)

    Kamada, H.; Polyzou, W. N.; Witała, H.; Miyagawa, K.

    2014-04-01

    We produce a Lorentz boosted two-body potential for particles of different mass that is phase equivalent to a given realistic non-relativistic two-body potential. The relativistic potential is related to the nonrelativistic potential using the Coester-Pieper-Serduke scheme, which ensures that the same scattering wave functions are obtained from the relativistic and non-relativistic potentials. This implies that the phase shifts are identical functions of the relative momentum. To construct the potential we use an iterative scheme that generalizes one that has been applied successfully to two-body systems with equal masses.

  3. Two-Body Electrodisintegration of $^3$He at High Momentum Transfer

    SciTech Connect

    R. Schiavilla; O. Benhar; A. Kievsky; L.E. Marcucci; M. Viviani

    2005-08-01

    The {sup 3}He (e,e{prime}p)d reaction is studied using an accurate three-nucleon bound state wave function, a model for the electromagnetic current operator including one- and two-body terms, and the Glauber approximation for the treatment of final state interactions. In contrast to earlier studies, the profile operator in the Glauber expansion is derived from a nucleon-nucleon scattering amplitude, which retains its full spin and isospin dependence and is consistent with phase-shift analyses of two-nucleon scattering data. The amplitude is boosted from the center-of-mass frame, where parameterizations for it are available, to the frame where rescattering occurs. Exact Monte Carlo methods are used to evaluate the relevant matrix elements of the electromagnetic current operator. The predicted cross section is found to be in quantitative agreement with the experimental data for values of the missing momentum p{sub m} in the range (0--700) MeV/c, but underestimates the data at p{sub m} {approx} 1 GeV/c by about a factor of two. However, the longitudinal-transverse asymmetry, measured up to p{sub m} {approx} 600 MeV/c, is well reproduced by theory. A critical comparison is carried out between the results obtained in the present work and those of earlier studies.

  4. HIGH TEMPERATURE INTERACTIONS BETWEEN RESIDUAL OIL ASH AND DISPERSED KAOLINITE POWDERS

    EPA Science Inventory

    The potential use of sorbents to manage ultrafine ash aerosol emissions from residual oil combustion was investigated using a downfired 82-kW-rated laboratory-scale refractory-lined combustor. The major constituents were vanadium (V), iron (Fe), nickel, (Ni) and zinc (Zn). Of the...

  5. Role of acidic residues in helices TH8-TH9 in membrane interactions of the diphtheria toxin T domain.

    PubMed

    Ghatak, Chiranjib; Rodnin, Mykola V; Vargas-Uribe, Mauricio; McCluskey, Andrew J; Flores-Canales, Jose C; Kurnikova, Maria; Ladokhin, Alexey S

    2015-04-01

    The pH-triggered membrane insertion of the diphtheria toxin translocation domain (T domain) results in transferring the catalytic domain into the cytosol, which is relevant to potential biomedical applications as a cargo-delivery system. Protonation of residues is suggested to play a key role in the process, and residues E349, D352 and E362 are of particular interest because of their location within the membrane insertion unit TH8-TH9. We have used various spectroscopic, computational and functional assays to characterize the properties of the T domain carrying the double mutation E349Q/D352N or the single mutation E362Q. Vesicle leakage measurements indicate that both mutants interact with the membrane under less acidic conditions than the wild-type. Thermal unfolding and fluorescence measurements, complemented with molecular dynamics simulations, suggest that the mutant E362Q is more susceptible to acid destabilization because of disruption of native intramolecular contacts. Fluorescence experiments show that removal of the charge in E362Q, and not in E349Q/D352N, is important for insertion of TH8-TH9. Both mutants adopt a final functional state upon further acidification. We conclude that these acidic residues are involved in the pH-dependent action of the T domain, and their replacements can be used for fine tuning the pH range of membrane interactions. PMID:25875295

  6. De novo design of protein-protein interactions through modification of inter-molecular helix-helix interface residues.

    PubMed

    Yagi, Sota; Akanuma, Satoshi; Yamagishi, Manami; Uchida, Tatsuya; Yamagishi, Akihiko

    2016-05-01

    For de novo design of protein-protein interactions (PPIs), information on the shape and chemical complementarity of their interfaces is generally required. Recent advances in computational PPI design have allowed for de novo design of protein complexes, and several successful examples have been reported. In addition, a simple and easy-to-use approach has also been reported that arranges leucines on a solvent-accessible region of an α-helix and places charged residues around the leucine patch to induce interactions between the two helical peptides. For this study, we adopted this approach to de novo design a new PPI between the helical bundle proteins sulerythrin and LARFH. A non-polar patch was created on an α-helix of LARFH around which arginine residues were introduced to retain its solubility. The strongest interaction found was for the LARFH variant cysLARFH-IV-3L3R and the sulerythrin mutant 6L6D (KD=0.16 μM). This artificial protein complex is maintained by hydrophobic and ionic interactions formed by the inter-molecular helical bundle structure. Therefore, by the simple and easy-to-use approach to create de novo interfaces on the α-helices, we successfully generated an artificial PPI. We also created a second LARFH variant with the non-polar patch surrounded by positively charged residues at each end. Upon mixing this LARFH variant with 6L6D, mesh-like fibrous nanostructures were observed by atomic force microscopy. Our method may, therefore, also be applicable to the de novo design of protein nanostructures. PMID:26867971

  7. IRBIT Interacts with the Catalytic Core of Phosphatidylinositol Phosphate Kinase Type Iα and IIα through Conserved Catalytic Aspartate Residues

    PubMed Central

    Ando, Hideaki; Hirose, Matsumi; Gainche, Laura; Kawaai, Katsuhiro; Bonneau, Benjamin; Ijuin, Takeshi; Itoh, Toshiki; Takenawa, Tadaomi; Mikoshiba, Katsuhiko

    2015-01-01

    Phosphatidylinositol phosphate kinases (PIPKs) are lipid kinases that generate phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), a critical lipid signaling molecule that regulates diverse cellular functions, including the activities of membrane channels and transporters. IRBIT (IP3R-binding protein released with inositol 1,4,5-trisphosphate) is a multifunctional protein that regulates diverse target proteins. Here, we report that IRBIT forms signaling complexes with members of the PIPK family. IRBIT bound to all PIPK isoforms in heterologous expression systems and specifically interacted with PIPK type Iα (PIPKIα) and type IIα (PIPKIIα) in mouse cerebellum. Site-directed mutagenesis revealed that two conserved catalytic aspartate residues of PIPKIα and PIPKIIα are involved in the interaction with IRBIT. Furthermore, phosphatidylinositol 4-phosphate, Mg2+, and/or ATP interfered with the interaction, suggesting that IRBIT interacts with catalytic cores of PIPKs. Mutations of phosphorylation sites in the serine-rich region of IRBIT affected the selectivity of its interaction with PIPKIα and PIPKIIα. The structural flexibility of the serine-rich region, located in the intrinsically disordered protein region, is assumed to underlie the mechanism of this interaction. Furthermore, in vitro binding experiments and immunocytochemistry suggest that IRBIT and PIPKIα interact with the Na+/HCO3− cotransporter NBCe1-B. These results suggest that IRBIT forms signaling complexes with PIPKIα and NBCe1-B, whose activity is regulated by PI(4,5)P2. PMID:26509711

  8. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

    PubMed Central

    Tse, Amanda; Verkhivker, Gennady M.

    2015-01-01

    Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating

  9. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution.

    PubMed

    Tse, Amanda; Verkhivker, Gennady M

    2015-01-01

    Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating

  10. Spin-dependent two-body interactions from gravitational self-force computations

    NASA Astrophysics Data System (ADS)

    Bini, Donato; Damour, Thibault; Geralico, Andrea

    2015-12-01

    We analytically compute, through the eight-and-a-half post-Newtonian order and the fourth-order in spin, the gravitational self-force correction to Detweiler's gauge invariant redshift function for a small mass in circular orbit around a Kerr black hole. Using the first law of mechanics for black hole binaries with spin [L. Blanchet, A. Buonanno and A. Le Tiec, Phys. Rev. D 87, 024030 (2013)] we transcribe our results into a knowledge of various spin-dependent couplings, as encoded within the spinning effective-one-body model of T. Damour and A. Nagar [Phys. Rev. D 90, 044018 (2014)]. We also compare our analytical results to the (corrected) numerical self-force results of A. G. Shah, J. L. Friedman and T. S. Keidl [Phys. Rev. D 86, 084059 (2012)], from which we show how to directly extract physically relevant spin-dependent couplings.

  11. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

    NASA Astrophysics Data System (ADS)

    Lipska, Agnieszka G.; Seidman, Steven R.; Sieradzan, Adam K.; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A.

    2016-05-01

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models.

  12. Few Residues within an Extensive Binding Interface Drive Receptor Interaction and Determine the Specificity of Arrestin Proteins*

    PubMed Central

    Vishnivetskiy, Sergey A.; Gimenez, Luis E.; Francis, Derek J.; Hanson, Susan M.; Hubbell, Wayne L.; Klug, Candice S.; Gurevich, Vsevolod V.

    2011-01-01

    Arrestins bind active phosphorylated forms of G protein-coupled receptors, terminating G protein activation, orchestrating receptor trafficking, and redirecting signaling to alternative pathways. Visual arrestin-1 preferentially binds rhodopsin, whereas the two non-visual arrestins interact with hundreds of G protein-coupled receptor subtypes. Here we show that an extensive surface on the concave side of both arrestin-2 domains is involved in receptor binding. We also identified a small number of residues on the receptor binding surface of the N- and C-domains that largely determine the receptor specificity of arrestins. We show that alanine substitution of these residues blocks the binding of arrestin-1 to rhodopsin in vitro and of arrestin-2 and -3 to β2-adrenergic, M2 muscarinic cholinergic, and D2 dopamine receptors in intact cells, suggesting that these elements critically contribute to the energy of the interaction. Thus, in contrast to arrestin-1, where direct phosphate binding is crucial, the interaction of non-visual arrestins with their cognate receptors depends to a lesser extent on phosphate binding and more on the binding to non-phosphorylated receptor elements. PMID:21471193

  13. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.

    PubMed

    Lipska, Agnieszka G; Seidman, Steven R; Sieradzan, Adam K; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A

    2016-05-14

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models. PMID:27179474

  14. Validation of Proposed Metrics for Two-Body Abrasion Scratch Test Analysis Standards

    NASA Technical Reports Server (NTRS)

    Kobrick, Ryan L.; Klaus, David M.; Street, Kenneth W., Jr.

    2011-01-01

    The objective of this work was to evaluate a set of standardized metrics proposed for characterizing a surface that has been scratched from a two-body abrasion test. This is achieved by defining a new abrasion region termed Zone of Interaction (ZOI). The ZOI describes the full surface profile of all peaks and valleys, rather than just measuring a scratch width as currently defined by the ASTM G 171 Standard. The ZOI has been found to be at least twice the size of a standard width measurement, in some cases considerably greater, indicating that at least half of the disturbed surface area would be neglected without this insight. The ZOI is used to calculate a more robust data set of volume measurements that can be used to computationally reconstruct a resultant profile for detailed analysis. Documenting additional changes to various surface roughness parameters also allows key material attributes of importance to ultimate design applications to be quantified, such as depth of penetration and final abraded surface roughness. Data are presented to show that different combinations of scratch tips and abraded materials can actually yield the same scratch width, but result in different volume displacement or removal measurements and therefore, the ZOI method is more discriminating than the ASTM method scratch width. Furthermore, by investigating the use of custom scratch tips for our specific needs, the usefulness of having an abrasion metric that can measure the displaced volume in this standardized manner, and not just by scratch width alone, is reinforced. This benefit is made apparent when a tip creates an intricate contour having multiple peaks and valleys within a single scratch. This work lays the foundation for updating scratch measurement standards to improve modeling and characterization of three-body abrasion test results.

  15. Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis

    NASA Astrophysics Data System (ADS)

    Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki

    2006-03-01

    Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.

  16. MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein–ligand fragment interaction, pathways and SNPs

    PubMed Central

    Tanramluk, Duangrudee; Narupiyakul, Lalita; Akavipat, Ruj; Gong, Sungsam; Charoensawan, Varodom

    2016-01-01

    Protein–ligand interaction analysis is an important step of drug design and protein engineering in order to predict the binding affinity and selectivity between ligands to the target proteins. To date, there are more than 100 000 structures available in the Protein Data Bank (PDB), of which ∼30% are protein–ligand (MW below 1000 Da) complexes. We have developed the integrative web server MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) with the aim of providing a user-friendly web interface to assist structural study and design of protein–ligand interactions. In brief, the server allows the users to input the chemical fragments and present all the unique molecular interactions to the target proteins with available three-dimensional structures in the PDB. The users can also link the ligands of interest to assess possible off-target proteins, human variants and pathway information using our all-in-one integrated tools. Taken together, we envisage that the server will facilitate and improve the study of protein–ligand interactions by allowing observation and comparison of ligand interactions with multiple proteins at the same time. (http://manoraa.org). PMID:27131358

  17. MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein-ligand fragment interaction, pathways and SNPs.

    PubMed

    Tanramluk, Duangrudee; Narupiyakul, Lalita; Akavipat, Ruj; Gong, Sungsam; Charoensawan, Varodom

    2016-07-01

    Protein-ligand interaction analysis is an important step of drug design and protein engineering in order to predict the binding affinity and selectivity between ligands to the target proteins. To date, there are more than 100 000 structures available in the Protein Data Bank (PDB), of which ∼30% are protein-ligand (MW below 1000 Da) complexes. We have developed the integrative web server MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) with the aim of providing a user-friendly web interface to assist structural study and design of protein-ligand interactions. In brief, the server allows the users to input the chemical fragments and present all the unique molecular interactions to the target proteins with available three-dimensional structures in the PDB. The users can also link the ligands of interest to assess possible off-target proteins, human variants and pathway information using our all-in-one integrated tools. Taken together, we envisage that the server will facilitate and improve the study of protein-ligand interactions by allowing observation and comparison of ligand interactions with multiple proteins at the same time. (http://manoraa.org). PMID:27131358

  18. Role of portal region lysine residues in electrostatic interactions between heart fatty acid binding protein and phospholipid membranes.

    PubMed

    Herr, F M; Aronson, J; Storch, J

    1996-01-30

    The structure of heart fatty acid binding protein (HFABP) is a flattened beta-barrel comprising 10 antiparallel beta-sheets capped by two alpha-helical segments. The helical cap region is hypothesized to behave as a portal "lid" for the entry and release of ligand from the binding pocket. The transfer of fatty acid from HFABP is thought to occur via effective collisional interactions with membranes, and these interactions are enhanced when transfer is to membranes of net negative charge, thus implying that specific basic residues on the surface of HFABP may govern the transfer process [Wootan, M. G., & Storch, J. (1994) J. Biol. Chem. 269, 10517-10523]. To directly examine the role of charged lysine residues on the HFABP surface in specific interactions with membranes, chemical modification and selective mutagenesis of HFABP were used. All surface lysine residues were neutralized by acetylation of recombinant HFABP with acetic anhydride. In addition, seven mutant HFABPs were generated that resulted in charge alterations in five distinct sites of HFABP. Modification of the protein did not significantly alter the structural or ligand binding properties of HFABP, as assessed by circular dichroism, fluorescence quantum yield, and ligand binding analyses. By using a resonance energy transfer assay, transfer of 2-(9-anthroyloxy)palmitate (2AP) from acetylated HFABP to membranes was significantly slower than transfer from native HFABP. In addition, in distinct contrast to transfer from native protein, the 2AP transfer rate from acetylated HFABP was not increased to acceptor membranes of increased negative charge. Transfer of 2AP from HFABP mutants involving K22, located on alpha-helix I (alpha-I) of the helical cap region, was 3-fold slower than transfer from wild-type protein, whereas rates from a mutant involving the K59 residue, located on the beta 2-turn of the barrel near the helical cap, were 2-fold faster than those of wild type. A double mutant involving K22 and K

  19. Amino Acid Residues of RegA Important for Interactions with the CbbR-DNA Complex of Rhodobacter sphaeroides

    PubMed Central

    Dangel, Andrew W.; Luther, Amanda

    2014-01-01

    CbbR and RegA (PrrA) are transcriptional regulators of the Calvin-Benson-Bassham (CBB) CO2 fixation pathway (cbbI and cbbII) operons of Rhodobacter sphaeroides. The CbbR and RegA proteins interact, but CbbR must be bound to the promoter DNA in order for RegA-CbbR protein-protein interactions to occur. RegA greatly enhances the ability of CbbR to bind the cbbI promoter or greatly enhances the stability of the CbbR/promoter complex. The N-terminal receiver domain and the DNA binding domain of RegA were shown to interact with CbbR. Residues in α-helix 7 and α-helix 8 of the DNA binding domain (helix-turn-helix) of RegA directly interacted with CbbR, with α-helix 7 positioned immediately above the DNA and α-helix 8 located in the major groove of the DNA. A CbbR protein containing only the DNA binding motif and the linker helix was capable of binding to RegA. In contrast, a truncated CbbR containing only the linker helix and recognition domains I and II (required for effector binding) was not able to interact with RegA. The accumulated results strongly suggest that the DNA binding domains of both proteins interact to facilitate optimal transcriptional control over the cbb operons. In vivo analysis, using constitutively active mutant CbbR proteins, further indicated that CbbR must interact with phosphorylated RegA in order to accomplish transcriptional activation. PMID:24957624

  20. Effect of residual attractive interactions in size asymmetric colloidal mixtures: Theoretical analysis and predictions.

    PubMed

    Germain, Ph

    2010-07-28

    We analyze the influence of residual attractions on the static and some dynamic properties of size asymmetric mixtures of "hard-sphere-like" colloids. These attractions, usually neglected in the theoretical analysis, are characterized by a very short range and a moderate strength reflecting the underlying microscopic structure of the colloidal particles. Their effect on the potentials of mean force is analyzed from analytical expressions obtained from low density expansions. The effective potential of the big particle fluid is next considered. An analytical expression is proposed for estimating the deviation with respect to the hard sphere depletion potential. This case is compared to that of mixtures with noninteracting depletants. The important consequences on the binodals and the glass transition lines of the effective fluid are discussed in both cases. This study is next extended to other properties-the specific heat and the low shear viscosity-which incorporate contributions from the two components of the binary mixture. PMID:20687684

  1. Effect of residual attractive interactions in size asymmetric colloidal mixtures: Theoretical analysis and predictions

    NASA Astrophysics Data System (ADS)

    Germain, Ph.

    2010-07-01

    We analyze the influence of residual attractions on the static and some dynamic properties of size asymmetric mixtures of "hard-sphere-like" colloids. These attractions, usually neglected in the theoretical analysis, are characterized by a very short range and a moderate strength reflecting the underlying microscopic structure of the colloidal particles. Their effect on the potentials of mean force is analyzed from analytical expressions obtained from low density expansions. The effective potential of the big particle fluid is next considered. An analytical expression is proposed for estimating the deviation with respect to the hard sphere depletion potential. This case is compared to that of mixtures with noninteracting depletants. The important consequences on the binodals and the glass transition lines of the effective fluid are discussed in both cases. This study is next extended to other properties—the specific heat and the low shear viscosity—which incorporate contributions from the two components of the binary mixture.

  2. Neutral weak-current two-body contributions in inclusive scattering from {sup 12}C

    SciTech Connect

    Lovato, Alessandro; Gandolfi, Stefano; Carlson, Joseph; Pieper, S. C.; Schiavilla, Rocco

    2014-05-01

    An {\\it ab initio} calculation of the sum rules of the neutral weak response functions in $^{12}$C is reported, based on a realistic Hamiltonian, including two- and three-nucleon potentials, and on realistic currents, consisting of one- and two-body terms. We find that the sum rules of the response functions associated with the longitudinal and transverse components of the (space-like) neutral current are largest and that a significant portion ($\\simeq 30$\\%) of the calculated strength is due to two-body terms. This fact may have implications for the MiniBooNE and other neutrino quasi-elastic scattering data on nuclei.

  3. Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels

    PubMed Central

    Yip, Kevin Y; Kim, Philip M; McDermott, Drew; Gerstein, Mark

    2009-01-01

    Background Proteins interact through specific binding interfaces that contain many residues in domains. Protein interactions thus occur on three different levels of a concept hierarchy: whole-proteins, domains, and residues. Each level offers a distinct and complementary set of features for computationally predicting interactions, including functional genomic features of whole proteins, evolutionary features of domain families and physical-chemical features of individual residues. The predictions at each level could benefit from using the features at all three levels. However, it is not trivial as the features are provided at different granularity. Results To link up the predictions at the three levels, we propose a multi-level machine-learning framework that allows for explicit information flow between the levels. We demonstrate, using representative yeast interaction networks, that our algorithm is able to utilize complementary feature sets to make more accurate predictions at the three levels than when the three problems are approached independently. To facilitate application of our multi-level learning framework, we discuss three key aspects of multi-level learning and the corresponding design choices that we have made in the implementation of a concrete learning algorithm. 1) Architecture of information flow: we show the greater flexibility of bidirectional flow over independent levels and unidirectional flow; 2) Coupling mechanism of the different levels: We show how this can be accomplished via augmenting the training sets at each level, and discuss the prevention of error propagation between different levels by means of soft coupling; 3) Sparseness of data: We show that the multi-level framework compounds data sparsity issues, and discuss how this can be dealt with by building local models in information-rich parts of the data. Our proof-of-concept learning algorithm demonstrates the advantage of combining levels, and opens up opportunities for further

  4. MOWGLI: prediction of protein-MannOse interacting residues With ensemble classifiers usinG evoLutionary Information.

    PubMed

    Pai, Priyadarshini P; Mondal, Sukanta

    2016-10-01

    Proteins interact with carbohydrates to perform various cellular interactions. Of the many carbohydrate ligands that proteins bind with, mannose constitute an important class, playing important roles in host defense mechanisms. Accurate identification of mannose-interacting residues (MIR) may provide important clues to decipher the underlying mechanisms of protein-mannose interactions during infections. This study proposes an approach using an ensemble of base classifiers for prediction of MIR using their evolutionary information in the form of position-specific scoring matrix. The base classifiers are random forests trained by different subsets of training data set Dset128 using 10-fold cross-validation. The optimized ensemble of base classifiers, MOWGLI, is then used to predict MIR on protein chains of the test data set Dtestset29 which showed a promising performance with 92.0% accurate prediction. An overall improvement of 26.6% in precision was observed upon comparison with the state-of-art. It is hoped that this approach, yielding enhanced predictions, could be eventually used for applications in drug design and vaccine development. PMID:26457920

  5. Distal residue-CO interaction in carbonmonoxy myoglobins: a molecular dynamics study of three distal mutants.

    PubMed Central

    Jewsbury, P; Kitagawa, T

    1995-01-01

    Six 90-ps molecular dynamics trajectories, two for each of three distal mutants of sperm whale carbonmonoxy myoglobin, are reported; solvent waters within 16 A of the active site have been included. In both His64GIn trajectories, the distal side chain remains part of the heme pocket, forming a "closed" conformation similar to that of the wild type 64N delta H tautomer. Despite a connectivity more closely resembling the N epsilon H histidine tautomer, close interactions with the carbonyl ligand similar to those observed for the wild type 64N epsilon H tautomer are prevented in this mutant by repulsive interactions between the carbonyl O and the 64O epsilon. The aliphatic distal side chain of the His64Leu mutant shows little interaction with the carbonyl ligand in either His64Leu trajectory. Solvent water molecules move into and out of the active site in the His64Gly mutant trajectories; during all the other carbonmonoxy myoglobin trajectories, including the wild type distal tautomers considered in an earlier work, solvent molecules rarely encroach closer than 6 A of the active site. These results are consistent with a recent structural interpretation of the wild type infrared spectrum, and the current reinterpretation that the distal-ligand interaction in carbonmonoxy myoglobin is largely electrostatic, not steric, in nature. Images FIGURE 5 FIGURE 7 PMID:7787018

  6. NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation

    PubMed Central

    2014-01-01

    Background The rapid growth of un-annotated missense variants poses challenges requiring novel strategies for their interpretation. From the thermodynamic point of view, amino acid changes can lead to a change in the internal energy of a protein and induce structural rearrangements. This is of great relevance for the study of diseases and protein design, justifying the development of prediction methods for variant-induced stability changes. Results Here we propose NeEMO, a tool for the evaluation of stability changes using an effective representation of proteins based on residue interaction networks (RINs). RINs are used to extract useful features describing interactions of the mutant amino acid with its structural environment. Benchmarking shows NeEMO to be very effective, allowing reliable predictions in different parts of the protein such as β-strands and buried residues. Validation on a previously published independent dataset shows that NeEMO has a Pearson correlation coefficient of 0.77 and a standard error of 1 Kcal/mol, outperforming nine recent methods. The NeEMO web server can be freely accessed from URL: http://protein.bio.unipd.it/neemo/. Conclusions NeEMO offers an innovative and reliable tool for the annotation of amino acid changes. A key contribution are RINs, which can be used for modeling proteins and their interactions effectively. Interestingly, the approach is very general, and can motivate the development of a new family of RIN-based protein structure analyzers. NeEMO may suggest innovative strategies for bioinformatics tools beyond protein stability prediction. PMID:25057121

  7. PTPRT regulates the interaction of Syntaxin-binding protein 1 with Syntaxin 1 through dephosphorylation of specific tyrosine residue

    SciTech Connect

    Lim, So-Hee; Moon, Jeonghee; Lee, Myungkyu; Lee, Jae-Ran

    2013-09-13

    Highlights: •PTPRT is a brain-specific, expressed, protein tyrosine phosphatase. •PTPRT regulated the interaction of Syntaxin-binding protein 1 with Syntaxin 1. •PTPRT dephosphorylated the specific tyrosine residue of Syntaxin-binding protein 1. •Dephosphorylation of Syntaxin-binding protein 1 enhanced the interaction with Syntaxin 1. •PTPRT appears to regulate the fusion of synaptic vesicle through dephosphorylation. -- Abstract: PTPRT (protein tyrosine phosphatase receptor T), a brain-specific tyrosine phosphatase, has been found to regulate synaptic formation and development of hippocampal neurons, but its regulation mechanism is not yet fully understood. Here, Syntaxin-binding protein 1, a key component of synaptic vesicle fusion machinery, was identified as a possible interaction partner and an endogenous substrate of PTPRT. PTPRT interacted with Syntaxin-binding protein 1 in rat synaptosome, and co-localized with Syntaxin-binding protein 1 in cultured hippocampal neurons. PTPRT dephosphorylated tyrosine 145 located around the linker between domain 1 and 2 of Syntaxin-binding protein 1. Syntaxin-binding protein 1 directly binds to Syntaxin 1, a t-SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein, and plays a role as catalysts of SNARE complex formation. Syntaxin-binding protein 1 mutant mimicking non-phosphorylation (Y145F) enhanced the interaction with Syntaxin 1 compared to wild type, and therefore, dephosphorylation of Syntaxin-binding protein 1 appeared to be important for SNARE-complex formation. In conclusion, PTPRT could regulate the interaction of Syntaxin-binding protein 1 with Syntaxin 1, and as a result, the synaptic vesicle fusion appeared to be controlled through dephosphorylation of Syntaxin-binding protein 1.

  8. Towards numerically robust multireference theories: The driven similarity renormalization group truncated to one- and two-body operators

    NASA Astrophysics Data System (ADS)

    Li, Chenyang; Evangelista, Francesco A.

    2016-04-01

    The first nonperturbative version of the multireference driven similarity renormalization group (MR-DSRG) theory [C. Li and F. A. Evangelista, J. Chem. Theory Comput. 11, 2097 (2015)] is introduced. The renormalization group structure of the MR-DSRG equations ensures numerical robustness and avoidance of the intruder-state problem, while the connected nature of the amplitude and energy equations guarantees size consistency and extensivity. We approximate the MR-DSRG equations by keeping only one- and two-body operators and using a linearized recursive commutator approximation of the Baker-Campbell-Hausdorff expansion [T. Yanai and G. K.-L. Chan, J. Chem. Phys. 124, 194106 (2006)]. The resulting linearized MR-DSRG scheme with one- and two-body operators [MR-LDSRG(2)] contains only 39 terms and scales as O ( N 2 NP 2 NH 2 ) where NH, NP, and N correspond to the number of hole, particle, and total orbitals, respectively. Benchmark MR-LDSRG(2) computations on the hydrogen fluoride and molecular nitrogen binding curves and the singlet-triplet splitting of p-benzyne yield results comparable in accuracy to those from multireference configuration interaction, Mukherjee multireference coupled cluster theory, and internally contracted multireference coupled cluster theory.

  9. Towards numerically robust multireference theories: The driven similarity renormalization group truncated to one- and two-body operators.

    PubMed

    Li, Chenyang; Evangelista, Francesco A

    2016-04-28

    The first nonperturbative version of the multireference driven similarity renormalization group (MR-DSRG) theory [C. Li and F. A. Evangelista, J. Chem. Theory Comput. 11, 2097 (2015)] is introduced. The renormalization group structure of the MR-DSRG equations ensures numerical robustness and avoidance of the intruder-state problem, while the connected nature of the amplitude and energy equations guarantees size consistency and extensivity. We approximate the MR-DSRG equations by keeping only one- and two-body operators and using a linearized recursive commutator approximation of the Baker-Campbell-Hausdorff expansion [T. Yanai and G. K.-L. Chan, J. Chem. Phys. 124, 194106 (2006)]. The resulting linearized MR-DSRG scheme with one- and two-body operators [MR-LDSRG(2)] contains only 39 terms and scales as O(N(2)NP (2)NH (2)) where NH, NP, and N correspond to the number of hole, particle, and total orbitals, respectively. Benchmark MR-LDSRG(2) computations on the hydrogen fluoride and molecular nitrogen binding curves and the singlet-triplet splitting of p-benzyne yield results comparable in accuracy to those from multireference configuration interaction, Mukherjee multireference coupled cluster theory, and internally contracted multireference coupled cluster theory. PMID:27131538

  10. Two-body Relaxation Driven Evolution of the Young Stellar Disk in the Galactic Center

    NASA Astrophysics Data System (ADS)

    Šubr, Ladislav; Haas, Jaroslav

    2014-05-01

    The center of our Galaxy hosts almost two hundred very young stars, a subset of which is orbiting the central supermassive black hole (SMBH) in a relatively thin disk-like structure. First analyses indicated a power-law surface density profile of the disk, ΣvpropR β with β = -2. Recently, however, doubts about this profile arose. In particular, it now seems to be better described by a sort of broken power law. By means of both analytical arguments and numerical N-body modeling, we show that such a broken power-law profile is a natural consequence of the two-body relaxation of the disk. Due to the small relative velocities of the nearby stars in co-planar Keplerian orbits around the SMBH, two-body relaxation is effective enough to affect the evolution of the disk on timescales comparable to its estimated age. In the inner, densest part of the disk, the profile becomes rather flat (β ≈ -1) while the outer parts keep imprints of the initial state. Our numerical models show that the observed projected surface density profile of the young stellar disk can result from two-body relaxation driven evolution of a disk with initial single power-law profile with -2 <~ β <~ -1.5. In addition, we suggest that two-body relaxation may have caused a significant radial migration of the S-stars toward the central SMBH, thus playing an important role in their formation scenario.

  11. Experiments driving theory: Gravitational wave detection and the two body problem in general relativity

    NASA Astrophysics Data System (ADS)

    Iyer, Bala R.

    2016-05-01

    Over the last two decades, the search for gravitational waves from coalescing compact binaries by detectors like LIGO and Virgo has crucially required and consequently spurred tremendous progress in the two body problem in general relativity. A broad brush overview of these major developments and the current status of these significant results is presented.

  12. Universal algorithms and programs for calculating the motion parameters in the two-body problem

    NASA Technical Reports Server (NTRS)

    Bakhshiyan, B. T.; Sukhanov, A. A.

    1979-01-01

    The algorithms and FORTRAN programs for computing positions and velocities, orbital elements and first and second partial derivatives in the two-body problem are presented. The algorithms are applicable for any value of eccentricity and are convenient for computing various navigation parameters.

  13. Singularity in the Laboratory Frame Angular Distribution Derived in Two-Body Scattering Theory

    ERIC Educational Resources Information Center

    Dick, Frank; Norbury, John W.

    2009-01-01

    The laboratory (lab) frame angular distribution derived in two-body scattering theory exhibits a singularity at the maximum lab scattering angle. The singularity appears in the kinematic factor that transforms the centre of momentum (cm) angular distribution to the lab angular distribution. We show that it is caused in the transformation by the…

  14. Two-body correlations and natural-orbital tomography in ultracold bosonic systems of definite parity

    NASA Astrophysics Data System (ADS)

    Kroenke, Sven; Schmelcher, Peter

    2016-05-01

    Deep insights into the structure of a many-body state can often be inferred from its natural orbitals (eigenvectors of the reduced one-body density operator) and their populations. These quantities allow e.g. to distinguish a Bose-Einstein condensate from a correlated many-body state and were utilized to understand many-body processes such as the decay of dark solitons due to dynamical quantum depletion. We explore the relationship between natural orbitals, one-body coherences and two-body correlations for a certain important class of bosonic many-body wave-functions with definite parity. The strength of two-body correlations at the parity-symmetry center is shown (i) to characterize the number state distribution and (ii) to control the structure of non-local two-body correlations. A recipe for the experimental reconstruction of the natural-orbital densities based on two-body correlation measurements is derived. These results are applied to decaying dark solitons.

  15. Selective determination of thiram residues in fruit and vegetables by hydrophilic interaction LC-MS.

    PubMed

    Ringli, Daniela; Schwack, Wolfgang

    2013-01-01

    Thiram belongs to the most important class of dithiocarbamate (DTC) fungicides including dimethyldithiocarbamates (DMDs), ethylenebis(dithiocarbamtes) (EBDs) and propylenebis(dithiocarbamates) (PBDs). During the surface extraction of fruit and vegetables for the LC-MS determination of residues of DMDs, EBDs and PBDs, thiram is reduced by the penicillamine buffer to the DMD anion, thus resulting in false-positive findings of DMD fungicides like ziram. Therefore, an alkaline sulfite buffer was applied for surface extraction, quantitatively transforming thiram into the DMD anion and a stable DMD-sulfite adduct that was used as a selective marker for thiram. Separation was performed isocratically on a ZIC-pHILIC column with acetonitrile-10 mM ammonium hydroxide solution (85/15). Mass selective detection was carried out on a single-quadrupole mass spectrometer coupled to an electrospray ionisation interface operating in negative mode. Using d12-thiram as the internal standard, recoveries of 80-108% were obtained from apples, tomatoes, grapes and sweet peppers, spiked in the range of 0.02-1 mg kg(-1). Limits of detection and quantification were 0.6 and 2 µg kg(-1), respectively. PMID:24070320

  16. Fujiwhara interaction of tropical cyclone scale vortices using a weighted residual collocation method

    NASA Astrophysics Data System (ADS)

    Walsh, Raymond P.; Alam, Jahrul M.

    2016-09-01

    The fundamental interaction between tropical cyclones was investigated through a series of water tank experiements by Fujiwhara [20, 21, 22]. However, a complete understanding of tropical cyclones remains an open research challenge although there have been numerous investigations through measurments with aircrafts/satellites, as well as with numerical simulations. This article presents a computational model for simulating the interaction between cyclones. The proposed numerical method is presented briefly, where the time integration is performed by projecting the discrete system onto a Krylov subspace. The method filters the large scale fluid dynamics using a multiresolution approximation, and the unresolved dynamics is modeled with a Smagorinsky type subgrid scale parameterization scheme. Numerical experiments with Fujiwhara interactions are considered to verify modeling accuracy. An excellent agreement between the present simulation and a reference simulation at Re = 5000 has been demonstrated. At Re = 37440, the kinetic energy of cyclones is seen consolidated into larger scales with concurrent enstrophy cascade, suggesting a steady increase of energy containing scales, a phenomena that is typical in two-dimensional turbulence theory. The primary results of this article suggest a novel avenue for addressing some of the computational challenges of mesoscale atmospheric circulations.

  17. Tyrosine residues 654 and 670 in {beta}-cat enin are crucial in regulation of Met-{beta}-catenin interactions

    SciTech Connect

    Zeng, Gang; Apte, Udayan; Micsenyi, Amanda; Bell, Aaron; Monga, Satdarshan P.S. . E-mail: smonga@pitt.edu

    2006-11-01

    {beta}-catenin, a key component of the canonical Wnt pathway, is also regulated by tyrosine phosphorylation that regulates its association to E-cadherin. Previously, we reported its association with the hepatocyte growth factor (HGF) receptor Met at the membrane. HGF induced Met-{beta}-catenin dissociation and nuclear translocation of {beta}-catenin, which was tyrosine-phosphorylation-dependent. Here, we further investigate the Met-{beta}-catenin interaction by selectively mutating several tyrosine residues, alone or in combination, in {beta}-catenin. The mutants were subcloned into FLAG-CMV vector and stably transfected into rat hepatoma cells, which were treated with HGF. All single or double-mutant-transfected cells continued to show HGF-induced nuclear translocation of FLAG-{beta}-catenin except the mutations affecting 654 and 670 simultaneously (Y654/670F), which coincided with the lack of formation of {beta}-catenin-TCF complex and DNA synthesis, in response to the HGF treatment. In addition, the Y654/670F-transfected cells also showed no phosphorylation of {beta}-catenin or dissociation from Met in response to HGF. Thus, intact 654 and 670 tyrosine residues in {beta}-catenin are crucial in HGF-mediated {beta}-catenin translocation, activation and mitogenesis.

  18. Structure-function studies on bacteriorhodopsin. IX. Substitutions of tryptophan residues affect protein-retinal interactions in bacteriorhodopsin

    SciTech Connect

    Mogi, T.; Marti, T.; Khorana, H.G. )

    1989-08-25

    Bacteriorhodopsin contains 8 tryptophan residues distributed across the membrane-embedded helices. To study their possible functions, we have replaced them one at a time by phenylalanine; in addition, Trp-137 and -138 have been replaced by cysteine. The mutants were prepared by cassette mutagenesis of the synthetic bacterio-opsin gene, expression and purification of the mutant apoproteins, renaturation, and chromophore regeneration. The replacement of Trp-10, Trp-12 (helix A), Trp-80 (helix C), and Trp-138 (helix E) by phenylalanine and of Trp-137 and Trp-138 by cysteine did not significantly alter the absorption spectra or affect their proton pumping. However, substitution of the remaining tryptophans by phenylalanine had the following effects. (1) Substitution of Trp-86 (helix C) and Trp-137 gave chromophores blue-shifted by 20 nm and resulted in reduced proton pumping to about 30%. (2) As also reported previously, substitution of Trp-182 and Trp-189 (helix F) caused large blue shifts (70 and 40 nm, respectively) in the chromophore and affected proton pumping. (3) The substitution of Trp-86 and Trp-182 by phenylalanine conferred acid instability on these mutants. The spectral shifts indicate that Trp-86, Trp-182, Trp-189, and possibly Trp-137 interact with retinal. It is proposed that these tryptophans, probably along with Tyr-57 (helix B) and Tyr-185 (helix F), form a retinal binding pocket. We discuss the role of tryptophan residues that are conserved in bacteriorhodopsin, halorhodopsin, and the related family of opsin proteins.

  19. Two Arginine Residues of Streptococcus gordonii Sialic Acid-Binding Adhesin Hsa Are Essential for Interaction to Host Cell Receptors

    PubMed Central

    Urano-Tashiro, Yumiko; Takahashi, Yukihiro; Oguchi, Riyo; Konishi, Kiyoshi

    2016-01-01

    Hsa is a large, serine-rich protein of Streptococcus gordonii DL1 that mediates binding to α2-3-linked sialic acid termini of glycoproteins, including platelet glycoprotein Ibα, and erythrocyte membrane protein glycophorin A, and band 3. The binding of Hsa to platelet glycoprotein Ibα contributes to the pathogenesis of infective endocarditis. This interaction appears to be mediated by a second non-repetitive region (NR2) of Hsa. However, the molecular details of the interaction between the Hsa NR2 region and these glycoproteins are not well understood. In the present study, we identified the amino acid residues of the Hsa NR2 region that are involved in sialic acid recognition. To identify the sialic acid-binding site of Hsa NR2 region, we prepared various mutants of Hsa NR2 fused with glutathione transferase. Fusion proteins harboring Arg340 to Asn (R340N) or Arg365 to Asn (R365N) substitutions in the NR2 domain exhibited significantly reduced binding to human erythrocytes and platelets. A sugar-binding assay showed that these mutant proteins abolished binding to α2-3-linked sialic acid. Furthermore, we established S. gordonii DL1 derivatives that encoded the corresponding Hsa mutant protein. In whole-cell assays, these mutant strains showed significant reductions in hemagglutination, in platelet aggregation, and in adhesion to human leukocytes. These results indicate that the Arg340 and Arg365 residues of Hsa play an important role in the binding of Hsa to α2-3-linked sialic acid-containing glycoproteins. PMID:27101147

  20. Two Arginine Residues of Streptococcus gordonii Sialic Acid-Binding Adhesin Hsa Are Essential for Interaction to Host Cell Receptors.

    PubMed

    Urano-Tashiro, Yumiko; Takahashi, Yukihiro; Oguchi, Riyo; Konishi, Kiyoshi

    2016-01-01

    Hsa is a large, serine-rich protein of Streptococcus gordonii DL1 that mediates binding to α2-3-linked sialic acid termini of glycoproteins, including platelet glycoprotein Ibα, and erythrocyte membrane protein glycophorin A, and band 3. The binding of Hsa to platelet glycoprotein Ibα contributes to the pathogenesis of infective endocarditis. This interaction appears to be mediated by a second non-repetitive region (NR2) of Hsa. However, the molecular details of the interaction between the Hsa NR2 region and these glycoproteins are not well understood. In the present study, we identified the amino acid residues of the Hsa NR2 region that are involved in sialic acid recognition. To identify the sialic acid-binding site of Hsa NR2 region, we prepared various mutants of Hsa NR2 fused with glutathione transferase. Fusion proteins harboring Arg340 to Asn (R340N) or Arg365 to Asn (R365N) substitutions in the NR2 domain exhibited significantly reduced binding to human erythrocytes and platelets. A sugar-binding assay showed that these mutant proteins abolished binding to α2-3-linked sialic acid. Furthermore, we established S. gordonii DL1 derivatives that encoded the corresponding Hsa mutant protein. In whole-cell assays, these mutant strains showed significant reductions in hemagglutination, in platelet aggregation, and in adhesion to human leukocytes. These results indicate that the Arg340 and Arg365 residues of Hsa play an important role in the binding of Hsa to α2-3-linked sialic acid-containing glycoproteins. PMID:27101147

  1. Validation of Proposed Metrics for Two-Body Abrasion Scratch Test Analysis Standards

    NASA Technical Reports Server (NTRS)

    Street, Kenneth W., Jr.; Kobrick, Ryan L.; Klaus, David M.

    2013-01-01

    Abrasion of mechanical components and fabrics by soil on Earth is typically minimized by the effects of atmosphere and water. Potentially abrasive particles lose sharp and pointed geometrical features through erosion. In environments where such erosion does not exist, such as the vacuum of the Moon, particles retain sharp geometries associated with fracturing of their parent particles by micrometeorite impacts. The relationship between hardness of the abrasive and that of the material being abraded is well understood, such that the abrasive ability of a material can be estimated as a function of the ratio of the hardness of the two interacting materials. Knowing the abrasive nature of an environment (abrasive)/construction material is crucial to designing durable equipment for use in such surroundings. The objective of this work was to evaluate a set of standardized metrics proposed for characterizing a surface that has been scratched from a two-body abrasion test. This is achieved by defining a new abrasion region termed Zone of Interaction (ZOI). The ZOI describes the full surface profile of all peaks and valleys, rather than just measuring a scratch width. The ZOI has been found to be at least twice the size of a standard width measurement; in some cases, considerably greater, indicating that at least half of the disturbed surface area would be neglected without this insight. The ZOI is used to calculate a more robust data set of volume measurements that can be used to computationally reconstruct a resultant profile for de tailed analysis. Documenting additional changes to various surface roughness par ameters also allows key material attributes of importance to ultimate design applications to be quantified, such as depth of penetration and final abraded surface roughness. Further - more, by investigating the use of custom scratch tips for specific needs, the usefulness of having an abrasion metric that can measure the displaced volume in this standardized

  2. Systematics of the release of residual nuclei from relativistic nucleus-nucleus interactions

    SciTech Connect

    Binns, W.R.; Garrard, T.L.; Israel, M.H.; Kertzmann, M.P.; Klarmann, J.; Stone, E.C.; Waddington, C.J.

    1987-11-01

    We have examined relativistic nuclei of krypton, xenon, holmium, and gold, accelerated in a partially stripped state to a maximum rigidity of about 5.6 GeV, interacting with targets of aluminum, carbon, and polyethylene. For each projectile and target combination we determined the total and partial charge changing cross sections for the production of lighter fragments. From these measurements we have developed a new representation of the dependence of the total charge changing cross sections on beam and target charge. We have also identified simple representations of the variation of the partial cross sections with the charge of the produced fragments and shown that they are dependent on the charge and energy of the beam. The fission of gold nuclei at high energies in these various targets has also been studied.

  3. Systematics of the release of residual nuclei from relativistic nucleus-nucleus interactions

    NASA Technical Reports Server (NTRS)

    Binns, W. R.; Israel, M. H.; Klarmann, J.; Garrard, T. L.; Kertzmann, M. P.

    1987-01-01

    Relativistic nuclei of krypton, xenon, holmium, and gold, accelerated in a partially stripped state to a maximum rigidity of about 5.6 GeV, interacting with targets of aluminum, carbon, and polyethylene are examined. For each projectile and target combination, determinations are made for the total and partial charge changing cross sections for the production of lighter fragments. From these measurements, a new representation of the dependence of the total charge changing cross sections on beam and target charge is developed. Simple representations of the variation of the partial cross sections were identified with the charge of the produced fragments and shown to be dependent on the charge and energy of the beam. The fission of gold nuclei at high energies in these various targets has also been studied.

  4. Number of Sialic Acid Residues in Ganglioside Headgroup Affects Interactions with Neighboring Lipids

    PubMed Central

    Frey, Shelli L.; Lee, Ka Yee C.

    2013-01-01

    Monolayers of binary mixtures of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and asialo-(GA1), disialo-(GD1b) and trisialo-(GT1b) gangliosides were used to determine the effect of ganglioside headgroup charge and geometry on its interactions with the neighboring zwitterionic lipid. Surface pressure versus molecular area isotherm measurements along with concurrent fluorescence microscopy of the monolayers at the air-water interface were complemented with atomic force microscopy imaging of monolayers deposited on solid substrates. Results were used to further develop a proposed geometric packing model that the complementary geometry of DPPC and monosialoganglioside GM1 headgroups affects their close molecular packing, inducing condensation of the layer at small mol % of ganglioside. For GA1, GD1b, and GT1b, a similar condensing effect, followed by a fluidizing effect is seen that varies with glycosphingolipid concentration, but results do not directly follow from geometric arguments because less DPPC is needed to condense ganglioside molecules with larger cross-sectional areas. The variations in critical packing mole ratios can be explained by global effects of headgroup charge and resultant dipole moments within the monolayer. Atomic force microscopy micrographs further support the model of ganglioside-induced DPPC condensation with condensed domains composed of a striped phase of condensed DPPC and DPPC/ganglioside geometrically packed complexes at low concentrations. PMID:24047994

  5. Number of sialic acid residues in ganglioside headgroup affects interactions with neighboring lipids.

    PubMed

    Frey, Shelli L; Lee, Ka Yee C

    2013-09-17

    Monolayers of binary mixtures of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and asialo-(GA1), disialo-(GD1b) and trisialo-(GT1b) gangliosides were used to determine the effect of ganglioside headgroup charge and geometry on its interactions with the neighboring zwitterionic lipid. Surface pressure versus molecular area isotherm measurements along with concurrent fluorescence microscopy of the monolayers at the air-water interface were complemented with atomic force microscopy imaging of monolayers deposited on solid substrates. Results were used to further develop a proposed geometric packing model that the complementary geometry of DPPC and monosialoganglioside GM1 headgroups affects their close molecular packing, inducing condensation of the layer at small mol % of ganglioside. For GA1, GD1b, and GT1b, a similar condensing effect, followed by a fluidizing effect is seen that varies with glycosphingolipid concentration, but results do not directly follow from geometric arguments because less DPPC is needed to condense ganglioside molecules with larger cross-sectional areas. The variations in critical packing mole ratios can be explained by global effects of headgroup charge and resultant dipole moments within the monolayer. Atomic force microscopy micrographs further support the model of ganglioside-induced DPPC condensation with condensed domains composed of a striped phase of condensed DPPC and DPPC/ganglioside geometrically packed complexes at low concentrations. PMID:24047994

  6. Two-body relaxation driven evolution of the young stellar disk in the galactic center

    SciTech Connect

    Šubr, Ladislav; Haas, Jaroslav

    2014-05-10

    The center of our Galaxy hosts almost two hundred very young stars, a subset of which is orbiting the central supermassive black hole (SMBH) in a relatively thin disk-like structure. First analyses indicated a power-law surface density profile of the disk, Σ∝R {sup β} with β = –2. Recently, however, doubts about this profile arose. In particular, it now seems to be better described by a sort of broken power law. By means of both analytical arguments and numerical N-body modeling, we show that such a broken power-law profile is a natural consequence of the two-body relaxation of the disk. Due to the small relative velocities of the nearby stars in co-planar Keplerian orbits around the SMBH, two-body relaxation is effective enough to affect the evolution of the disk on timescales comparable to its estimated age. In the inner, densest part of the disk, the profile becomes rather flat (β ≈ –1) while the outer parts keep imprints of the initial state. Our numerical models show that the observed projected surface density profile of the young stellar disk can result from two-body relaxation driven evolution of a disk with initial single power-law profile with –2 ≲ β ≲ –1.5. In addition, we suggest that two-body relaxation may have caused a significant radial migration of the S-stars toward the central SMBH, thus playing an important role in their formation scenario.

  7. Integrals of motion for the classical two-body problem with drag

    NASA Technical Reports Server (NTRS)

    Jezewski, D. J.; Mittleman, D.

    1983-01-01

    Integrals of motion for the two-body problem with drag are obtained by operating on the second-order vector differential equation describing the motion. The force field consists of an inverse-square gravitational attraction and a drag force proportional to the velocity vector and inversely proportional to the square of the distance to the attracting center. The developed integrals are the analogs of the Keplerian scalar energy, the vector angular momentum, and the Laplace vector.

  8. Two-body physics in quasi-low-dimensional atomic gases under spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Wang, Jing-Kun; Yi, Wei; Zhang, Wei

    2016-06-01

    One of the most dynamic directions in ultracold atomic gas research is the study of low-dimensional physics in quasi-low-dimensional geometries, where atoms are confined in strongly anisotropic traps. Recently, interest has significantly intensified with the realization of synthetic spin-orbit coupling (SOC). As a first step toward understanding the SOC effect in quasi-low-dimensional systems, the solution of two-body problems in different trapping geometries and different types of SOC has attracted great attention in the past few years. In this review, we discuss both the scattering-state and the bound-state solutions of two-body problems in quasi-one and quasi-two dimensions. We show that the degrees of freedom in tightly confined dimensions, in particular with the presence of SOC, may significantly affect system properties. Specifically, in a quasi-one-dimensional atomic gas, a one-dimensional SOC can shift the positions of confinement-induced resonances whereas, in quasitwo- dimensional gases, a Rashba-type SOC tends to increase the two-body binding energy, such that more excited states in the tightly confined direction are occupied and the system is driven further away from a purely two-dimensional gas. The effects of the excited states can be incorporated by adopting an effective low-dimensional Hamiltonian having the form of a two-channel model. With the bare parameters fixed by two-body solutions, this effective Hamiltonian leads to qualitatively different many-body properties compared to a purely low-dimensional model.

  9. Specific Inter-residue Interactions as Determinants of Human Monoacylglycerol Lipase Catalytic Competency: A ROLE FOR GLOBAL CONFORMATIONAL CHANGES.

    PubMed

    Tyukhtenko, Sergiy; Karageorgos, Ioannis; Rajarshi, Girija; Zvonok, Nikolai; Pavlopoulos, Spiro; Janero, David R; Makriyannis, Alexandros

    2016-02-01

    The serine hydrolase monoacylglycerol lipase (MGL) functions as the main metabolizing enzyme of 2-arachidonoyl glycerol, an endocannabinoid signaling lipid whose elevation through genetic or pharmacological MGL ablation exerts therapeutic effects in various preclinical disease models. To inform structure-based MGL inhibitor design, we report the direct NMR detection of a reversible equilibrium between active and inactive states of human MGL (hMGL) that is slow on the NMR time scale and can be modulated in a controlled manner by pH, temperature, and select point mutations. Kinetic measurements revealed that hMGL substrate turnover is rate-limited across this equilibrium. We identify a network of aromatic interactions and hydrogen bonds that regulates hMGL active-inactive state interconversion. The data highlight specific inter-residue interactions within hMGL modulating the enzymes function and implicate transitions between active (open) and inactive (closed) states of the hMGL lid domain in controlling substrate access to the enzymes active site. PMID:26555264

  10. Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin, 1998 Annual Report.

    SciTech Connect

    James, Brenda B.; Pearsons, Todd N.; McMichael, Geoffrey A.

    1999-12-01

    Select ecological interactions and spring chinook salmon residual/precocial abundance were monitored in 1998 as part of the Yakima/Klickitat Fisheries Project's supplementation monitoring program. Monitoring these variables is part of an effort to help evaluate the factors that contribute to, or limit supplementation success. The ecological interactions that were monitored were prey consumption, competition for food, and competition for space. The abundance of spring chinook salmon life-history forms that have the potential to be influenced by supplementation and that have important ecological and genetic roles were monitored (residuals and precocials). Residual spring chinook salmon do not migrate to the ocean during the normal emigration period and continue to rear in freshwater. Precocials are those salmon that precocially mature in freshwater. The purpose of sampling during 1998 was to collect baseline data one year prior to the release of hatchery spring chinook salmon which occurred during the spring of 1999. All sampling that the authors report on here was conducted in upper Yakima River during summer and fall 1998. The stomach fullness of juvenile spring chinook salmon during the summer and fall averaged 12%. The food competition index suggested that mountain whitefish (0.59), rainbow trout (0.55), and redside shiner (0.55) were competing for food with spring chinook salmon. The space competition index suggested that rainbow trout (0.31) and redside shiner (0.39) were competing for space with spring chinook salmon but mountain whitefish (0.05) were not. Age-0 spring chinook salmon selected a fairly narrow range of microhabitat parameters in the summer and fall relative to what was available. Mean focal depths and velocities for age 0 spring chinook salmon during the summer were 0.5 m {+-} 0.2 m and 0.26 m/s {+-} 0.19 m/s, and during the fall 0.5 m {+-} 0.2 m and 0.24 m/s {+-} 0.18 m/s. Among potential competitors, age 1+ rainbow trout exhibited the greatest

  11. Characterization of conserved arginine residues on Cdt1 that affect licensing activity and interaction with Geminin or Mcm complex.

    PubMed

    You, Zhiying; Ode, Koji L; Shindo, Mayumi; Takisawa, Haruhiko; Masai, Hisao

    2016-05-01

    All organisms ensure once and only once replication during S phase through a process called replication licensing. Cdt1 is a key component and crucial loading factor of Mcm complex, which is a central component for the eukaryotic replicative helicase. In higher eukaryotes, timely inhibition of Cdt1 by Geminin is essential to prevent rereplication. Here, we address the mechanism of DNA licensing using purified Cdt1, Mcm and Geminin proteins in combination with replication in Xenopus egg extracts. We mutagenized the 223th arginine of mouse Cdt1 (mCdt1) to cysteine or serine (R-S or R-C, respectively) and 342nd and 346th arginines constituting an arginine finger-like structure to alanine (RR-AA). The RR-AA mutant of Cdt1 could not only rescue the DNA replication activity in Cdt1-depleted extracts but also its specific activity for DNA replication and licensing was significantly increased compared to the wild-type protein. In contrast, the R223 mutants were partially defective in rescue of DNA replication and licensing. Biochemical analyses of these mutant Cdt1 proteins indicated that the RR-AA mutation disabled its functional interaction with Geminin, while R223 mutations resulted in ablation in interaction with the Mcm2∼7 complex. Intriguingly, the R223 mutants are more susceptible to the phosphorylation-induced inactivation or chromatin dissociation. Our results show that conserved arginine residues play critical roles in interaction with Geminin and Mcm that are crucial for proper conformation of the complexes and its licensing activity. PMID:26940553

  12. The distal residue-CO interaction in carbonmonoxy myoglobins: a molecular dynamics study of two distal histidine tautomers.

    PubMed Central

    Jewsbury, P; Kitagawa, T

    1994-01-01

    Four independent 90 ps molecular dynamics simulations of sperm-whale wild-type carbonmonoxy myoglobin (MbCO) have been calculated using a new AMBER force field for the haem prosthetic group. Two trajectories have the distal 64N delta nitrogen protonated, and two have the 64N epsilon nitrogen protonated; all water molecules within 16 A of the carbonyl O are included. In three trajectories, the distal residue remains part of the haem pocket, with the protonated distal nitrogen pointing into the active site. This is in contrast with the neutron diffraction crystal structure, but is consistent with the solution phase CO stretching frequencies (upsilon CO) of MbCO and various of its mutants. There are significant differences in the "closed" pocket structures found for each tautomer: the 64N epsilon H trajectories both show stable distal-CO interactions, whereas the 64N delta H tautomer) has a weaker interaction resulting in a more mobile distal side chain. One trajectory (a 64N delta H tautomer) has the distal histidine moving out into the "solvent", leaving the pocket in an "open" structure, with a large unhindered entrance to the active site. These trajectories suggest that the three upsilon CO frequencies observed for wild-type MbCO in solution, rather than representing significantly different Fe-C-O geometries as such, arise from three different haem pocket structures, each with different electric fields at the ligand. Each pocket structure corresponds to a different distal histidine conformer: the A3 band to the 64N epsilon H tautomer, the A1,2 band to the 64N delta H tautomer, and the A0 band to the absence of any significant interaction with the distal side chain. PMID:7696465

  13. Carboxymethylation of methionine residues in bovine pituitary luteinizing hormone and its subunits. Effects on the binding activity with receptor sites and interactions between subunits.

    PubMed Central

    Cheng, K W

    1976-01-01

    The reaction of iodoacetic acid with bovine lutropin (luteinizing hormone) at pH 3.0 was specific for methionine residues; it was slow and reached its equilibrium after 12 h at 37 degrees C. The number of modified methionine residues increased proportionately with the amount of the alkylating reagent in the reaction mixture. In the presence of a 20-fold molar excess of iodoacetic acid with respect to methionine, essentially all methionine residues in both subunits of bovine lutropin were carboxymethylated. Studies of various recombinations of modified and native alpha and beta subunits showed that methionine residues in bovine lutropin were not essential for interactions between subunits. Various recombinants were characterized by polyacrylamide-gel electrophoresis and gel filtration of Sephadex G-100. Immunological cross-reactivity by radioimmunoassay of the recombinants of modified alpha and beta subunits was relatively similar to that of the native subunits. However, the biological activity measured by receptor-site binding of the recombinants of alpha and beta chains with a total of three alkylated methionine residues was less than 5% of the activity of native lutropin. It is noteworthy that recombinants of a modified subunit and a native counterpart subunit regenerated 20-30 % of biological activity. These findings suggested that at least 1-2 methionine residues in each subunit are involved in the hormone-receptor interaction for bovine lutropin. Images PLATE 1 PMID:187169

  14. Probing RNA-protein interactions using pyrene-labeled oligodeoxynucleotides: Qbeta replicase efficiently binds small RNAs by recognizing pyrimidine residues.

    PubMed

    Preuss, R; Dapprich, J; Walter, N G

    1997-10-31

    Binding of small RNAs by the RNA-dependent RNA polymerase of coliphage Qbeta was studied utilizing a fluorometric assay. A DNA oligonucleotide probe of sequence 5'-d(TTTTTCC) was 5'-end-labeled with pyrene. In this construct, the proximal thymine residues efficiently quench the fluorophore emission in solution. Upon stoichiometric binding of one probe per polymerase molecule, the pyrene steady-state fluorescence increases by two orders of magnitude, the fluorescence anisotropy increases, and a long fluorescence lifetime component of 140 ns appears. With addition of replicable RNA, steady-state fluorescence decreases in a concentration dependent manner and the long lifetime component is lost. This observation most likely reflects displacement of the pyrene-labeled probe from the proposed nucleic acid binding site II of Qbeta replicase. The effect was utilized to access binding affinities of different RNAs to this site in a reverse titration assay format. In 10 mM sodium phosphate (pH 7.0), 100 mM NaCl, at 16 degrees C, equilibrium dissociation constants for different template midi- and minivariant RNAs were calculated to be in the nanomolar range. In general, the minus and plus strands, concomitantly synthesized by Qbeta replicase during replication, exhibited discriminative affinities, while their hybrid bound less efficiently than either of the single strands. Different non-replicable tRNAs also bound to the polymerase with comparable dissociation constants. By titration with DNA homo-oligonucleotides it was shown that the probed site on Qbeta replicase does not require a 2' hydroxyl group for binding nucleic acids, but recognizes pyrimidine residues. Its interaction with thymine is lost in an A.T base-pair, while that with cytosine is retained after Watson-Crick base-pairing. These findings can explain the affinities of RNA-Qbeta replicase interactions reported here and in earlier investigations. The sensitivity of the described fluorometric assay allows

  15. Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin.

    PubMed

    Kuo, Hsiou-Ting; Liu, Shing-Lung; Chiu, Wen-Chieh; Fang, Chun-Jen; Chang, Hsien-Chen; Wang, Wei-Ren; Yang, Po-An; Li, Jhe-Hao; Huang, Shing-Jong; Huang, Shou-Ling; Cheng, Richard P

    2015-05-01

    β-Sheet is one of the major protein secondary structures. Oppositely charged residues are frequently observed across neighboring strands in antiparallel sheets, suggesting the importance of cross-strand ion pairing interactions. The charged amino acids Asp, Glu, Arg, and Lys have different numbers of hydrophobic methylenes linking the charged functionality to the backbone. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on lateral cross-strand ion pairing interactions at non-hydrogen-bonded positions, β-hairpin peptides containing Zbb-Agx (Zbb = Asp, Glu, Aad in increasing length; Agx = Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by NMR methods. The fraction folded population and folding energy were derived from the chemical shift deviation data. Peptides with high fraction folded populations involved charged residue side chain lengths that supported high strand propensity. Double mutant cycle analysis was used to determine the interaction energy for the potential lateral ion pairs. Minimal interaction was observed between residues with short side chains, most likely due to the diffused positive charge on the guanidinium group, which weakened cross-strand electrostatic interactions with the carboxylate side chain. Only the Aad-Arg/Agh interactions with long side chains clearly exhibited stabilizing energetics, possibly relying on hydrophobics. A survey of a non-redundant protein structure database revealed that the statistical sheet pair propensity followed the trend Asp-Arg < Glu-Arg, implying the need for matching long side chains. This suggested the need for long side chains on both guanidinium-bearing and carboxylate-bearing residues to stabilize the β-hairpin motif. PMID:25646959

  16. Low-energy structure studies of odd-odd deformed nuclei and the coriolis and residual interactions

    SciTech Connect

    Dewberry, R.A.

    1980-08-01

    The nuclear level structure of /sup 176/Lu, /sup 170/Tm, /sup 166/Ho, and /sup 160/Tb have been studied by means of the /sup 177/Hf(t,..cap alpha..)/sup 176/Lu, /sup 171/Yb(t,..cap alpha..)/sup 170/Tm, /sup 167/Er(t,..cap alpha..)/sup 166/Ho, and /sup 161/Dy(t,..cap alpha..)/sup 160/Tb reactions and with the use of previously published (d,p) spectroscopy and gamma transitions from the (n,..gamma..) reactions. The (t,..cap alpha..) reactions have been performed and analyzed with 17 MeV tritons and the Los Alamos Q3D spectrometer. Eighty-one new rotational states in excited proton configurations or vibrational excited states are proposed. An independent parameterization of the Coriolis interaction is presented, which leads to satisfactory results in reproducing experimental single-particle transfer reaction cross-sections by theoretical calculations. The anomalous population of the excited neutron configurations (404 reduces to -624 up arrow) in /sup 176/Lu and (411 reduces to +- 512 up arrow) in /sup 170/Tm, and the anomalously low (t,..cap alpha..) cross-sections of the (411 up arrow +- 633 up arrow) configuration in /sup 166/Ho are observed. Qualitative explanation of the anomalies is presented in terms of the mixing of states which satisfy the requirement delta/sub I'/,/sub I/delta/sub K'/,/sub K/. Off-diagonal H/sub INT/ matrix elements are calculated, which show that the residual interaction cannot be used to account for the magnitude of the cross-sections observed.

  17. Simultaneous determination of residues of dipyrone metabolites in goat tissues by hydrophilic interaction liquid chromatography tandem mass spectrometry.

    PubMed

    Zhang, Chong; Zhang, Lifang; Cao, Suqing; Jiang, Zhaoling; Wu, Hao; Yan, Ming; Zhang, Xiaoxiao; Jiang, Shanxiang; Xue, Feiqun

    2016-04-01

    A reliable LC-MS/MS method with high sensitivity was developed and validated for the determination of dipyrone (DIP) metabolites in goat muscle, fat, liver, and kidney samples. Analytes were extracted using acetonitrile mixed with ammonia solution. After dehydration and evaporation to dryness, extracts were purified using an Oasis MAX cartridge. Chromatographic separation was performed on a hydrophilic interaction liquid chromatography column. The analytes were then detected using triple-quadrupole mass spectrometry in positive electrospray ionization and multiple reaction monitoring mode. Calibration plots were constructed using matrix-matched standards and showed good linearity. Limits of quantification for 4-methylaminoantipyrine (MAA), 4-formylaminoantipyrine (FAA), and 4-acetylaminoantipyrone (AAA) ranged from 0.4 μg kg(-1) to 6 μg kg(-1), while those for 4-aminoantipyrone (AA) ranged from 10 μg kg(-1) to 125 μg kg(-1) in all tissues. The developed method was successfully applied in the determination of DIP metabolite residues in actual goat tissues. PMID:26593468

  18. Identification of residues crucial for the interaction between human neuroglobin and the α-subunit of heterotrimeric Gi protein

    PubMed Central

    Takahashi, Nozomu; Wakasugi, Keisuke

    2016-01-01

    Mammalian neuroglobin (Ngb) protects neuronal cells under conditions of oxidative stress. We previously showed that human Ngb acts as a guanine nucleotide dissociation inhibitor (GDI) for the α-subunits of heterotrimeric Gi/o proteins and inhibits the decrease in cAMP concentration, leading to protection against cell death. In the present study, we used an eukaryotic expression vector driving high-level expression of human wild-type Ngb or Ngb mutants that either exhibit or lack GDI activities in human cells. We demonstrate that the GDI activity of human Ngb is tightly correlated with its neuroprotective activity. We further demonstrate that Glu53, Glu60, and Glu118 of human Ngb are crucial for both the neuroprotective activity and interaction with Gαi1. Moreover, we show that Lys46, Lys70, Arg208, Lys209, and Lys210 residues of Gαi1 are important for binding to human Ngb. We propose a molecular docking model of the complex between human Ngb and Gαi1. PMID:27109834

  19. Low oxygen affinity in reptilian hemoglobin D: prediction of residue interactions in Geochelone carbonaria HbD by homology modeling.

    PubMed

    Lutfullah, Ghosia; Khalil, Hilal Shahid; Amin, Farhat; Azhar, Noreen

    2008-04-01

    The homology model of hemoglobin D from Geochelone carbonaria, the red-footed tortoise was predicted using the 3D structure coordinates of Geochelone gigantea hemoglobin D as the template. The model was built using the program, MODELLER (8v1) and evaluated with PROCHECK and PROSA. The present study features an in-depth analysis of the 3D model and its conformational changes brought about with variations in its environment. These structural changes are correlated with its ability to adapt to different environmental constraints enabling the organism to better suit to its natural habitat. The model shows additional contacts between amino acid pairs of alpha-119 and beta-55, alpha-35 and beta-124, alpha-103 and beta-112, alpha-115 and beta-116, alpha-120 and beta-52, alpha-120 and beta-55, alpha-36 and beta-127 which are not found in human hemoglobin. It is predicted that these contacts may result in T-state stabilization thus lowering oxygen affinity. Furthermore, decrease in the interaction of phosphate heteroatoms with the amino acid residues of G. carbonaria Hb was also predicted in this study. PMID:18085430

  20. A novel anti-aldolase C antibody specifically interacts with residues 85–102 of the protein

    PubMed Central

    Langellotti, Simona; Romano, Maurizio; Guarnaccia, Corrado; Granata, Vincenzo; Orrù, Stefania; Zagari, Adriana; Baralle, Francisco E; Salvatore, Francesco

    2014-01-01

    Aldolase C is a brain-specific glycolytic isozyme whose complete repertoire of functions are obscure. This lack of knowledge can be addressed using molecular tools that discriminate the protein from the homologous, ubiquitous paralog aldolase A. The anti-aldolase C antibodies currently available are polyclonal and not highly specific. We obtained the novel monoclonal antibody 9F against human aldolase C, characterized its isoform specificity and tested its performance. First, we investigated the specificity of 9F for aldolase C. Then, using bioinformatic tools coupled to molecular cloning and chemical synthesis approaches, we produced truncated human aldolase C fragments, and assessed 9F binding to these fragments by western blot and ELISA assays. This strategy revealed that residues 85–102 harbor the epitope-containing region recognized by 9F. The efficiency of 9F was demonstrated also for immunoprecipitation assays. Finally, surface plasmon resonance revealed that the protein has a high affinity toward the epitope-containing peptide. Taken together, our findings show that epitope recognition is sequence-driven and is independent of the three-dimensional structure. In conclusion, given its specific molecular interaction, 9F is a novel and powerful tool to investigate aldolase C’s functions in the brain. PMID:24525694

  1. Phase-space structure of the Buckingham's two-body problem

    NASA Astrophysics Data System (ADS)

    Pricopi, D.; Popescu, E.

    2016-06-01

    In this paper, we study the global flow for the two-body problem associated to the Buckingham potential. For this, using McGehee-type transformations, we write the regularized equations of motion. Then, reducing the 4-dimensional phase space to a 2-dimension one, the global flow in the phase plane is described for all possible values of the parameters of the potential and those of the energy and angular momentum constants. Every phase trajectory is interpreted in terms of physical motion, our problem being depicted both geometrically and physically.

  2. Construction of Effective Electromagnetic Currents for Two-Body Quasipotential Equations

    SciTech Connect

    Dmitri Krioukov

    1998-09-01

    A systematic algebraic approach for the construction of effective electro-magnetic currents consistent with relativistic two-body quasipotential equations is presented. This approach generalizes the Mandelstam formalism and applies it to a generic quasipotential reduction method. The use of Ward-Takahashi identities for the effective currents guarantees conservation of current matrix elements involving any combination of bound and scattering states. This approach is shown to reproduce previous results for current matrix elements for the particular cases of the Gross and Blankenbecler-Sugar equations. A generic method of truncation of the quasipotential effective current with respect to the number of boson exchanges is introduced.

  3. Data-adaptive unfolding of nonergodic spectra: Two-Body Random Ensemble

    NASA Astrophysics Data System (ADS)

    Fossion, R.; Torres Vargas, G.; Velázquez, V.; López Vieyra, J. C.

    2015-01-01

    The statistics of spectral fluctuations is sensitive to the unfolding procedure that separates global from local properties. Previously, we presented a parameter-free and data- adaptive unfolding method that we demonstrated to be highly effective for standard random- matrix ensembles from Random Matrix Theory (RMT). More general ensembles often break the ergodicity property, which leads to ambiguities between individual-spectrum averaged and ensemble-averaged fluctuation measures. Here, we apply our data-adaptive unfolding to a nonergodic Two-Body Random Ensemble (TBRE). In the present approach, both fluctuation measures can be calculated simultaneously within the same unfolding step, and possible arbitrarities introduced by traditional unfolding procedures are avoided.

  4. Two-body potential model based on cosine series expansion for ionic materials

    SciTech Connect

    Oda, Takuji; Weber, William J.; Tanigawa, Hisashi

    2015-09-23

    There is a method to construct a two-body potential model for ionic materials with a Fourier series basis and we examine it. For this method, the coefficients of cosine basis functions are uniquely determined by solving simultaneous linear equations to minimize the sum of weighted mean square errors in energy, force and stress, where first-principles calculation results are used as the reference data. As a validation test of the method, potential models for magnesium oxide are constructed. The mean square errors appropriately converge with respect to the truncation of the cosine series. This result mathematically indicates that the constructed potential model is sufficiently close to the one that is achieved with the non-truncated Fourier series and demonstrates that this potential virtually provides minimum error from the reference data within the two-body representation. The constructed potential models work appropriately in both molecular statics and dynamics simulations, especially if a two-step correction to revise errors expected in the reference data is performed, and the models clearly outperform two existing Buckingham potential models that were tested. Moreover, the good agreement over a broad range of energies and forces with first-principles calculations should enable the prediction of materials behavior away from equilibrium conditions, such as a system under irradiation.

  5. C P -violating polarization asymmetry in charmless two-body decays of beauty baryons

    NASA Astrophysics Data System (ADS)

    He, Min; He, Xiao-Gang; Li, Guan-Nan

    2015-08-01

    Several baryons containing a heavy b-quark, the b-baryons, have been discovered. The charmless two-body decays of b-baryons can provide a new platform for C P violating studies in a similar way provided by charmless two-body decays of B-meson. There are new C P violating observables related to baryon polarization in b-baryon decays. We show that in the flavor S U (3 ) limit, there exists relations involving different combinations of the decay amplitudes compared with those in C P violating rate asymmetry. These new relations therefore provide interesting tests for the mechanism of C P violations in the standard model (SM) and flavor S U (3 ) symmetry. Such tests could complement the b-meson decay studies which hint at a better flavor S U (3 ) conservation in b-hadron decays than in kaon and hyperon decays. Future data from LHCb can provide new information about C P violation in the SM.

  6. Two-body potential model based on cosine series expansion for ionic materials

    DOE PAGESBeta

    Oda, Takuji; Weber, William J.; Tanigawa, Hisashi

    2015-09-23

    There is a method to construct a two-body potential model for ionic materials with a Fourier series basis and we examine it. For this method, the coefficients of cosine basis functions are uniquely determined by solving simultaneous linear equations to minimize the sum of weighted mean square errors in energy, force and stress, where first-principles calculation results are used as the reference data. As a validation test of the method, potential models for magnesium oxide are constructed. The mean square errors appropriately converge with respect to the truncation of the cosine series. This result mathematically indicates that the constructed potentialmore » model is sufficiently close to the one that is achieved with the non-truncated Fourier series and demonstrates that this potential virtually provides minimum error from the reference data within the two-body representation. The constructed potential models work appropriately in both molecular statics and dynamics simulations, especially if a two-step correction to revise errors expected in the reference data is performed, and the models clearly outperform two existing Buckingham potential models that were tested. Moreover, the good agreement over a broad range of energies and forces with first-principles calculations should enable the prediction of materials behavior away from equilibrium conditions, such as a system under irradiation.« less

  7. Applications of the Kustaanheimo-Stieffel transformation of the perturbed two-body problem

    NASA Technical Reports Server (NTRS)

    Bond, V. R.

    1973-01-01

    The Newtonian differential equations of motion for the two-body problem can be transformed into four linear harmonic-oscillator equations by simultaneously applying the regularization step dt/ds = r and the Kustaanheimo-Stieffel (KS) transformation. The regularization step changes the independent variable from time to a new variable s, and the KS transformation transforms the position and velocity vectors from Cartesian space into a four-dimensional space. A derivation of a uniform, regular solution for the perturbed two-body problem in the four-dimensional space is presented. The variation-of-parameters technique is used to develop expressions for the derivatives of ten elements (which are constants in the unperturbed motion) for the general case that includes both perturbations which can arise from a potential and perturbations which cannot be derived from a potential. This ten-element solution has mixed secular terms that degrade the long-term accuracy during numerical integration. Therefore, to eliminate these terms, the solution is modified by introducing two additional elements.

  8. Non-singular orbital elements for special perturbations in the two-body problem

    NASA Astrophysics Data System (ADS)

    Baù, Giulio; Bombardelli, Claudio; Peláez, Jesús; Lorenzini, Enrico

    2015-12-01

    Seven spatial elements and a time element are proposed as the state variables of a new special perturbation method for the two-body problem. The new elements hold for zero eccentricity and inclination and for negative values of the total energy. They are developed by combining a spatial transformation into projective coordinates (as in the Burdet-Ferrándiz regularization) with a time transformation in which the exponent of the orbital radius is equal to one instead of two (as commonly done in the literature). By following this approach, we discover a new linearization of the two-body problem, from which the orbital elements can be generated by the variation of parameters method. The geometrical significance of the spatial quantities is revealed by a new intermediate frame which differs from a local vertical local horizontal frame by one rotation in the instantaneous orbital plane. Four elements parametrize the attitude in space of this frame, which in turn defines the orientation of the orbital plane and fixes the departure direction for the longitude of the propagated body. The remaining three elements determine the motion along the radial unit vector and the orbital longitude. The performance of the method, tested using a series of benchmark orbit propagation scenarios, is extremely good when compared to several regularized formulations, some of which have been modified and improved here for the first time.

  9. A new set of integrals of motion to propagate the perturbed two-body problem

    NASA Astrophysics Data System (ADS)

    Baù, Giulio; Bombardelli, Claudio; Peláez, Jesús

    2013-05-01

    A formulation of the perturbed two-body problem that relies on a new set of orbital elements is presented. The proposed method represents a generalization of the special perturbation method published by Peláez et al. (Celest Mech Dyn Astron 97(2):131-150, 2007) for the case of a perturbing force that is partially or totally derivable from a potential. We accomplish this result by employing a generalized Sundman time transformation in the framework of the projective decomposition, which is a known approach for transforming the two-body problem into a set of linear and regular differential equations of motion. Numerical tests, carried out with examples extensively used in the literature, show the remarkable improvement of the performance of the new method for different kinds of perturbations and eccentricities. In particular, one notable result is that the quadratic dependence of the position error on the time-like argument exhibited by Peláez's method for near-circular motion under the J2 perturbation is transformed into linear. Moreover, the method reveals to be competitive with two very popular element methods derived from the Kustaanheimo-Stiefel and Sperling-Burdet regularizations.

  10. The importance of residues 195-206 of human blood clotting factor VII in the interaction of factor VII with tissue factor

    SciTech Connect

    Wildgoose, P.; Kisiel, W.; Kazim, A.L. )

    1990-09-01

    Previous studies indicated that human and bovine factor VII exhibit 71% amino acid sequence identity. In the present study, competition binding experiments revealed that the interaction of human factor VII with cell-surface human tissue factor was not inhibited by 100-fold molar excess of bovine factor VII. This finding indicated that bovine and human factor VII are not structurally homologous in the region(s) where human factor VII interacts with human tissue factor. On this premise, the authors synthesized three peptides corresponding to regions of human factor VII that exhibited marked structural dissimilarity to bovine factor VII; these regions of dissimilarity included residues 195-206, 263-274, and 314-326. Peptide 195-206 inhibited the interaction of factor VII with cell-surface tissue factor and the activation of factor X by a complex of factor VIIa and tissue factor half-maximally at concentrations of 1-2 mM. A structurally rearranged form of peptide 195-206 containing an aspartimide residue inhibited these reactions half-maximally at concentrations of 250-300 {mu}M. In contrast, neither peptide 263-274 nor peptide 314-326, at 2 mM concentration, significantly affected either factor VIIa interaction with tissue factor or factor VIIa-mediated activation of factor X. The data provide presumptive evidence that residues 195-206 of human factor VII are involved in the interaction of human factor VII with the extracellular domain of human tissue factor apoprotein.

  11. Baseline Residual Kidney Function and Its Ensuing Rate of Decline Interact to Predict Mortality of Peritoneal Dialysis Patients

    PubMed Central

    Pérez Fontán, Miguel; Remón Rodríguez, César; da Cunha Naveira, Marta; Borràs Sans, Mercè; Rodríguez Suárez, Carmen; Quirós Ganga, Pedro; Sánchez Alvarez, Emilio; Rodríguez-Carmona, Ana

    2016-01-01

    Background Baseline residual kidney function (RKF) and its rate of decline during follow-up are purported to be reliable outcome predictors of patients undergoing Peritoneal Dialysis (PD). The independent contribution of each of these factors has not been elucidated. Method We report a multicenter, longitudinal study of 493 patients incident on PD and satisfying two conditions: a glomerular filtration rate (GFR) ≥1 mL/minute and a daily diuresis ≥300 mL. The main variables were the GFR (mean of urea and creatinine clearances) at PD inception and the GFR rate of decline during follow-up. The main outcome variable was patient mortality. The secondary outcome variables were: PD technique failure and risk of peritoneal infection. The statistical analysis was based on a multivariate approach, placing an emphasis on the interactions between the two main study variables. Main Results Baseline GFR and its rate of decline performed well as independent predictors of both patient mortality and risk of peritoneal infection. These two main study variables maintained a moderate correlation with each other (r2 = 0.12, p<0.0005), and interacted clearly, as predictors of patient mortality. A low baseline GFR followed by a fast decline portended the worst survival outcome (adjusted HR 3.84, 95%CI 1.81–8.14, p<0.0005)(Ref. baseline GFR above median plus rate of decline below median). In general, the rate of decline of RKF had a greater effect on mortality than baseline GFR, which had no detectable effect on survival when the decline of RKF was slow (HR 1.17, 95% CI 0.81–2.22, p = 0.22). Conversely, a relatively high GFR at the start of PD still carried a significant risk of mortality, when RKF declined rapidly (HR 1.89, 95% CI 1.05–3.72, p = 0.028). Conclusion The risk-benefit balance of an early versus late start of PD cannot be evaluated without taking into consideration the rate of decline of RKF. This circumstance may contribute to explain the controversial results

  12. First results with charmless two-body B-decays at LHCb, and future prospects

    SciTech Connect

    2011-02-22

    LHCb is an experiment which is designed to perform flavour physics measurements at the LHC. Charged two-body charmless B decays (e.g. B^0 -> Kpi, pipi, B_s->KK, etc) receive significant contributions from loop diagrams and are thus sensitive probes of New Physics. Study of these modes is therefore an important physics goal of LHCb. First results will be presented, using around 37 pb^{-1} of data collected at \\sqrt{s}=7 TeV in 2010. These results illustrate the power of the LHCb trigger system and particle identification capabilities of the RICH detectors in isolating clean samples of each final state, and include preliminary measurements of direct CP-violation in certain key modes. The prospects for these measurements in the coming run will be presented. A brief survey will also be given of results and prospect in other areas of the LHCb physics programme.

  13. Opposite charged two-body system of identical counterrotating black holes

    NASA Astrophysics Data System (ADS)

    Cabrera-Munguia, I.; Lämmerzahl, Claus; López, L. A.; Macías, Alfredo

    2013-10-01

    A four-parametric exact solution describing a two-body system of identical Kerr-Newman counterrotating black holes endowed with opposite electric/magnetic charges is presented. The axis conditions are solved in order to really describe two black holes separated by a massless strut. Moreover, the explicit form of the horizon half length parameter σ in terms of physical Komar parameters, i.e., Komar’s mass M, electric charge QE, angular momentum J, and a coordinate distance R is derived. Additionally, magnetic charges QB arise from the rotation of electrically charged black holes. As a consequence, in order to account for the contribution to the mass of the magnetic charge, the usual Smarr mass formula should be generalized, as it is proposed by A. Tomimatsu, Prog. Theor. Phys. 72, 73 (1984).

  14. Geography of the rotational resonances and their stability in the ellipsoidal full two body problem

    NASA Astrophysics Data System (ADS)

    Jafari Nadoushan, Mahdi; Assadian, Nima

    2016-02-01

    A fourth-order Hamiltonian describing the planar full two body problem is obtained, allowing for a mapping out of the geography of spin-spin-orbit resonances. The expansion of the mutual potential function up to the fourth-order results in the angles to come through one single harmonic and consequently the rotation of both bodies and mutual orbit are coupled. Having derived relative equilibria, stability analysis showed that the stability conditions are independent of physical and orbital characteristics. Simultaneously chaotic motion of bodies is investigated through the Chirikov diffusion utilizing geographic information of the complete resonances. The results show that simultaneous chaos among the binary asteroids is not expected to be prevalent due to the mass distribution of primary in compare with secondary. If mass distribution of bodies is of the same order, simultaneous chaos and global instability are achievable.

  15. First results with charmless two-body B-decays at LHCb, and future prospects

    ScienceCinema

    None

    2011-04-25

    LHCb is an experiment which is designed to perform flavour physics measurements at the LHC. Charged two-body charmless B decays (e.g. B^0 -> Kpi, pipi, B_s->KK, etc) receive significant contributions from loop diagrams and are thus sensitive probes of New Physics. Study of these modes is therefore an important physics goal of LHCb. First results will be presented, using around 37 pb^{-1} of data collected at \\sqrt{s}=7 TeV in 2010. These results illustrate the power of the LHCb trigger system and particle identification capabilities of the RICH detectors in isolating clean samples of each final state, and include preliminary measurements of direct CP-violation in certain key modes. The prospects for these measurements in the coming run will be presented. A brief survey will also be given of results and prospect in other areas of the LHCb physics programme.

  16. Parametric study of two-body floating-point wave absorber

    NASA Astrophysics Data System (ADS)

    Amiri, Atena; Panahi, Roozbeh; Radfar, Soheil

    2016-03-01

    In this paper, we present a comprehensive numerical simulation of a point wave absorber in deep water. Analyses are performed in both the frequency and time domains. The converter is a two-body floating-point absorber (FPA) with one degree of freedom in the heave direction. Its two parts are connected by a linear mass-spring-damper system. The commercial ANSYS-AQWA software used in this study performs well in considering validations. The velocity potential is obtained by assuming incompressible and irrotational flow. As such, we investigated the effects of wave characteristics on energy conversion and device efficiency, including wave height and wave period, as well as the device diameter, draft, geometry, and damping coefficient. To validate the model, we compared our numerical results with those from similar experiments. Our study results can clearly help to maximize the converter's efficiency when considering specific conditions.

  17. Treatment of the two-body Coulomb problem as a short-range potential

    NASA Astrophysics Data System (ADS)

    Gasaneo, G.; Ancarani, L. U.

    2009-12-01

    The scattering wave function and the transition amplitude for the two-body Coulomb problem are written as power series of the Sommerfeld parameter. Making use of a mathematical study of the nth derivatives of Kummer function with respect to its first parameter, the series coefficients are expressed analytically in terms of multivariable hypergeometric functions. We establish the connection with the Born series based on the free particle Green’s function and show its applicability to long-range potentials. We also relate our analysis to recent works on the distorted-wave theory for the Coulomb problem. For the transition amplitude, the Born series is presented and compared to the series obtained from the exact well-known Rutherford result. Since the two series differ, care must be taken when extracting the relevant information about the scattering. Finally, implications for three-body problems are discussed.

  18. Numerical integration of a relativistic two-body problem via a multiple scales method

    NASA Astrophysics Data System (ADS)

    Abouelmagd, Elbaz I.; Elshaboury, S. M.; Selim, H. H.

    2016-01-01

    We offer an analytical study on the dynamics of a two-body problem perturbed by small post-Newtonian relativistic term. We prove that, while the angular momentum is not conserved, the motion is planar. We also show that the energy is subject to small changes due to the relativistic effect. We also offer a periodic solution to this problem, obtained by a method based on the separation of time scales. We demonstrate that our solution is more general than the method developed in the book by Brumberg (Essential Relativistic Celestial Mechanics, Hilger, Bristol, 1991). The practical applicability of this model may be in studies of the long-term evolution of relativistic binaries (neutron stars or black holes).

  19. Proton-Nucleus Elastic Cross Sections Using Two-Body In-Medium Scattering Amplitudes

    NASA Technical Reports Server (NTRS)

    Tripathi, R. K.; Wilson, John W.; Cucinotta, Francis A.

    2001-01-01

    Recently, a method was developed of extracting nucleon-nucleon (NN) cross sections in the medium directly from experiment. The in-medium NN cross sections form the basic ingredients of several heavy-ion scattering approaches including the coupled-channel approach developed at the Langley Research Center. The ratio of the real to the imaginary part of the two-body scattering amplitude in the medium was investigated. These ratios are used in combination with the in-medium NN cross sections to calculate elastic proton-nucleus cross sections. The agreement is excellent with the available experimental data. These cross sections are needed for the radiation risk assessment of space missions.

  20. Dark energy in the two-body problem: The local group of galaxies

    NASA Astrophysics Data System (ADS)

    Emelyanov, N. V.; Kovalyov, M. Yu.; Chernin, A. D.

    2015-06-01

    The two-body problem of classical mechanics can be extended in a natural way by introducing a universal dark-energy background, which acts as a third dynamical factor. For real systems of galaxies, the corresponding additional acceleration is described by general relativity in the Newtonian limit, in which deviations from the Minkowski metric are very small. It is shown that this acceleration has the same form in different inertial and non-inertial reference frames. The invariance of the acceleration produced by dark energy reflects the fact that, according to its mechanical properties, dark energy is a vacuum that is comoving with any motion. In this generalized formulation, as in the classical case, the two-body problem with a dark-energy background reduces to the motion of a single body in a central field. Two problems of this kind are considered for the Local Group of galaxies. The first, "internal," problem concerns the binary system formed by the main bodies of the Local Group: our galaxy and M31. The subject of the second, "external," problem is the binary system formed by the Local Group as a whole and its closest neighbor, the Virgo Cluster. In the internal problem, the effect of the dark energy is that the binary system is not bound if its mass does not exceed 3 × 1012 M⊙, which is allowed by the observational data. The external problem demonstrates the possibility of an evolutionary scenario in which a group could initially be located in the volume of a cluster, but then leave it and, moving away with an acceleration created by dark energy, arrive at the observed distance from the cluster.

  1. Energy spectra of massive two-body decay products and mass measurement

    NASA Astrophysics Data System (ADS)

    Agashe, Kaustubh; Franceschini, Roberto; Hong, Sungwoo; Kim, Doojin

    2016-04-01

    We have recently established a new method for measuring the mass of unstable particles produced at hadron colliders based on the analysis of the energy distribution of a mass less product from their two-body decays. The central ingredient of our proposal is the remarkable result that, for an unpolarized decaying particle, the location of the peak in the energy distribution of the observed decay product is identical to the (fixed) value of the energy that this particle would have in the rest-frame of the decaying particle, which, in turn, is a simple function of the involved masses. In addition, we utilized the property that this energy distribution is symmetric around the location of peak when energy is plotted on a logarithmic scale. The general strategy was demonstrated in several specific cases, including both beyond the standard model particles, as well as for the top quark. In the present work, we generalize this method to the case of a massive decay product from a two-body decay; this procedure is far from trivial because (in general) both the above-mentioned properties are no longer valid. Nonetheless, we propose a suitably modified parametrization of the energy distribution that was used successfully for the massless case, which can deal with the massive case as well. We test this parametrization on concrete examples of energy spectra of Z bosons from the decay of a heavier supersymmetric partner of top quark (stop) into a Z boson and a lighter stop. After establishing the accuracy of this parametrization, we study a realistic application for the same process, but now including dominant backgrounds and using foreseeable statistics at LHC14, in order to determine the performance of this method for an actual mass measurement. The upshot of our present and previous work is that, in spite of energy being a Lorentz-variant quantity, its distribution emerges as a powerful tool for mass measurement at hadron colliders.

  2. Elicitin-Induced Distal Systemic Resistance in Plants is Mediated Through the Protein-Protein Interactions Influenced by Selected Lysine Residues.

    PubMed

    Uhlíková, Hana; Obořil, Michal; Klempová, Jitka; Šedo, Ondrej; Zdráhal, Zbyněk; Kašparovský, Tomáš; Skládal, Petr; Lochman, Jan

    2016-01-01

    Elicitins are a family of small proteins with sterol-binding activity that are secreted by Phytophthora and Pythium sp. classified as oomycete PAMPs. Although α- and β-elicitins bind with the same affinity to one high affinity binding site on the plasma membrane, β-elicitins (possessing 6-7 lysine residues) are generally 50- to 100-fold more active at inducing distal HR and systemic resistance than the α-isoforms (with only 1-3 lysine residues). To examine the role of lysine residues in elicitin biological activity, we employed site-directed mutagenesis to prepare a series of β-elicitin cryptogein variants with mutations on specific lysine residues. In contrast to direct infiltration of protein into leaves, application to the stem revealed a rough correlation between protein's charge and biological activity, resulting in protection against Phytophthora parasitica. A detailed analysis of proteins' movement in plants showed no substantial differences in distribution through phloem indicating differences in consequent apoplastic or symplastic transport. In this process, an important role of homodimer formation together with the ability to form a heterodimer with potential partner represented by endogenous plants LTPs is suggested. Our work demonstrates a key role of selected lysine residues in these interactions and stresses the importance of processes preceding elicitin recognition responsible for induction of distal systemic resistance. PMID:26904041

  3. Elicitin-Induced Distal Systemic Resistance in Plants is Mediated Through the Protein–Protein Interactions Influenced by Selected Lysine Residues

    PubMed Central

    Uhlíková, Hana; Obořil, Michal; Klempová, Jitka; Šedo, Ondrej; Zdráhal, Zbyněk; Kašparovský, Tomáš; Skládal, Petr; Lochman, Jan

    2016-01-01

    Elicitins are a family of small proteins with sterol-binding activity that are secreted by Phytophthora and Pythium sp. classified as oomycete PAMPs. Although α- and β-elicitins bind with the same affinity to one high affinity binding site on the plasma membrane, β-elicitins (possessing 6–7 lysine residues) are generally 50- to 100-fold more active at inducing distal HR and systemic resistance than the α-isoforms (with only 1–3 lysine residues). To examine the role of lysine residues in elicitin biological activity, we employed site-directed mutagenesis to prepare a series of β-elicitin cryptogein variants with mutations on specific lysine residues. In contrast to direct infiltration of protein into leaves, application to the stem revealed a rough correlation between protein’s charge and biological activity, resulting in protection against Phytophthora parasitica. A detailed analysis of proteins’ movement in plants showed no substantial differences in distribution through phloem indicating differences in consequent apoplastic or symplastic transport. In this process, an important role of homodimer formation together with the ability to form a heterodimer with potential partner represented by endogenous plants LTPs is suggested. Our work demonstrates a key role of selected lysine residues in these interactions and stresses the importance of processes preceding elicitin recognition responsible for induction of distal systemic resistance. PMID:26904041

  4. Water-soluble LYNX1 Residues Important for Interaction with Muscle-type and/or Neuronal Nicotinic Receptors*

    PubMed Central

    Lyukmanova, Ekaterina N.; Shulepko, Mikhail A.; Buldakova, Svetlana L.; Kasheverov, Igor E.; Shenkarev, Zakhar O.; Reshetnikov, Roman V.; Filkin, Sergey Y.; Kudryavtsev, Denis S.; Ojomoko, Lucy O.; Kryukova, Elena V.; Dolgikh, Dmitry A.; Kirpichnikov, Mikhail P.; Bregestovski, Piotr D.; Tsetlin, Victor I.

    2013-01-01

    Human LYNX1, belonging to the Ly6/neurotoxin family of three-finger proteins, is membrane-tethered with a glycosylphosphatidylinositol anchor and modulates the activity of nicotinic acetylcholine receptors (nAChR). Recent preparation of LYNX1 as an individual protein in the form of water-soluble domain lacking glycosylphosphatidylinositol anchor (ws-LYNX1; Lyukmanova, E. N., Shenkarev, Z. O., Shulepko, M. A., Mineev, K. S., D'Hoedt, D., Kasheverov, I. E., Filkin, S. Y., Krivolapova, A. P., Janickova, H., Dolezal, V., Dolgikh, D. A., Arseniev, A. S., Bertrand, D., Tsetlin, V. I., and Kirpichnikov, M. P. (2011) NMR structure and action on nicotinic acetylcholine receptors of water-soluble domain of human LYNX1. J. Biol. Chem. 286, 10618–10627) revealed the attachment at the agonist-binding site in the acetylcholine-binding protein (AChBP) and muscle nAChR but outside it, in the neuronal nAChRs. Here, we obtained a series of ws-LYNX1 mutants (T35A, P36A, T37A, R38A, K40A, Y54A, Y57A, K59A) and examined by radioligand analysis or patch clamp technique their interaction with the AChBP, Torpedo californica nAChR and chimeric receptor composed of the α7 nAChR extracellular ligand-binding domain and the transmembrane domain of α1 glycine receptor (α7-GlyR). Against AChBP, there was either no change in activity (T35A, T37A), slight decrease (K40A, K59A), and even enhancement for the rest mutants (most pronounced for P36A and R38A). With both receptors, many mutants lost inhibitory activity, but the increased inhibition was observed for P36A at α7-GlyR. Thus, there are subtype-specific and common ws-LYNX1 residues recognizing distinct targets. Because ws-LYNX1 was inactive against glycine receptor, its “non-classical” binding sites on α7 nAChR should be within the extracellular domain. Micromolar affinities and fast washout rates measured for ws-LYNX1 and its mutants are in contrast to nanomolar affinities and irreversibility of binding for α-bungarotoxin and

  5. The second-sphere residue T263 is important for the function and catalytic activity of PTP1B via interaction with the WPD-loop.

    PubMed

    Xiao, Peng; Wang, Xiao; Wang, Hong-Mei; Fu, Xiao-Lei; Cui, Fu-ai; Yu, Xiao; Wen, Shi-shuai; Bi, Wen-Xiang; Sun, Jin-Peng

    2014-12-01

    Protein tyrosine phosphatases have diverse substrate specificities and intrinsic activities that lay the foundations for the fine-tuning of a phosphorylation network to precisely regulate cellular signal transduction. All classical PTPs share common catalytic mechanisms, and the important catalytic residues in the first sphere of their active sites have been well characterized. However, little attention has been paid to the second-sphere residues that are potentially important in defining the intrinsic activity and substrate specificity of PTPs. Here, we find that a conserved second-sphere residue, Thr263, located in the surface Q-loop is important for both the function and activity of PTPs. Using PTP1B as a study model, we found that mutations of Thr263 impaired the negative regulation role of PTP1B in insulin signaling. A detailed mechanistic study utilizing steady-state kinetics, Brønsted analysis and pH dependence in the presence of pNPP or phosphopeptide substrates revealed that Thr263 is required for the stabilization of the leaving group during catalysis. Further crystallographic studies and structural comparison revealed that Thr263 regulates the general acid function through modulation of the WPD-loop by the T263:F182/Y/H interaction pair, which is conserved in 26 out of 32 classical PTPs. In addition, the hydrophobic interaction between Thr263 and Arg1159 of the insulin receptor contributes to the substrate specificity of PTP1B. Taken together, our findings demonstrate the general role of the second-sphere residue Thr263 in PTP catalysis. Our findings suggest that the second sphere residues of PTP active site may play important roles in PTP-mediated function in both normal and diseased states. PMID:25450460

  6. Effect of D to E mutation of the RGD motif in rhodostomin on its activity, structure, and dynamics: importance of the interactions between the D residue and integrin.

    PubMed

    Chen, Chiu-Yueh; Shiu, Jia-Hau; Hsieh, Yao-Husn; Liu, Yu-Chen; Chen, Yen-Chin; Chen, Yi-Chun; Jeng, Wen-Yih; Tang, Ming-Jer; Lo, Szecheng J; Chuang, Woei-Jer

    2009-09-01

    Rhodostomin (Rho) is a snake venom protein containing an RGD motif that specifically inhibits the integrin-binding function. Rho produced in Pichia pastoris inhibits platelet aggregation with a K(I) of 78 nM as potent as native Rho. In contrast, its D51E mutant inhibits platelet aggregation with a K(I) of 49 muM. Structural analysis of Rho and its D51E mutant showed that they have the same tertiary fold with three two-stranded antiparallel beta-sheets. There are no structural backbone differences between the RG[D/E] loop which extends outward from the protein core and the RG[D/E] sequence at its apex in a four-residue RG[D/E]M type I turn. Two minor differences between Rho and its D51E mutant were only found from their backbone dynamics and 3D structures. The R(2) value of E51 is 13% higher than that of the D51 residue. A difference in the charge separation of 1.76 A was found between the sidechains of positive (R49) and negative residues (D51 or E51).The docking of Rho into integrin alphavbeta3 showed that the backbone amide and carbonyl groups of the D51 residue of Rho were formed hydrogen bonds with the integrin residues R216 and R214, respectively. In contrast, these hydrogen bonds were absent in the D51E mutant-integrin complex. Our findings suggest that the interactions between both the sidechain and backbone of the D residue of RGD-containing ligands and integrin are important for their binding. PMID:19280603

  7. Medium modified two-body scattering amplitude from proton-nucleus total cross-sections

    NASA Technical Reports Server (NTRS)

    Tripathi, R. K.; Wilson, J. W.; Cucinotta, F. A.

    2001-01-01

    Recently (R.K. Tripathi, J.W. Wilson, F.A. Cucinotta, Nucl. Instr. and Meth. B 145 (1998) 277; R.K. Tripathi, F.A. Cucinotta, J.W. Wilson, NASA-TP-1998-208438), we have extracted nucleon-nucleon (N-N) cross-sections in the medium directly from experiment. The in-medium N-N cross-sections form the basic ingredients of several heavy-ion scattering approaches including the coupled-channel approach developed at the NASA Langley Research Center. Here, we investigate the ratio of real to imaginary part of the two-body scattering amplitude in the medium. These ratios are used in combination with the in-medium N-N cross-sections to calculate total proton-nucleus cross-sections. The agreement is excellent with the available experimental data. These cross-sections are needed for the radiation risk assessment of space missions. c2001 Elsevier Science B.V. All rights reserved.

  8. The Effective-One-Body Approach to the General Relativistic Two Body Problem

    NASA Astrophysics Data System (ADS)

    Damour, Thibault; Nagar, Alessandro

    The two-body problem in General Relativity has been the subject of many analytical investigations. After reviewing some of the methods used to tackle this problem (and, more generally, the N-body problem), we focus on a new, recently introduced approach to the motion and radiation of (comparable mass) binary systems: the Effective One Body (EOB) formalism. We review the basic elements of this formalism, and discuss some of its recent developments. Several recent comparisons between EOB predictions and Numerical Relativity (NR) simulations have shown the aptitude of the EOB formalism to provide accurate descriptions of the dynamics and radiation of various binary systems (comprising black holes or neutron stars) in regimes that are inaccessible to other analytical approaches (such as the last orbits and the merger of comparable mass black holes). In synergy with NR simulations, post-Newtonian (PN) theory and Gravitational Self-Force (GSF) computations, the EOB formalism is likely to provide an efficient way of computing the very many accurate template waveforms that are needed for Gravitational Wave (GW) data analysis purposes.

  9. Two-body and three-body contacts for identical Bosons near unitarity.

    PubMed

    Smith, D Hudson; Braaten, Eric; Kang, Daekyoung; Platter, Lucas

    2014-03-21

    In a recent experiment with ultracold trapped Rb85 atoms, Makotyn et al. studied a quantum-degenerate Bose gas in the unitary limit where its scattering length is infinitely large. We show that the observed momentum distributions are compatible with a universal relation that expresses the high-momentum tail in terms of the two-body contact C2 and the three-body contact C3. We determine the contact densities for the unitary Bose gas with number density n to be C2 ≈ 20 n(4/3) and C3 ≈ 2n(5/3). We also show that the observed atom loss rate is compatible with that from 3-atom inelastic collisions, which gives a contribution proportional to C3, but the loss rate is not compatible with that from 2-atom inelastic collisions, which gives a contribution proportional to C2. We point out that the contacts C2 and C3 could be measured independently by using the virial theorem near and at unitarity, respectively. PMID:24702333

  10. Probing the influence of hypermodified residues within the tRNA3(Lys) anticodon stem loop interacting with the A-loop primer sequence from HIV-1.

    PubMed

    Galindo-Murillo, Rodrigo; Davis, Darrell R; Cheatham, Thomas E

    2016-03-01

    Replication of the HIV-1 virus requires reverse transcription of the viral RNA genome, a process that is specifically initiated by human tRNA3(Lys) packaged within the infectious virion. The primary binding site for the tRNA involves the 3' 18 nucleotides with an additional interaction between an adenine rich loop (A-loop) in the template and the anticodon stem-loop region of the tRNA3(Lys). The loop of the tRNA primer contains two hypermodified base residues and a pseudouridine that are required for a proper binding and activity. Here, we investigate the influence on the structure, dynamics and binding stability of the three modified residues (mnm(5)s(2)U34, t(6)A37 and Ψ39) using extensive molecular dynamics and Quantum Theory of Atoms in Molecules (QTAIM) analysis. Consistent with experiment, the results suggest that the three modified residues are required for faithful binding. Residues mnm(5)s(2)U34 and Ψ39 have a major influence in stabilizing the anticodon loop whereas mnm(5)s(2)U34 and t(6)A37 appear to stabilize the formation of the complex of tRNA3(Lys) with the HIV-1 A-loop. PMID:26655694

  11. On the Accuracy of Sequence-Based Computational Inference of Protein Residues Involved in Interactions with DNA

    PubMed Central

    Gou, Zhenkun; Kuznetsov, Igor B.

    2009-01-01

    Methods for computational inference of DNA-binding residues in DNA-binding proteins are usually developed using classification techniques trained to distinguish between binding and non-binding residues on the basis of known examples observed in experimentally determined high-resolution structures of protein-DNA complexes. What degree of accuracy can be expected when a computational methods is applied to a particular novel protein remains largely unknown. We test the utility of classification methods on the example of Kernel Logistic Regression (KLR) predictors of DNA-binding residues. We show that predictors that utilize sequence properties of proteins can successfully predict DNA-binding residues in proteins from a novel structural class. We use Multiple Linear Regression (MLR) to establish a quantitative relationship between protein properties and the expected accuracy of KLR predictors. Present results indicate that in the case of novel proteins the expected accuracy provided by an MLR model is close to the actual accuracy and can be used to assess the overall confidence of the prediction. PMID:20209034

  12. Role of Acidic Residues in Helices TH8–TH9 in Membrane Interactions of the Diphtheria Toxin T Domain

    PubMed Central

    Ghatak, Chiranjib; Rodnin, Mykola V.; Vargas-Uribe, Mauricio; McCluskey, Andrew J.; Flores-Canales, Jose C.; Kurnikova, Maria; Ladokhin, Alexey S.

    2015-01-01

    The pH-triggered membrane insertion of the diphtheria toxin translocation domain (T domain) results in transferring the catalytic domain into the cytosol, which is relevant to potential biomedical applications as a cargo-delivery system. Protonation of residues is suggested to play a key role in the process, and residues E349, D352 and E362 are of particular interest because of their location within the membrane insertion unit TH8–TH9. We have used various spectroscopic, computational and functional assays to characterize the properties of the T domain carrying the double mutation E349Q/D352N or the single mutation E362Q. Vesicle leakage measurements indicate that both mutants interact with the membrane under less acidic conditions than the wild-type. Thermal unfolding and fluorescence measurements, complemented with molecular dynamics simulations, suggest that the mutant E362Q is more susceptible to acid destabilization because of disruption of native intramolecular contacts. Fluorescence experiments show that removal of the charge in E362Q, and not in E349Q/D352N, is important for insertion of TH8–TH9. Both mutants adopt a final functional state upon further acidification. We conclude that these acidic residues are involved in the pH-dependent action of the T domain, and their replacements can be used for fine tuning the pH range of membrane interactions. PMID:25875295

  13. Complex interactions among residues within pore region determine the K+ dependence of a KAT1-type potassium channel AmKAT1.

    PubMed

    Yang, Guangzhe; Sentenac, Hervé; Véry, Anne-Aliénor; Su, Yanhua

    2015-08-01

    KAT1-type channels mediate K(+) influx into guard cells that enables stomatal opening. In this study, a KAT1-type channel AmKAT1 was cloned from the xerophyte Ammopiptanthus mongolicus. In contrast to most KAT1-type channels, its activation is strongly dependent on external K(+) concentration, so it can be used as a model to explore the mechanism for the K(+) -dependent gating of KAT1-type channels. Domain swapping between AmKAT1 and KAT1 reveals that the S5-pore-S6 region controls the K(+) dependence of AmKAT1, and residue substitutions show that multiple residues within the S5-Pore linker and Pore are involved in its K(+) -dependent gating. Importantly, complex interactions occur among these residues, and it is these interactions that determine its K(+) dependence. Finally, we analyzed the potential mechanism for the K(+) dependence of AmKAT1, which could originate from the requirement of K(+) occupancy in the selectivity filter to maintain its conductive conformation. These results provide new insights into the molecular basis of the K(+) -dependent gating of KAT1-type channels. PMID:26032087

  14. Transmembrane Domain Interactions and Residue Proline 378 Are Essential for Proper Structure, Especially Disulfide Bond Formation, in the Human Vitamin K-Dependent γ-Glutamyl Carboxylase†

    PubMed Central

    Tie, Jian-Ke; Zheng, Mei-Yan; Hsiao, Kuang-Ling N.; Perera, Lalith; Stafford, Darrel W.; Straight, David L.

    2009-01-01

    We used recombinant techniques to create a two-chain form (residues 1–345 and residues 346–758) of the vitamin K-dependent γ-glutamyl carboxylase, a glycoprotein located in the endoplasmic reticulum containing five transmembrane domains. The two-chain carboxylase had carboxylase and epoxidase activities similar to those of one-chain carboxylase. In addition, it had normal affinity for the propeptide of factor IX. We employed this molecule to investigate formation of the one disulfide bond in carboxylase, the transmembrane structure of carboxylase, and the potential interactions among the carboxylase’s transmembrane domains. Our results indicate that the two peptides of the two-chain carboxylase are joined by a disulfide bond. Proline 378 is important for the structure necessary for disulfide formation. Results with the P378L carboxylase indicate that noncovalent bonds maintain the two-chain structure even when the disulfide bond is disrupted. As we had previously proposed, the fifth transmembrane domain of carboxylase is the last and only transmembrane domain in the C-terminal peptide of the two-chain carboxylase. We show that the noncovalent association between the two chains of carboxylase involves an interaction between the fifth transmembrane domain and the second transmembrane domain. Results of a homology model of transmembrane domains 2 and 5 suggest that not only do these two domains associate but that transmembrane domain 2 may interact with another transmembrane domain. This latter interaction may be mediated at least in part by a motif of glycine residues in the second transmembrane domain. PMID:18498174

  15. The interaction between natural organic matter in raw waters and pesticide residues: a three dimensional excitation-emission matrix (3DEEM) fluorescence investigation.

    PubMed

    Beale, David J; Porter, Nichola A; Roddick, Felicity A

    2013-01-01

    This paper examines the interaction between dissolved natural organic matter and pesticide residues, both of which are found in raw water sources, using three dimensional excitation-emission matrix (3DEEM) fluorescence spectroscopy. It was observed that pesticide residue at 0.1 mg L(-1) formed a complex with humic-like fluorophores that are commonly found in raw water samples. Applying 3DEEM fluorescence to investigate the humic fractions, it was found that identification of changes in water sources was possible, and, importantly, the presence of a number of pesticides was able to be determined. In addition, the formation of this complex, and the influence of soluble cations and anions upon it, was shown to impact the efficiency of analytical extraction procedures for pesticides; however, 3DEEM fluorescence could be an approach to account for such losses. PMID:23752373

  16. Residual Symmetry and Explicit Soliton-Cnoidal Wave Interaction Solutions of the (2+1)-Dimensional KdV-mKdV Equation

    NASA Astrophysics Data System (ADS)

    Cheng, Wenguang; Li, Biao

    2016-04-01

    The truncated Painlevé method is developed to obtain the nonlocal residual symmetry and the Bäcklund transformation for the (2+1)-dimensional KdV-mKdV equation. The residual symmetry is localised after embedding the (2+1)-dimensional KdV-mKdV equation to an enlarged one. The symmetry group transformation of the enlarged system is computed. Furthermore, the (2+1)-dimensional KdV-mKdV equation is proved to be consistent Riccati expansion (CRE) solvable. The soliton-cnoidal wave interaction solution in terms of the Jacobi elliptic functions and the third type of incomplete elliptic integral is obtained by using the consistent tanh expansion (CTE) method, which is a special form of CRE.

  17. The role of N-terminal and C-terminal Arg residues from BK on interaction with kinin B2 receptor.

    PubMed

    Filippelli-Silva, Rafael; Martin, Renan P; Rodrigues, Eliete S; Nakaie, Clovis R; Oliveira, Laerte; Pesquero, João B; Shimuta, Suma I

    2016-04-01

    Bradykinin (BK) is a nonapeptide important for several physiological processes such as vasodilatation, increase in vascular permeability and release of inflammatory mediators. BK performs its actions by coupling to and activating the B2 receptor, a family A G-protein coupled receptor. Using a strategy which allows systematical monitoring of BK R1 and R9 residues and B2 receptor acidic residues Glu5.35(226) and Asp6.58(298), our study aims at clarifying the BK interaction profile with the B2 receptor [receptor residue numbers are normalized according to Ballesteros and Weinstein, Methods Neurosci. 25 (1995), pp. 366-428) followed by receptor sequence numbering in brackets]. N- and C-terminal analogs of BK (-A1, -G1, -K1, -E1 and BK-A9) were tested against wild type B2, Glu5.35(226)Ala and Asp6.58(298)Ala B2 mutant receptors for their affinity and capability to elicit responses by mechanical recordings of isolated mice stomach fundus, measuring intracellular calcium mobilization, and competitive fluorimetric binding assays. BK showed 2- and 15-fold decreased potency for Glu5.35(226) and Asp6.58(298) B2 mutant receptors, respectively. In B2-Glu5.35(226)Ala BK analogs showed milder reduction in evaluated parameters. On the other hand, in the B2-Asp6.58(298)Ala mutant, no N-terminal analog was able to elicit any response. However, the BK-A9 analog presented higher affinity parameters than BK in the latter mutant. These findings provide enough support for defining a novel interaction role of BK-R9 and Asp6.58(298) receptor residues. PMID:26584354

  18. Modified Kepler's law, escape speed, and two-body problem in modified Newtonian dynamics-like theories

    NASA Astrophysics Data System (ADS)

    Zhao, Hongsheng; Li, Baojiu; Bienaymé, Olivier

    2010-11-01

    We derive a simple analytical expression for the two-body force in a subclass of modified Newtonian dynamics (MOND) theories and make testable predictions in the modification to the two-body orbital period, shape, precession rate, escape speed, etc. We demonstrate the applications of the modified Kepler’s law in the timing of satellite orbits around the Milky Way, and checking the feasibility of MOND in the orbit of the large Magellanic cloud, the M31 galaxy, and the merging bullet clusters. MOND appears to be consistent with satellite orbits although with a tight margin. Our results on two-bodies are also generalized to restricted three-body, many-body problems, rings, and shells.

  19. Hydrophilic Residues Are Crucial for Ribosomal Protein L11 (RPL11) Interaction with Zinc Finger Domain of MDM2 and p53 Protein Activation*

    PubMed Central

    Zhang, Qi; Xiao, Hui; Chai, Sergio C.; Hoang, Quyen Q.; Lu, Hua

    2011-01-01

    Ribosomal protein L11 (RPL11) has been shown to activate p53 by binding to MDM2 and negating its p53 suppression activity in response to ribosomal stress. Although a mutation at Cys-305 within the zinc finger domain of MDM2 has been shown to drastically impair MDM2 interaction with RPL11 and thus escapes the inhibition by this ribosomal protein, it still remains elusive whether RPL11 inactivates MDM2 via direct action on this zinc finger domain and what is the chemical nature of this specific interaction. To define the roles of the MDM2 zinc finger in association with RPL11, we conducted hydrogen-deuterium exchange mass spectrometry, computational modeling, circular dichroism, and mutational analyses of the zinc finger domain of MDM2 and human RPL11. Our study reveals that RPL11 forms a stable complex with MDM2 in vitro through direct contact with its zinc finger. This binding is disrupted by single mutations of non-cysteine amino acids within the zinc finger domain of MDM2. Basic residues in RPL11 are crucial for the stable binding and RPL11 suppression of MDM2 activity toward p53. These results provide the first line of evidence for the specific interaction between RPL11 and the zinc finger of MDM2 via hydrophilic residues as well as a molecular foundation for better understanding RPL11 inhibition of MDM2 function. PMID:21903592

  20. Quantum oscillation signatures of spin-orbit interactions controlling the residual nodal bilayer-splitting in underdoped high-Tc cuprates

    NASA Astrophysics Data System (ADS)

    Harrison, Neil; Shekhter, Arkady

    2015-03-01

    We investigate the origin of the small residual nodal bilayer-splitting in the underdoped high-Tc superconductor YBa2Cu3O6+x using the results of recently published angle-resolved quantum oscillation data [Sebastian et al., Nature 511, 61 (2014)]. A crucial clue to the origin of the residual bilayer-splitting is found to be provided by the anomalously small Zeeman-splitting of some of the observed cyclotron orbits. We show that such an anomalously Zeeman-splitting (or small effective g-factor) for a subset of orbits can be explained by spin-orbit interactions, which become significant in the nodal regions as a result of the vanishing bilayer coupling. The primary effect of spin-orbit interactions is to cause quasiparticles traversing the nodal region of the Brillouin zone to undergo a spin flip. We suggest that the Rashba-like spin-orbit interactions, naturally present in bilayer systems, have the right symmetry and magnitude to give rise to a network of coupled orbits consistent with experimental observations in underdoped YBa2Cu3O6+x. This work is supported by the DOEm BES proposal LANLF100, while the magnet lab is supported by the NSF and Florida State.

  1. Identification of Conserved Amino Acid Residues of the Salmonella σS Chaperone Crl Involved in Crl-σS Interactions

    PubMed Central

    Monteil, Véronique; Kolb, Annie; D'Alayer, Jacques; Beguin, Pierre; Norel, Françoise

    2010-01-01

    Proteins that bind σ factors typically attenuate the function of the σ factor by restricting its access to the RNA polymerase (RNAP) core enzyme. An exception to this general rule is the Crl protein that binds the stationary-phase sigma factor σS (RpoS) and enhances its affinity for the RNAP core enzyme, thereby increasing expression of σS-dependent genes. Analyses of sequenced bacterial genomes revealed that crl is less widespread and less conserved at the sequence level than rpoS. Seventeen residues are conserved in all members of the Crl family. Site-directed mutagenesis of the crl gene from Salmonella enterica serovar Typhimurium and complementation of a Δcrl mutant of Salmonella indicated that substitution of the conserved residues Y22, F53, W56, and W82 decreased Crl activity. This conclusion was further confirmed by promoter binding and abortive transcription assays. We also used a bacterial two-hybrid system (BACTH) to show that the four substitutions in Crl abolish Crl-σS interaction and that residues 1 to 71 in σS are dispensable for Crl binding. In Escherichia coli, it has been reported that Crl also interacts with the ferric uptake regulator Fur and that Fur represses crl transcription. However, the Salmonella Crl and Fur proteins did not interact in the BACTH system. In addition, a fur mutation did not have any significant effect on the expression level of Crl in Salmonella. These results suggest that the relationship between Crl and Fur is different in Salmonella and E. coli. PMID:20008066

  2. Developing an Acidic Residue Reactive and Sulfoxide-Containing MS-Cleavable Homobifunctional Cross-Linker for Probing Protein-Protein Interactions.

    PubMed

    Gutierrez, Craig B; Yu, Clinton; Novitsky, Eric J; Huszagh, Alexander S; Rychnovsky, Scott D; Huang, Lan

    2016-08-16

    Cross-linking mass spectrometry (XL-MS) has become a powerful strategy for defining protein-protein interactions and elucidating architectures of large protein complexes. However, one of the inherent challenges in MS analysis of cross-linked peptides is their unambiguous identification. To facilitate this process, we have previously developed a series of amine-reactive sulfoxide-containing MS-cleavable cross-linkers. These MS-cleavable reagents have allowed us to establish a common robust XL-MS workflow that enables fast and accurate identification of cross-linked peptides using multistage tandem mass spectrometry (MS(n)). Although amine-reactive reagents targeting lysine residues have been successful, it remains difficult to characterize protein interaction interfaces with little or no lysine residues. To expand the coverage of protein interaction regions, we present here the development of a new acidic residue-targeting sulfoxide-containing MS-cleavable homobifunctional cross-linker, dihydrazide sulfoxide (DHSO). We demonstrate that DHSO cross-linked peptides display the same predictable and characteristic fragmentation pattern during collision induced dissociation as amine-reactive sulfoxide-containing MS-cleavable cross-linked peptides, thus permitting their simplified analysis and unambiguous identification by MS(n). Additionally, we show that DHSO can provide complementary data to amine-reactive reagents. Collectively, this work not only enlarges the range of the application of XL-MS approaches but also further demonstrates the robustness and applicability of sulfoxide-based MS-cleavability in conjunction with various cross-linking chemistries. PMID:27417384

  3. Developing an Acidic Residue Reactive and Sulfoxide-Containing MS-Cleavable Homobifunctional Cross-Linker for Probing Protein–Protein Interactions

    PubMed Central

    2016-01-01

    Cross-linking mass spectrometry (XL-MS) has become a powerful strategy for defining protein–protein interactions and elucidating architectures of large protein complexes. However, one of the inherent challenges in MS analysis of cross-linked peptides is their unambiguous identification. To facilitate this process, we have previously developed a series of amine-reactive sulfoxide-containing MS-cleavable cross-linkers. These MS-cleavable reagents have allowed us to establish a common robust XL-MS workflow that enables fast and accurate identification of cross-linked peptides using multistage tandem mass spectrometry (MSn). Although amine-reactive reagents targeting lysine residues have been successful, it remains difficult to characterize protein interaction interfaces with little or no lysine residues. To expand the coverage of protein interaction regions, we present here the development of a new acidic residue-targeting sulfoxide-containing MS-cleavable homobifunctional cross-linker, dihydrazide sulfoxide (DHSO). We demonstrate that DHSO cross-linked peptides display the same predictable and characteristic fragmentation pattern during collision induced dissociation as amine-reactive sulfoxide-containing MS-cleavable cross-linked peptides, thus permitting their simplified analysis and unambiguous identification by MSn. Additionally, we show that DHSO can provide complementary data to amine-reactive reagents. Collectively, this work not only enlarges the range of the application of XL-MS approaches but also further demonstrates the robustness and applicability of sulfoxide-based MS-cleavability in conjunction with various cross-linking chemistries. PMID:27417384

  4. The full two-body-problem: Simulation, analysis, and application to the dynamics, characteristics, and evolution of binary asteroid systems

    NASA Astrophysics Data System (ADS)

    Fahnestock, Eugene Gregory

    The Full Two-Body-Problem (F2BP) describes the dynamics of two unconstrained rigid bodies in close proximity, having arbitrary spatial distribution of mass, charge, or similar field quantity, and interacting through a mutual potential dependent on that distribution. While the F2BP has applications in areas as wide ranging as molecular dynamics to satellite formation flying, this dissertation focuses on its application to natural bodies in space with nontrivial mass distribution interacting through mutual gravitational potential, i.e. binary asteroids. This dissertation first describes further development and implementation of methods for accurate and efficient F2BP propagation based upon a flexible method for computing the mutual potential between bodies modeled as homogenous polyhedra. Next application of these numerical tools to the study of binary asteroid (66391) 1999 KW4 is summarized. This system typifies the largest class of NEO binaries, which includes nearly half of them, characterized by a roughly oblate spheroid primary rotating rapidly and roughly triaxial ellipsoid secondary in on-average synchronous rotation. Thus KW4's dynamics generalize to any member of that class. Analytical formulae are developed which separately describe the effects of primary oblateness and secondary triaxial ellipsoid shape on frequencies of system motions revealed through the F2BP simulation. These formulae are useful for estimating inertia elements and highest-level internal mass distributions of bodies in any similar system, simply from standoff observation of these motion frequencies. Finally precise dynamical simulation and analysis of the motion of test particles within the time-varying gravity field of the F2BP system is detailed. This Restricted Full-detail Three-Body-Problem encompasses exploration of three types of particle motion within a binary asteroid: (1) Orbital motion such as that for a spacecraft flying within the system about the primary, secondary, or

  5. Proton-hydrogen reaction in an effectively two-body model

    SciTech Connect

    Pupyshev, V. V.

    2013-02-15

    A model of total interaction between a proton incident to a hydrogen atom and the proton that is the nucleus of this atom is proposed. This interaction is assumed to be the sum of the short-range nuclear Reid potential and the long-range Thomas-Fermi potential induced by the Coulomb interaction of the electron with the nucleus of the hydrogen atom. The explicit low-energy asymptotic behavior of the cross section for the proton-hydrogen reaction leading to deuteron production is found. It is shown that this cross section increases in inverse proportion to the collision energy for the proton and hydrogen atom in its zero limit.

  6. Essential role of extracellular charged residues of the human CCK(1) receptor for interactions with SR 146131, SR 27897 and CCK-8S.

    PubMed

    Gouldson, P; Legoux, P; Carillon, C; Dumont, X; Le Fur, G; Ferrara, P; Shire, D

    2000-02-18

    We hypothesized that charge-charge interactions may be important for the binding of the human cholecystokinin type 1 (CCK(1)) receptor-specific non-peptide full agonist SR 146131, (2-[4-(4-chloro-2, 5-dimethoxyphenyl)-5-(2-cyclohexyl-ethyl)-thiazol-2-ylcarbamoyl ]-5, 7-dimethyl-indol-1-yl-1-acetic acid), the competitive antagonist SR 27897, (1-[2-(4-(2-chlorophenyl)thiazol-2-yl) aminocarbonyl indoyl] acetic acid) and the natural octapeptide CCK-8S to the CCK(1) receptor. Alanine replacement studies of positively charged residues in the extracellular domains of the receptor showed that only the R336A mutation affected SR 146131 potency of mutated receptors transiently expressed in monkey kidney epithelial COS-7 cells. Two residues, Lys(115) and Lys(187), were implicated in SR 27897 binding. Only the replacement of Lys(115), Arg(197) and Arg(336) significantly affected CCK-8S binding or activity. These results clearly indicated the importance of certain charged residues, but not others, in SR 146131, SR 27897 and CCK-8S binding. Furthermore, although these molecules probably occupy different binding sites on the CCK(1) receptor, we show that a small non-peptide agonist, SR 146131, can stimulate the dual signaling pathways mediated by the CCK(1) receptor. PMID:10688974

  7. Conserved transmembrane glycine residues in the Shigella flexneri polysaccharide co-polymerase protein WzzB influence protein-protein interactions.

    PubMed

    Papadopoulos, Magdalene; Tran, Elizabeth Ngoc Hoa; Murray, Gerald Laurence; Morona, Renato

    2016-06-01

    The O antigen (Oag) component of lipopolysaccharides (LPS) is crucial for virulence and Oag chain-length regulation is controlled by the polysaccharide co-polymerase class 1 (PCP1) proteins. Crystal structure analyses indicate that structural conservation among PCP1 proteins is highly maintained, however the mechanism of Oag modal-chain-length control remains to be fully elucidated. Shigella flexneri PCP1 protein WzzBSF confers a modal-chain length of 10-17 Oag repeat units (RUs), whereas the Salmonella enterica Typhimurium PCP1 protein WzzBST confers a modal-chain length of ~16-28 Oag RUs. Both proteins share >70 % overall sequence identity and contain two transmembrane (TM1 and TM2) regions, whereby a conserved proline-glycine-rich motif overlapping the TM2 region is identical in both proteins. Conserved glycine residues within TM2 are functionally important, as glycine to alanine substitutions at positions 305 and 311 confer very short Oag modal-chain length (~2-6 Oag RUs). In this study, WzzBSF was co-expressed with WzzBST in S. flexneri and a single intermediate modal-chain length of ~11-21 Oag RUs was observed, suggesting the presence of Wzz:Wzz interactions. Interestingly, co-expression of WzzBSF with WzzBG305A/G311A conferred a bimodal LPS Oag chain length (despite over 99 % protein sequence identity), and we hypothesized that the proteins fail to interact. Co-purification assays detected His6-WzzBSF co-purifying with FLAG-tagged WzzBST but not with FLAG-tagged WzzBG305A/G311A, supporting our hypothesis. These data indicate that the conserved glycine residues in TM2 are involved in Wzz:Wzz interactions, and provide insight into key interactions that drive Oag modal length control. PMID:27028755

  8. Bulged residues promote the progression of a loop–loop interaction to a stable and inhibitory antisense–target RNA complex

    PubMed Central

    Kolb, Fabrice A.; Westhof, Eric; Ehresmann, Chantal; Ehresmann, Bernard; Wagner, E. Gerhart H.; Romby, Pascale

    2001-01-01

    In several groups of bacterial plasmids, antisense RNAs regulate copy number through inhibition of replication initiator protein synthesis. These RNAs are characterized by a long hairpin structure interrupted by several unpaired residues or bulged loops. In plasmid R1, the inhibitory complex between the antisense RNA (CopA) and its target mRNA (CopT) is characterized by a four-way junction structure and a side-by-side helical alignment. This topology facilitates the formation of a stabilizer intermolecular helix between distal regions of both RNAs, essential for in vivo control. The bulged residues in CopA/CopT were shown to be required for high in vitro binding rate and in vivo activity. This study addresses the question of why removal of bulged nucleotides blocks stable complex formation. Structure mapping, modification interference, and molecular modeling of bulged-less mutant CopA–CopT complexes suggests that, subsequent to loop–loop contact, helix propagation is prevented. Instead, a fully base paired loop–loop interaction is formed, inducing a continuous stacking of three helices. Consequently, the stabilizer helix cannot be formed, and stable complex formation is blocked. In contrast to the four-way junction topology, the loop–loop interaction alone failed to prevent ribosome binding at its loading site and, thus, inhibition of RepA translation was alleviated. PMID:11470871

  9. Peptide aromatic interactions modulated by fluorinated residues: Synthesis, structure and biological activity of Somatostatin analogs containing 3-(3′,5′difluorophenyl)-alanine

    PubMed Central

    Martín-Gago, Pablo; Rol, Álvaro; Todorovski, Toni; Aragón, Eric; Martin-Malpartida, Pau; Verdaguer, Xavier; Vallès Miret, Mariona; Fernández-Carneado, Jimena; Ponsati, Berta; Macias, Maria J.; Riera, Antoni

    2016-01-01

    Somatostatin is a 14-residue peptide hormone that regulates the endocrine system by binding to five G-protein-coupled receptors (SSTR1–5). We have designed six new Somatostatin analogs with L-3-(3′,5′-difluorophenyl)-alanine (Dfp) as a substitute of Phe and studied the effect of an electron-poor aromatic ring in the network of aromatic interactions present in Somatostatin. Replacement of each of the Phe residues (positions 6, 7 and 11) by Dfp and use of a D-Trp8 yielded peptides whose main conformations could be characterized in aqueous solution by NMR. Receptor binding studies revealed that the analog with Dfp at position 7 displayed a remarkable affinity to SSTR2 and SSTR3. Analogs with Dfp at positions 6 or 11 displayed a π-π interaction with the Phe present at 11 or 6, respectively. Interestingly, these analogs, particularly [D-Trp8,L-Dfp11]-SRIF, showed high selectivity towards SSTR2, with a higher value than that of Octreotide and a similar one to that of native Somatostatin. PMID:27271737

  10. Peptide aromatic interactions modulated by fluorinated residues: Synthesis, structure and biological activity of Somatostatin analogs containing 3-(3',5'difluorophenyl)-alanine.

    PubMed

    Martín-Gago, Pablo; Rol, Álvaro; Todorovski, Toni; Aragón, Eric; Martin-Malpartida, Pau; Verdaguer, Xavier; Vallès Miret, Mariona; Fernández-Carneado, Jimena; Ponsati, Berta; Macias, Maria J; Riera, Antoni

    2016-01-01

    Somatostatin is a 14-residue peptide hormone that regulates the endocrine system by binding to five G-protein-coupled receptors (SSTR1-5). We have designed six new Somatostatin analogs with L-3-(3',5'-difluorophenyl)-alanine (Dfp) as a substitute of Phe and studied the effect of an electron-poor aromatic ring in the network of aromatic interactions present in Somatostatin. Replacement of each of the Phe residues (positions 6, 7 and 11) by Dfp and use of a D-Trp8 yielded peptides whose main conformations could be characterized in aqueous solution by NMR. Receptor binding studies revealed that the analog with Dfp at position 7 displayed a remarkable affinity to SSTR2 and SSTR3. Analogs with Dfp at positions 6 or 11 displayed a π-π interaction with the Phe present at 11 or 6, respectively. Interestingly, these analogs, particularly [D-Trp8,L-Dfp11]-SRIF, showed high selectivity towards SSTR2, with a higher value than that of Octreotide and a similar one to that of native Somatostatin. PMID:27271737

  11. β- transitions of 16 7N9 → 16 8O8 with optimized SDI residual interaction using pnTDA and TDA approximations

    NASA Astrophysics Data System (ADS)

    Pahlavani, M. R.; Firoozi, B.

    2015-11-01

    Within a developed particle-hole approach, a systematic study of the β- transition from the ground state of the 16N nucleus to the ground and some exited states of the 16O nucleus has been carried out. The energy spectrum and the wave functions of pure configuration of the 16N and 16O nuclei are numerically obtained using the mean-field shell model with respect to the Woods-Saxon nuclear potential accompanying spin-orbit and Coulomb interaction. Considering SDI residual interaction, mixed configuration of ground and excited pnTDA and TDA states are extracted for the aforementioned nucleus. These energy spectra and corresponding eigenstates are highly correspondent to the experimental energy spectrum and eigenstates after adjusting the residual potential parameters using the Nelder-Mead (NM) algorithm. In this approach, the endpoint energy, log ft and the partial half-lives of some possible transitions are calculated. The obtained results using the optimized SDI approach are reasonably close to the available experimental data.

  12. Quasiforbidden two-body Förster resonances in a cold Cs Rydberg gas

    NASA Astrophysics Data System (ADS)

    Pelle, B.; Faoro, R.; Billy, J.; Arimondo, E.; Pillet, P.; Cheinet, P.

    2016-02-01

    Cold Rydberg atoms are known to display dipole-dipole interaction-allowed resonances, also called Förster resonances, which lead to an efficient energy transfer when the proper electric field is used. This electric field also enables resonances, which do not respect the dipole-dipole selection rules under zero field. A few of these quasiforbidden resonances have been observed but they are often overlooked. Here we show that in cold 133Cs atoms there is a large number of these resonances that display a significant transfer efficiency due to their strong interactions, even at low electric field. We also develop a graphical method enabling us to find all possible resonances simultaneously. The resulting dramatic increase in the total number of addressable resonant energy transfers at different electric fields could have implications in the search for few-body interactions or macromolecules built from Rydberg atoms.

  13. Residue Substitutions Near the Redox Center of Bacillus subtilis Spx Affect RNA Polymerase Interaction, Redox Control, and Spx-DNA Contact at a Conserved cis-Acting Element

    PubMed Central

    Lin, Ann A.; Walthers, Don

    2013-01-01

    Spx, a member of the ArsC protein family, is a regulatory factor that interacts with RNA polymerase (RNAP). It is highly conserved in Gram-positive bacteria and controls transcription on a genome-wide scale in response to oxidative stress. The structural requirements for RNAP interaction and promoter DNA recognition by Spx were examined through mutational analysis. Residues near the CxxC redox disulfide center of Spx functioned in RNAP α subunit interaction and in promoter DNA binding. R60E and C10A mutants were shown previously to confer defects in transcriptional activation, but both were able to interact with RNAP. R92, which is conserved in ArsC-family proteins, is likely involved in redox control of Spx, as the C10A mutation, which blocks disulfide formation, was epistatic to the R92A mutation. The R91A mutation reduced transcriptional activation and repression, suggesting a defect in RNAP interaction, which was confirmed by interaction assays using an epitope-tagged mutant protein. Protein-DNA cross-linking detected contact between RNAP-bound Spx and the AGCA element at −44 that is conserved in Spx-controlled genes. This interaction caused repositioning of the RNAP σA subunit from a −35-like element upstream of the trxB (thioredoxin reductase) promoter to positions −36 and −11 of the core promoter. The study shows that RNAP-bound Spx contacts a conserved upstream promoter sequence element when bound to RNAP. PMID:23813734

  14. Adsorption of charged protein residues on an inorganic nanosheet: Computer simulation of LDH interaction with ion channel

    NASA Astrophysics Data System (ADS)

    Tsukanov, Alexey A.; Psakhie, Sergey G.

    2016-08-01

    Quasi-two-dimensional and hybrid nanomaterials based on layered double hydroxides (LDH), cationic clays, layered oxyhydroxides and hydroxides of metals possess large specific surface area and strong electrostatic properties with permanent or pH-dependent electric charge. Such nanomaterials may impact cellular electrostatics, changing the ion balance, pH and membrane potential. Selective ion adsorption/exchange may alter the transmembrane electrochemical gradient, disrupting potential-dependent cellular processes. Cellular proteins as a rule have charged residues which can be effectively adsorbed on the surface of layered hydroxide based nanomaterials. The aim of this study is to attempt to shed some light on the possibility and mechanisms of protein "adhesion" an LDH nanosheet and to propose a new direction in anticancer medicine, based on physical impact and strong electrostatics. An unbiased molecular dynamics simulation was performed and the combined process free energy estimation (COPFEE) approach was used.

  15. Quantum few-body problem with internal structure. I. Two-body problem

    SciTech Connect

    Kuperin, Yu.A.; Makarov, K.A.; Merkur'ev, S.P.; Motovilov, A.K.; Pavlov, B.S.

    1988-12-01

    The methods of the theory of extensions to an auxiliary Hilbert space are used to construct in the two-particle sector a scattering theory for particles possessing internal structure. The analytic properties of the amplitudes of resonance scattering and Green's functions corresponding to a class of singular energy-dependent interactions are investigated.

  16. A Combined Genetic-Proteomic Approach Identifies Residues within Dengue Virus NS4B Critical for Interaction with NS3 and Viral Replication

    PubMed Central

    Chatel-Chaix, Laurent; Fischl, Wolfgang; Scaturro, Pietro; Cortese, Mirko; Kallis, Stephanie; Bartenschlager, Marie; Fischer, Bernd

    2015-01-01

    ABSTRACT Dengue virus (DENV) infection causes the most prevalent arthropod-borne viral disease worldwide. Approved vaccines are not available, and targets suitable for the development of antiviral drugs are lacking. One possible drug target is nonstructural protein 4B (NS4B), because it is absolutely required for virus replication; however, its exact role in the DENV replication cycle is largely unknown. With the aim of mapping NS4B determinants critical for DENV replication, we performed a reverse genetic screening of 33 NS4B mutants in the context of an infectious DENV genome. While the majority of these mutations were lethal, for several of them, we were able to select for second-site pseudoreversions, most often residing in NS4B and restoring replication competence. To identify all viral NS4B interaction partners, we engineered a fully viable DENV genome encoding an affinity-tagged NS4B. Mass spectrometry-based analysis of the NS4B complex isolated from infected cells identified the NS3 protease/helicase as a major interaction partner of NS4B. By combining the genetic complementation map of NS4B with a replication-independent expression system, we identified the NS4B cytosolic loop—more precisely, amino acid residue Q134—as a critical determinant for NS4B-NS3 interaction. An alanine substitution at this site completely abrogated the interaction and DENV RNA replication, and both were restored by pseudoreversions A69S and A137V. This strict correlation between the degree of NS4B-NS3 interaction and DENV replication provides strong evidence that this viral protein complex plays a pivotal role during the DENV replication cycle, hence representing a promising target for novel antiviral strategies. IMPORTANCE With no approved therapy or vaccine against dengue virus infection, the viral nonstructural protein 4B (NS4B) represents a possible drug target, because it is indispensable for virus replication. However, little is known about its precise structure and

  17. 1H/15N HSQC NMR studies of ligand carboxylate group interactions with arginine residues in complexes of brodimoprim analogues and Lactobacillus casei dihydrofolate reductase.

    PubMed

    Morgan, W D; Birdsall, B; Nieto, P M; Gargaro, A R; Feeney, J

    1999-02-16

    1H and 15N NMR studies have been undertaken on complexes of Lactobacillus casei dihydrofolate reductase (DHFR) formed with analogues of the antibacterial drug brodimoprim (2,4-diamino-5-(3', 5'-dimethoxy-4'-bromobenzyl)pyrimidine) in order to monitor interactions between carboxylate groups on the ligands and basic residues in the protein. These analogues had been designed by computer modeling with carboxylated alkyl chains introduced at the 3'-O position in order to improve their binding properties by making additional interactions with basic groups in the protein. Specific interactions between ligand carboxylate groups and the conserved Arg57 residue have been detected in studies of 1H/15N HSQC spectra of complexes of DHFR with both the 4-carboxylate and the 4, 6-dicarboxylate brodimoprim analogues. The spectra from both complexes showed four resolved signals for the four NHeta protons of the guanidino group of Arg57, and this is consistent with hindered rotation in the guanidino group resulting from interactions with the 4-carboxylate group in each analogue. In the spectra of each complex, one of the protons from each of the two NH2 groups and both nitrogens are considerably deshielded compared to the shielding values normally observed for such nuclei. This pattern of deshielding is that expected for a symmetrical end-on interaction of the carboxylate oxygens with the NHeta12 and NHeta22 guanidino protons. The differences in the degree of deshielding between the complexes of the two structurally similar brodimoprim analogues and the methotrexate indicates that the shielding is very sensitive to geometry, most probably to hydrogen bond lengths. The 1H/15N HSQC spectrum of the DHFR complex with the brodimoprim-6-carboxylate analogue does not feature any deshielded Arg NHeta protons and this argues against a similar interaction with the Arg57 in this case. It has not proved possible to determine whether the 6-carboxylate in this analogue is interacting directly with

  18. Flavodoxin-mediated electron transfer from photosystem I to ferredoxin-NADP+ reductase in Anabaena: role of flavodoxin hydrophobic residues in protein-protein interactions.

    PubMed

    Goñi, Guillermina; Serrano, Ana; Frago, Susana; Hervás, Manuel; Peregrina, José Ramón; De la Rosa, Miguel A; Gómez-Moreno, Carlos; Navarro, José A; Medina, Milagros

    2008-01-29

    Three surface hydrophobic residues located at the Anabaena flavodoxin (Fld) putative complex interface with its redox partners were replaced by site-directed mutagenesis. The effects of these replacements on Fld interaction with both its physiological electron donor, photosystem I (PSI), and its electron acceptor, ferredoxin-NADP+ reductase (FNR), were analyzed. Trp57, Ile59, and Ile92 contributed to the optimal orientation and tightening of the FNR:Fld and PSI:Fld complexes. However, these side chains did not appear to be involved in crucial specific interactions, but rather contributed to the obtainment of the optimal orientation and distance of the redox centers required for efficient electron transfer. This supports the idea that the interaction of Fld with its partners is less specific than that of ferredoxin and that more than one orientation is efficient for electron transfer in these transient complexes. Additionally, for some of the analyzed processes, WT Fld seems not to be the most optimized molecular species. Therefore, subtle changes at the isoalloxazine environment not only influence the Fld binding abilities, but also modulate the electron exchange processes by producing different orientations and distances between the redox centers. Finally, the weaker apoflavodoxin interaction with FNR suggests that the solvent-accessible region of FMN plays a role either in complex formation with FNR or in providing the adequate conformation of the FNR binding region in Fld. PMID:18177021

  19. The Role of a Second-Shell Residue in Modifying Substrate and Inhibitor Interactions in the SHV β-Lactamase: A Study of Ambler Position Asn276†

    PubMed Central

    Drawz, Sarah M.; Bethel, Christopher R.; Hujer, Kristine M.; Hurless, Kelly N.; Distler, Anne M.; Caselli, Emilia; Prati, Fabio; Bonomo, Robert A.

    2014-01-01

    Inhibitor-resistant class A β-lactamases of the TEM and SHV families that arise by single amino acid substitutions are a significant threat to the efficacy of β-lactam/β-lactamase inhibitor combinations. To better understand the basis of the inhibitor-resistant phenotype in SHV, we performed mutagenesis to examine the role of a second-shell residue, Asn276. Of the 19 variants expressed in Escherichia coli, only the Asn276Asp enzyme demonstrated reduced susceptibility to ampicillin/clavulanate (MIC increased from 50/2 → 50/8 μg/mL) while maintaining high-level resistance to ampicillin (MIC = 8192 μg/mL). Steady-state kinetic analyses of Asn276Asp revealed slightly diminished kcat/Km for all substrates tested. In contrast, we observed a 5-fold increase in Ki for clavulanate (7.4 ± 0.9 μM for Asn276Asp vs 1.4 ± 0.2 μM for SHV-1) and a 40% reduction in kinact/KI (0.013 ± 0.002 μM−1 s−1 for Asn276Asp vs 0.021 ± 0.004 μM−1 s−1 for SHV-1). Timed electrospray ionization mass spectrometry of clavulanate-inhibited SHV-1 and SHV Asn276Asp showed nearly identical mass adducts, arguing for a similar pathway of inactivation. Molecular modeling shows that novel electrostatic interactions are formed between Arg244Nη2 and both 276AspOδ1 and Oδ2; these new forces restrict the spatial position of Arg244, a residue important in the recognition of the C3/C4 carboxylate of β-lactam substrates and inhibitors. Testing the functional consequences of this interaction, we noted considerable free energy costs (+ΔΔG) for substrates and inhibitors. A rigid carbapenem (meropenem) was most affected by the Asn276Asp substitution (46-fold increase in Ki vs SHV-1). We conclude that residue 276 is an important second-shell residue in class A β-lactamase-mediated resistance to substrates and inhibitors, and only Asn is able to precisely modulate the conformational flexibility of Arg244 required for successful evolution in nature. PMID:19351161

  20. Site-directed mutagenesis of amino acid residues of D1 protein interacting with phosphatidylglycerol affects the function of plastoquinone QB in photosystem II.

    PubMed

    Endo, Kaichiro; Mizusawa, Naoki; Shen, Jian-Ren; Yamada, Masato; Tomo, Tatsuya; Komatsu, Hirohisa; Kobayashi, Masami; Kobayashi, Koichi; Wada, Hajime

    2015-12-01

    Recent X-ray crystallographic analysis of photosystem (PS) II at 1.9-Å resolution identified 20 lipid molecules in the complex, five of which are phosphatidylglycerol (PG). In this study, we mutagenized amino acid residues S232 and N234 of D1, which interact with two of the PG molecules (PG664 and PG694), by site-directed mutagenesis in Synechocystis sp. PCC 6803 to investigate the role of the interaction in PSII. The serine and asparagine residues at positions 232 and 234 from the N-terminus were mutagenized to alanine and aspartic acid, respectively, and a mutant carrying both amino acid substitutions was also produced. Although the obtained mutants, S232A, N234D, and S232AN234D, exhibited normal growth, they showed decreased photosynthetic activities and slower electron transport from QA to QB than the control strain. Thermoluminescence analysis suggested that this slower electron transfer in the mutants was caused by more negative redox potential of QB, but not in those of QA and S2. In addition, the levels of extrinsic proteins, PsbV and PsbU, were decreased in PSII monomer purified from the S232AN234D mutant, while that of Psb28 was increased. In the S232AN234D mutant, the content of PG in PSII was slightly decreased, whereas that of monogalactosyldiacylglycerol was increased compared with the control strain. These results suggest that the interactions of S232 and N234 with PG664 and PG694 are important to maintain the function of QB and to stabilize the binding of extrinsic proteins to PSII. PMID:25921208

  1. Pump-Probe Spectroscopy of Two-Body Correlations in Ultracold Gases

    SciTech Connect

    Koch, Christiane P.; Kosloff, Ronnie

    2009-12-31

    We suggest pump-probe spectroscopy to study pair correlations that determine the many-body dynamics in weakly interacting, dilute ultracold gases. A suitably chosen, short laser pulse depletes the pair density locally, creating a 'hole' in the electronic ground state. The dynamics of this nonstationary pair density is monitored by a time-delayed probe pulse. The resulting transient signal allows us to spectrally decompose the hole and to map out the pair correlation function.

  2. Maize Root Lectins Mediate the Interaction with Herbaspirillum seropedicae via N-Acetyl Glucosamine Residues of Lipopolysaccharides

    PubMed Central

    Balsanelli, Eduardo; Tuleski, Thalita Regina; de Baura, Valter Antonio; Yates, Marshall Geoffrey; Chubatsu, Leda Satie; de Oliveira Pedrosa, Fabio; de Souza, Emanuel Maltempi; Monteiro, Rose Adele

    2013-01-01

    Herbaspirillum seropedicae is a plant growth-promoting diazotrophic betaproteobacterium which associates with important crops, such as maize, wheat, rice and sugar-cane. We have previously reported that intact lipopolysaccharide (LPS) is required for H. seropedicae attachment and endophytic colonization of maize roots. In this study, we present evidence that the LPS biosynthesis gene waaL (codes for the O-antigen ligase) is induced during rhizosphere colonization by H. seropedicae. Furthermore a waaL mutant strain lacking the O-antigen portion of the LPS is severely impaired in colonization. Since N-acetyl glucosamine inhibits H. seropedicae attachment to maize roots, lectin-like proteins from maize roots (MRLs) were isolated and mass spectrometry (MS) analysis showed that MRL-1 and MRL-2 correspond to maize proteins with a jacalin-like lectin domain, while MRL-3 contains a B-chain lectin domain. These proteins showed agglutination activity against wild type H. seropedicae, but failed to agglutinate the waaL mutant strain. The agglutination reaction was severely diminished in the presence of N-acetyl glucosamine. Moreover addition of the MRL proteins as competitors in H. seropedicae attachment assays decreased 80-fold the adhesion of the wild type to maize roots. The results suggest that N-acetyl glucosamine residues of the LPS O-antigen bind to maize root lectins, an essential step for efficient bacterial attachment and colonization. PMID:24130823

  3. Maize root lectins mediate the interaction with Herbaspirillum seropedicae via N-acetyl glucosamine residues of lipopolysaccharides.

    PubMed

    Balsanelli, Eduardo; Tuleski, Thalita Regina; de Baura, Valter Antonio; Yates, Marshall Geoffrey; Chubatsu, Leda Satie; Pedrosa, Fabio de Oliveira; de Souza, Emanuel Maltempi; Monteiro, Rose Adele

    2013-01-01

    Herbaspirillum seropedicae is a plant growth-promoting diazotrophic betaproteobacterium which associates with important crops, such as maize, wheat, rice and sugar-cane. We have previously reported that intact lipopolysaccharide (LPS) is required for H. seropedicae attachment and endophytic colonization of maize roots. In this study, we present evidence that the LPS biosynthesis gene waaL (codes for the O-antigen ligase) is induced during rhizosphere colonization by H. seropedicae. Furthermore a waaL mutant strain lacking the O-antigen portion of the LPS is severely impaired in colonization. Since N-acetyl glucosamine inhibits H. seropedicae attachment to maize roots, lectin-like proteins from maize roots (MRLs) were isolated and mass spectrometry (MS) analysis showed that MRL-1 and MRL-2 correspond to maize proteins with a jacalin-like lectin domain, while MRL-3 contains a B-chain lectin domain. These proteins showed agglutination activity against wild type H. seropedicae, but failed to agglutinate the waaL mutant strain. The agglutination reaction was severely diminished in the presence of N-acetyl glucosamine. Moreover addition of the MRL proteins as competitors in H. seropedicae attachment assays decreased 80-fold the adhesion of the wild type to maize roots. The results suggest that N-acetyl glucosamine residues of the LPS O-antigen bind to maize root lectins, an essential step for efficient bacterial attachment and colonization. PMID:24130823

  4. Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin; Yakima/Klickitat Fisheries Project Monitoring and Evaluation, 2001-2002 Annual Report.

    SciTech Connect

    Pearsons, Todd N.; James, Brenda B.; Johnson, Christopher L.

    2003-05-01

    This report examines some of the factors that can influence the success of supplementation, which is currently being tested in the Yakima Basin using upper Yakima stock of spring chinook salmon. Supplementation success in the Yakima Basin is defined relative to four topic areas: natural production, genetics, ecological interactions, and harvest (Busack et al. 1997). The success of spring chinook salmon supplementation in the Yakima Basin is dependent, in part, upon fish culture practices and favorable physical and biological conditions in the natural environment (Busack et al. 1997). Shortfalls in either of these two topics (i.e., failure in culturing many fish that have high long-term fitness or environmental conditions that constrain spring chinook salmon production) will cause supplementation success to be limited. For example, inadvertent selection or propagation of spring chinook that residualize or precocially mature may hinder supplementation success. Spring chinook salmon that residualize (do not migrate during the normal migration period) may have lower survival rates than migrants and, additionally, may interact with wild fish and cause unacceptable impacts to non-target taxa. Large numbers of precocials (nonanadromous spawners) may increase competition for females and significantly skew ratios of offspring sired by nonanadromous males, which could result in more nonanadromous spring chinook in future generations. Conditions in the natural environment may also limit the success of spring chinook supplementation. For example, intra or interspecific competition may constrain spring chinook salmon production. Spring chinook salmon juveniles may compete with each other for food or space or compete with other species that have similar ecological requirements. Monitoring of spring chinook salmon residuals, precocials, prey abundance, carrying capacity, and competition will help researchers interpret why supplementation is working or not working (Busack et al

  5. Mutation of a single residue, β-glutamate-20, alters protein–lipid interactions of light harvesting complex II

    PubMed Central

    Kwa, Lee Gyan; Wegmann, Dominik; Brügger, Britta; Wieland, Felix T; Wanner, Gerhard; Braun, Paula

    2008-01-01

    It is well established that assembly of the peripheral antenna complex, LH2, is required for proper photosynthetic membrane biogenesis in the purple bacterium Rhodobacter sphaeroides. The underlying interactions are, as yet, not understood. Here we examined the relationship between the morphology of the photosynthetic membrane and the lipid–protein interactions at the LH2–lipid interface. The non-bilayer lipid, phosphatidylethanolamine, is shown to be highly enriched in the boundary lipid phase of LH2. Sequence alignments indicate a putative lipid binding site, which includes β-glutamate-20 and the adjacent carotenoid end group. Replacement of β-glutamate-20 with alanine results in significant reduction of phosphatidylethanolamine and concomitant raise in phosphatidylcholine in the boundary lipid phase of LH2 without altering the lipid composition of the bulk phase. The morphology of the LH2 housing membrane is, however, unaffected by the amino acid replacement. In contrast, simultaneous modification of glutamate-20 and exchange of the carotenoid sphaeroidenone with neurosporene results in significant enlargement of the vesicular membrane invaginations. These findings suggest that the LH2 complex, specifically β-glutamate-20 and the carotenoids' polar head group, contribute to the shaping of the photosynthetic membrane by specific interactions with surrounding lipid molecules. PMID:18034796

  6. Two-body pion absorption on {sup 3}He at threshold

    SciTech Connect

    Lee, T.S.H.; Kiang, L.L.; Riska, D.O.

    1995-08-01

    We showed that a drastic reduction of the ratio of the rates of the reactions {sup 3}He({pi}{sup -},nn) and {sup 3}He({pi}{sup -},np) for stopped pions is obtained once the effect of the short-range two-nucleon components of the axial charge operator for nuclear systems is taken into account. In a calculation using realistic models of nucleon-nucleon interactions in the construction of these short-range components of the axial charge operator, the predicted ratios can be brought to within 10-20% of the empirical value. A paper describing our results was published.

  7. Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks.

    PubMed

    Stetz, Gabrielle; Verkhivker, Gennady M

    2016-08-22

    Although molecular mechanisms of allosteric regulation in the Hsp70 chaperones have been extensively studied at both structural and functional levels, the current understanding of allosteric inhibition of chaperone activities by small molecules is still lacking. In the current study, using a battery of computational approaches, we probed allosteric inhibition mechanisms of E. coli Hsp70 (DnaK) and human Hsp70 proteins by small molecule inhibitors PET-16 and novolactone. Molecular dynamics simulations and binding free energy analysis were combined with network-based modeling of residue interactions and allosteric communications to systematically characterize and compare molecular signatures of the apo form, substrate-bound, and inhibitor-bound chaperone complexes. The results suggested a mechanism by which the allosteric inhibitors may leverage binding energy hotspots in the interaction networks to stabilize a specific conformational state and impair the interdomain allosteric control. Using the network-based centrality analysis and community detection, we demonstrated that substrate binding may strengthen the connectivity of local interaction communities, leading to a dense interaction network that can promote an efficient allosteric communication. In contrast, binding of PET-16 to DnaK may induce significant dynamic changes and lead to a fractured interaction network and impaired allosteric communications in the DnaK complex. By using a mechanistic-based analysis of distance fluctuation maps and allosteric propensities of protein residues, we determined that the allosteric network in the PET-16 complex may be small and localized due to the reduced communication and low cooperativity of the substrate binding loops, which may promote the higher rates of substrate dissociation and the decreased substrate affinity. In comparison with the significant effect of PET-16, binding of novolactone to HSPA1A may cause only moderate network changes and preserve allosteric

  8. The One-Body and Two-Body Density Matrices of Finite Nuclei and Center-of-Mass Correlations

    SciTech Connect

    Shebeko, A.; Papakonstantinou, P.; Mavrommatis, E.

    2006-04-26

    A method is presented for the calculation of the one-body (1DM) and two-body (2DM) density matrices and their Fourier transforms in momentum space, that is consistent with the requirement for translational invariance (TI), in the case of a nucleus (a finite self-bound system). We restore TI by using the so-called fixed center-of-mass (CM) approximation for constructing an intrinsic nuclear ground state wavefunction (WF) by starting from a non-translationally invariant (nTI) WF and applying a projection prescription. We discuss results for the one-body (OBMD) and two-body (TBMD) momentum distributions of the 4He nucleus calculated with the Slater determinant of the harmonic oscillator (HO) orbitals, as the initial nTI WF. Effects of such an inclusion of CM correlations are found to be quite important in the momentum distributions.

  9. The Two-Body Problem in the Point Mass Approximation Field. II. Escape and Near-Escape Dynamics

    NASA Astrophysics Data System (ADS)

    Mioc, Vasile; Stavinschi, Magda

    The study of the two-body problem in the point mass approximation field (featured by the potential A/r+Br2, with r=distance between particles, and A, B=real nonzero constants) is continued by tackling the situation r→∞. The infinity singularity is blown up via McGehee-type transformations, and the infinity manifold is pasted on the phase space. The fictitious flow on this manifold is described, and the local flow near infinity, too.

  10. f and g series solutions to a post-Newtonian two-body problem with parameters β and γ

    NASA Astrophysics Data System (ADS)

    Qin, Song-He; Liu, Jing-Xi; Zhong, Ze-Hao; Xie, Yi

    2016-01-01

    Classical Newtonian f and g series for a Keplerian two-body problem are extended for the case of a post-Newtonian two-body problem with parameters β and γ. These two parameters are introduced to parameterize the post-Newtonian approximation of alternative theories of gravity and they are both equal to 1 in general relativity. Up to the order of 30, we obtain all of the coefficients of the series in their exact forms without any cutoff for significant figures. The f and g series for the post-Newtonian two-body problem are also compared with a Runge-Kutta order 7 integrator. Although the f and g series have no superiority in terms of accuracy or efficiency at the order of 7, the discrepancy in the performances of these two methods is not quite distinct. However, the f and g series have the advantage of flexibility for going to higher orders. Some examples of relativistic advance of periastron are given and the effect of gravitational radiation on the scheme of f and g series is evaluated.

  11. Development of a two-body wet abrasion test method with attention to the effects of reused abradant

    SciTech Connect

    Blau, Peter Julian; Dehoff, Ryan R

    2012-01-01

    Abrasive wear is among the most common and costliest causes for material wastage, and it occurs in many forms. A simple method has been developed to quantify the response of metals and alloys to two-body wet abrasion. A metallographic polishing machine was modified to create a disk-on-flat sliding test rig. Adhesive-backed SiC grinding papers were used under fixed load and speed to rank the abrasive wear of seven alloy steels, some of which are candidates for drill cones for geothermal drilling. Standardized two-body abrasion tests, like those described in ASTM G132, feed unused abrasive into the contact; however, the current work investigated whether useful rankings could still be obtained with a simpler testing configuration in which specimens repeatedly slide on the same wear path under water-lubricated conditions. Tests using abrasive grit sizes of 120 and 180 resulted in the same relative ranking of the alloys although the coarser grit produced more total wear. Wear decreased when the same abrasive disk was re-used for up to five runs, but the relative rankings of the steels remained the same. This procedure was presented to ASTM Committee G2 on Wear and Erosion as a potential standard test for wet two-body abrasive wear.

  12. Electrodynamic two-body problem for prescribed initial data on a straight line

    NASA Astrophysics Data System (ADS)

    Deckert, D.-A.; Hinrichs, G.

    2016-05-01

    Electrodynamic interaction between point charges can be described by a system of ODEs involving advanced and retarded delays - the so-called Fokker-Schwarzschild-Tetrode (FST) equations. In special situations, approximate equations can be derived which are purely retarded. Upon omission of the terms describing radiation friction, these are called Synge equations. In both cases, few mathematical results are available on existence and uniqueness of solutions. We investigate the situation of two like point-charges in 3 + 1 space-time dimensions restricted to motion on a straight line. We give a priori estimates on the asymptotic motion and, using a Leray-Schauder argument, prove: 1) Existence of solutions to the FST equations on the future or past half-line given finite trajectory segments; 2) Global existence of the Synge equations for Cauchy data; 3) Global existence of a FST toy model. Furthermore, we give a sufficient criterion that uniquely distinguishes solutions by means of finite trajectory segments.

  13. Proton scattering by a hydrogen atom in an effectively two-body model

    SciTech Connect

    Pupyshev, V. V.

    2013-02-15

    It is assumed that the total potential of proton interaction with a hydrogen atom is the sum of the short-range nuclear soft-core Reid potential and the long-range Thomas-Fermi potential. A quantum mechanical analysis of low-energy features of the phase shift and cross section for elastic proton scattering on a hydrogen atom is given for the case of zero total angular momentum. The calculations performed in the present study within a nonlinear version of the variable-phase approach ultimately revealed that, because of a long-range character of the asymptotic behavior of the Thomas-Fermi potential, the respective cross section at low energies oscillates but has a finite number of zeros.

  14. Interaction of biochar and organic residues from sugarcane industry in soil chemical attributes and greenhouse gases emissions.

    NASA Astrophysics Data System (ADS)

    Fernanda Abbruzzini, Thalita; Feola Conz, Rafaela; Pellegrino Cerri, Carlos Eduardo

    2014-05-01

    Researchers have highlighted the importance of providing soil quality in agricultural systems, besides mitigating greenhouse gases (GHG) emissions to the atmosphere and increasing soil carbon sequestration. Therefore, several studies have demonstrated the effectiveness of biochar as a soil conditioner, both in relation to increased C sequestration and improvements in soil chemical, physical and biological attributes, resulting in better conditions for plant growth. The aim of this study was to assess the impact of applying biochar produced from sugarcane straw to soils in relation to changes in soil chemical attributes and mitigation of greenhouse gases emissions into the atmosphere. To do so, we conducted a laboratory incubation under controlled environmental conditions (ie temperature and humidity) with and without the application of filter cake and vinasse (ie organic residues from sugarcane industry) and rates of biochar application (0, 10, 20 and 50 Mg ha-1). The fluxes of CO2, N2O and CH4 of each incubation unity were measured periodically (in days 1, 2, 5, 9, 13, 16, 20, 24, 28, 30, 47, 60, 91, 105, 123, 130, 138 and 150). Each treatment consisted of eight replicates with destructive samples evaluated at 30, 60, 90 and 150 days after incubation to characterize the chemical attributes of the incubated soil, besides GHG (CO2, N2O and CH4) emissions. In general, there was an increase in carbon dioxide (CO2) fluxes over time due to the application of filter cake and vinasse and increasing dose of biochar. Regarding nitrous oxide (N2O) emissions, there was an increase of 82.35% with the application of vinasse and filter cake compared to the control treatment. However, different doses of biochar (10, 20 and 50 Mg ha-1) reduced N2O emissions by 29, 38.7 and 70.9%, respectively. The methane (CH4) flux was negligible in all treatments. We observed improvements in soil chemical attributes, such as higher pH, a substantial increase in the soil CEC, reduced exchangeable

  15. Aromatic–aromatic interactions between residues in KCa3.1 pore helix and S5 transmembrane segment control the channel gating process

    PubMed Central

    Garneau, Line; Klein, Hélène; Lavoie, Marie-France; Brochiero, Emmanuelle; Parent, Lucie

    2014-01-01

    The Ca2+-activated potassium channel KCa3.1 is emerging as a therapeutic target for a large variety of health disorders. One distinguishing feature of KCa3.1 is that the channel open probability at saturating Ca2+ concentrations (Pomax) is low, typically 0.1–0.2 for KCa3.1 wild type. This observation argues for the binding of Ca2+ to the calmodulin (CaM)–KCa3.1 complex, promoting the formation of a preopen closed-state configuration leading to channel opening. We have previously shown that the KCa3.1 active gate is most likely located at the level of the selectivity filter. As Ca2+-dependent gating of KCa3.1 originates from the binding of Ca2+ to CaM in the C terminus, the hypothesis of a gate located at the level of the selectivity filter requires that the conformational change initiated in the C terminus be transmitted to the S5 and S6 transmembrane helices, with a resulting effect on the channel pore helix directly connected to the selectivity filter. A study was thus undertaken to determine to what extent the interactions between the channel pore helix with the S5 and S6 transmembrane segments contribute to KCa3.1 gating. Molecular dynamics simulations first revealed that the largest contact area between the pore helix and the S5 plus S6 transmembrane helices involves residue F248 at the C-terminal end of the pore helix. Unitary current recordings next confirmed that modulating aromatic–aromatic interactions between F248 and W216 of the S5 transmembrane helical segment and/or perturbing the interactions between F248 and residues in S6 surrounding the glycine hinge G274 cause important changes in Pomax. This work thus provides the first evidence for a key contribution of the pore helix in setting Pomax by stabilizing the channel closed configuration through aromatic–aromatic interactions involving F248 of the pore helix. We propose that the interface pore helix/S5 constitutes a promising site for designing KCa3.1 potentiators. PMID:24470490

  16. Interaction of acid mine drainage with Ordinary Portland Cement blended solid residues generated from active treatment of acid mine drainage with coal fly ash.

    PubMed

    Gitari, Wilson M; Petrik, Leslie F; Key, David L; Okujeni, Charles

    2011-01-01

    Fly ash (FA) has been investigated as a possible treatment agent for Acid mine drainage (AMD) and established to be an alternative, cheap and economically viable agent compared to the conventional alkaline agents. However, this treatment option also leads to generation of solid residues (SR) that require disposal and one of the proposed disposal method is a backfill in coal mine voids. In this study, the interaction of the SR with AMD that is likely to be present in such backfill scenario was simulated by draining columns packed with SR and SR + 6% Ordinary Portland Cement (OPC) unsaturated with simulated AMD over a 6 month period. The evolving geochemistry of the liquid/solid (L/S) system was evaluated in-terms of the mineral phases likely or controlling contaminants attenuation at the different pH regimes generated. Stepwise acidification of the percolates was observed as the drainage progressed. Two pH buffer zones were observed (7.5-9 and 3-4) for SR and (11.2-11.3 and 3.5-4) for SR + 6% OPC. The solid residue cores (SR) appeared to have a significant buffering capacity, maintaining a neutral to slightly alkaline pH in the leachates for an extended period of time (97 days: L/S 4.3) while SR + 6% OPC reduced this neutralization capacity to 22 days (L/S 1.9). Interaction of AMD with SR or SR + 6% OPC generated alkaline conditions that favored precipitation of Fe, Al, Mn-(oxy) hydroxides, Fe and Ca-Al hydroxysulphates that greatly contributed to the contaminants removal. However, precipitation of these phases was restricted to the pH of the leachates remaining at neutral to circum-neutral levels. Backfill of mine voids with SR promises to be a feasible technology for the disposal of the SR but its success will greatly depend on the disposal scenario, AMD generated and the alkalinity generating potential of the SR. A disadvantage would be the possible re-dissolution of the precipitated phases at pH < 4 that would release the contaminants back to the water column

  17. Determination of aminoglycoside residues in kidney and honey samples by hydrophilic interaction chromatography-tandem mass spectrometry.

    PubMed

    Kumar, Praveen; Rúbies, Antoni; Companyó, Ramon; Centrich, Francesc

    2012-10-01

    Two methods based on liquid chromatography-tandem mass spectrometry were developed for the determination of ten aminoglycosides (streptomycin, dihydrostreptomycin, spectinomycin, apramycin, paromomycin, kanamycin A, gentamycin C1, gentamycin C2/C2a, gentamycin C1a, and neomycin B) in kidney samples from food-producing animals and in honey samples. The methods involved extraction with an aqueous solution (for the kidney samples) or sample dissolution in water (for the honey samples), solid-phase extraction with a weak cation exchange cartridge and injection of the eluate into a liquid chromatography-tandem mass spectrometry system. A zwitterionic hydrophilic interaction chromatography column was used for separation of aminoglycosides and a triple quadrupole mass analyzer was used for detection. The methods were validated according to Decision 2002/657/EC. The limits of quantitation ranged from 2 to 125 μg/kg in honey and 25 to 264 μg/kg in the kidney samples. Interday precision (RSD%) ranged from 6 to 26% in honey and 2 to 21% in kidney. Trueness, expressed as the percentage of error, ranged from 7 to 20% in honey and 1 to 11% in kidney. PMID:23065931

  18. Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state

    NASA Astrophysics Data System (ADS)

    Stan, George; Brooks, Bernard R.; Lorimer, George H.; Thirumalai, D.

    2006-03-01

    We have used a bioinformatic approach to predict the natural substrate proteins for the Escherichia coli chaperonin GroEL based on two simple criteria. Natural substrate proteins should contain binding motifs similar in sequence to the mobile loop peptide of GroES that displaces the binding motif during the chaperonin cycle. Secondly, each substrate protein should contain multiple copies of the binding motif so that the chaperonin can perform "work" on the substrate protein. To validate these criteria, we have used a database of 252 proteins that have been experimentally shown to interact with the chaperonin machinery in vivo. More than 80% are identified by these criteria. The binding motifs of all 79 proteins in the database with a known three-dimensional structure are buried (<50% solvent-accessible surface area) in the native state. Our results show that the binding motifs are inaccessible in the native state but become solvent-exposed in unfolded state, thus enabling GroEL to distinguish between unfolded and native states. The structures of the binding motif in the native states of the substrate proteins include -helices, -strands, and random coils. The diversity of secondary structures implies that there are large and varied conformational transitions in the recognition motifs after their displacement by the mobile loops of GroES. chaperonin | E. coli | natural substrates | recognition motif

  19. LEDGIN-mediated Inhibition of Integrase-LEDGF/p75 Interaction Reduces Reactivation of Residual Latent HIV.

    PubMed

    Vranckx, Lenard S; Demeulemeester, Jonas; Saleh, Suha; Boll, Annegret; Vansant, Gerlinde; Schrijvers, Rik; Weydert, Caroline; Battivelli, Emilie; Verdin, Eric; Cereseto, Anna; Christ, Frauke; Gijsbers, Rik; Debyser, Zeger

    2016-06-01

    Persistence of latent, replication-competent Human Immunodeficiency Virus type 1 (HIV-1) provirus is the main impediment towards a cure for HIV/AIDS (Acquired Immune Deficiency Syndrome). Therefore, different therapeutic strategies to eliminate the viral reservoirs are currently being explored. We here propose a novel strategy to reduce the replicating HIV reservoir during primary HIV infection by means of drug-induced retargeting of HIV integration. A novel class of integration inhibitors, referred to as LEDGINs, inhibit the interaction between HIV integrase and the LEDGF/p75 host cofactor, the main determinant of lentiviral integration site selection. We show for the first time that LEDGF/p75 depletion hampers HIV-1 reactivation in cell culture. Next we demonstrate that LEDGINs relocate and retarget HIV integration resulting in a HIV reservoir that is refractory to reactivation by different latency-reversing agents. Taken together, these results support the potential of integrase inhibitors that modulate integration site targeting to reduce the likeliness of viral rebound. PMID:27428435

  20. The effect of cholesterol on the long-range network of interactions established among sea anemone Sticholysin II residues at the water-membrane interface.

    PubMed

    García-Linares, Sara; Alm, Ida; Maula, Terhi; Gavilanes, José G; Slotte, Johan Peter; Martínez-Del-Pozo, Álvaro

    2015-04-01

    Actinoporins are α-pore forming proteins with therapeutic potential, produced by sea anemones. Sticholysin II (StnII) from Stichodactyla helianthus is one of its most extensively characterized members. These proteins remain stably folded in water, but upon interaction with lipid bilayers, they oligomerize to form a pore. This event is triggered by the presence of sphingomyelin (SM), but cholesterol (Chol) facilitates pore formation. Membrane attachment and pore formation require changes involving long-distance rearrangements of residues located at the protein-membrane interface. The influence of Chol on membrane recognition, oligomerization, and/or pore formation is now studied using StnII variants, which are characterized in terms of their ability to interact with model membranes in the presence or absence of Chol. The results obtained frame Chol not only as an important partner for SM for functional membrane recognition but also as a molecule which significantly reduces the structural requirements for the mentioned conformational rearrangements to occur. However, given that the DOPC:SM:Chol vesicles employed display phase coexistence and have domain boundaries, the observed effects could be also due to the presence of these different phases on the membrane. In addition, it is also shown that the Arg51 guanidinium group is strictly required for membrane recognition, independently of the presence of Chol. PMID:25815890

  1. The Effect of Cholesterol on the Long-Range Network of Interactions Established among Sea Anemone Sticholysin II Residues at the Water-Membrane Interface

    PubMed Central

    García-Linares, Sara; Alm, Ida; Maula, Terhi; Gavilanes, José G.; Slotte, Johan Peter; Martínez-del-Pozo, Álvaro

    2015-01-01

    Actinoporins are α-pore forming proteins with therapeutic potential, produced by sea anemones. Sticholysin II (StnII) from Stichodactyla helianthus is one of its most extensively characterized members. These proteins remain stably folded in water, but upon interaction with lipid bilayers, they oligomerize to form a pore. This event is triggered by the presence of sphingomyelin (SM), but cholesterol (Chol) facilitates pore formation. Membrane attachment and pore formation require changes involving long-distance rearrangements of residues located at the protein-membrane interface. The influence of Chol on membrane recognition, oligomerization, and/or pore formation is now studied using StnII variants, which are characterized in terms of their ability to interact with model membranes in the presence or absence of Chol. The results obtained frame Chol not only as an important partner for SM for functional membrane recognition but also as a molecule which significantly reduces the structural requirements for the mentioned conformational rearrangements to occur. However, given that the DOPC:SM:Chol vesicles employed display phase coexistence and have domain boundaries, the observed effects could be also due to the presence of these different phases on the membrane. In addition, it is also shown that the Arg51 guanidinium group is strictly required for membrane recognition, independently of the presence of Chol. PMID:25815890

  2. Backbone and side chain NMR assignments of Geobacillus stearothermophilus ZapA allow identification of residues that mediate the interaction of ZapA with FtsZ.

    PubMed

    Nogueira, Maria Luiza C; Sforça, Mauricio Luis; Chin, Yanni K-Y; Mobli, Mehdi; Handler, Aaron; Gorbatyuk, Vitaliy Y; Robson, Scott A; King, Glenn F; Gueiros-Filho, Frederico J; Zeri, Ana Carolina de Mattos

    2015-10-01

    Bacterial division begins with the formation of a contractile protein ring at midcell, which constricts the bacterial envelope to generate two daughter cells. The central component of the division ring is FtsZ, a tubulin-like protein capable of self-assembling into filaments which further associate into a higher order structure known as the Z ring. Proteins that bind to FtsZ play a crucial role in the formation and regulation of the Z ring. One such protein is ZapA, a widely conserved 21 kDa homodimeric protein that associates with FtsZ filaments and promotes their bundling. Although ZapA was discovered more than a decade ago, the structural details of its interaction with FtsZ remain unknown. In this work, backbone and side chain NMR assignments for the Geobacillus stearothermophilus ZapA homodimer are described. We titrated FtsZ into (15)N(2)H-ZapA and mapped ZapA residues whose resonances are perturbed upon FtsZ binding. This information provides a structural understanding of the interaction between FtsZ and ZapA. PMID:25967379

  3. Elimination of secular terms from the differential equations for the elements of perturbed two-body motion

    NASA Technical Reports Server (NTRS)

    Bond, Victor R.; Fraietta, Michael F.

    1991-01-01

    In 1961, Sperling linearized and regularized the differential equations of motion of the two-body problem by changing the independent variable from time to fictitious time by Sundman's transformation (r = dt/ds) and by embedding the two-body energy integral and the Laplace vector. In 1968, Burdet developed a perturbation theory which was uniformly valid for all types of orbits using a variation of parameters approach on the elements which appeared in Sperling's equations for the two-body solution. In 1973, Bond and Hanssen improved Burdet's set of differential equations by embedding the total energy (which is a constant when the potential function is explicitly dependent upon time.) The Jacobian constant was used as an element to replace the total energy in a reformulation of the differential equations of motion. In the process, another element which is proportional to a component of the angular momentum was introduced. Recently trajectories computed during numerical studies of atmospheric entry from circular orbits and low thrust beginning in near-circular orbits exhibited numerical instability when solved by the method of Bond and Gottlieb (1989) for long time intervals. It was found that this instability was due to secular terms which appear on the righthand sides of the differential equations of some of the elements. In this paper, this instability is removed by the introduction of another vector integral called the delta integral (which replaces the Laplace Vector) and another scalar integral which removes the secular terms. The introduction of these integrals requires a new derivation of the differential equations for most of the elements. For this rederivation, the Lagrange method of variation of parameters is used, making the development more concise. Numerical examples of this improvement are presented.

  4. Identification of residues in the CH2/CH3 domain interface of IgA essential for interaction with the human fcalpha receptor (FcalphaR) CD89.

    PubMed

    Pleass, R J; Dunlop, J I; Anderson, C M; Woof, J M

    1999-08-13

    Cellular receptors for IgA (FcalphaR) mediate important protective functions. An extensive panel of site-directed mutant IgAs was used to identify IgA residues critical for FcalphaR (CD89) binding and triggering. Although a tailpiece-deleted IgA1 was able to bind and trigger CD89, antibodies featuring CH3 domain exchanges between human IgA1 and IgG1 could not, indicating that both domains but not the tailpiece are required for FcalphaR recognition. To further investigate the role of the interdomain region, numerous IgA1s, each with a point substitution in either of two interdomain loops (Leu-257-Gly-259 in Calpha2; Pro-440-Phe-443 in Calpha3), were generated. With only one exception (G259R), substitutions produced either ablation (L257R, P440A, A442R, F443R) or marked reduction (P440R) in CD89 binding and triggering. Further support for involvement of these interdomain loops was provided by interspecies comparisons of IgA. Thus a human IgA1 mutant, LA441-442MN, which mimicked the mouse IgA loop sequence through substitution of two adjacent residues in the Calpha3 loop, was found, like mouse IgA, not to bind CD89. In contrast, bovine IgA1, identical to human IgA1 within these interdomain loops despite numerous differences elsewhere in the Fc region, did bind CD89. We have thus identified motifs in the interdomain region of IgA Fc critical for FcalphaR binding and triggering, significantly enhancing present understanding of the molecular basis of the IgA-FcalphaR interaction. PMID:10438530

  5. The Two-Body Problem in the Point Mass Approximation Field. I. Collision and Near-Collision Dynamics

    NASA Astrophysics Data System (ADS)

    Mioc, Vasile; Stavinschi, Magda

    Newton's theorem about the point mass approximation is fully correct only in fields with potentials of the form A/r+Br2. Here r is the distance between particles, and A, B are real parameters. A systematic qualitative study of the two-body problem in such a field is being started here. The equations of motion are written in Hamiltonian formalism, and the first integrals of energy and angular momentum are pointed out. Using McGehee's transformation, the motion equations are regularized, and the collision singularity is replaced by the collision manifold. The flow on this manifold and in its neighbourhood is depicted.

  6. Complete angular distribution measurements of two-body deuteron photodisintegration between 0.5 and 3 GeV

    SciTech Connect

    M. Mirazita; F. Ronchetti; P. Rossi; E. De Sanctis; CLAS Collaboration

    2004-07-12

    Nearly complete angular distributions of the two-body deuteron photodisintegration differential cross section have been measured using the CEBAF Large Acceptance Spectrometer detector and the tagged photon beam at the Thomas Jefferson National Accelerator Facility. The data cover photon energies between 0.5 and 3.0 GeV and center-of-mass proton scattering angles 10{sup o}-160{sup o}. The data show a persistent forward-backward angle asymmetry over the explored energy range, and are well described by the nonperturbative quark gluon string model.

  7. Identification of the basic amino acid residues on the PsbP protein involved in the electrostatic interaction with photosystem II.

    PubMed

    Nishimura, Taishi; Uno, Chihiro; Ido, Kunio; Nagao, Ryo; Noguchi, Takumi; Sato, Fumihiko; Ifuku, Kentaro

    2014-09-01

    The PsbP protein is an extrinsic subunit of photosystem II (PSII) that is essential for photoautotrophic growth in higher plants. Several crystal structures of PsbP have been reported, but the binding topology of PsbP in PSII has not yet been clarified. In this study, we report that the basic pocket of PsbP, which consists of conserved Arg48, Lys143, and Lys160, is important for the electrostatic interaction with the PSII complex. Our release-reconstitution experiment showed that the binding affinities of PsbP-R48A, -K143A, and -K160A mutated proteins to PSII were lower than that of PsbP-WT, and triple mutations of these residues greatly diminished the binding affinity to PSII. Even when maximum possible binding had occurred, the R48A, K143A, and K160A proteins showed a reduced ability to restore the rate of oxygen evolution at low chloride concentrations. Fourier transform infrared resonance (FTIR) difference spectroscopy results were consistent with the above finding, and suggested that these mutated proteins were not able to induce the normal conformational change around the Mn cluster during S1 to S2 transition. Finally, chemical cross-linking experiments suggested that the interaction between the N-terminus of PsbP with PsbE was inhibited by these mutations. These data suggest that the basic pocket of PsbP is important for proper association and interaction with PSII. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy. PMID:24388917

  8. Direct identification of a distinct site of interaction between the carboxyl-terminal residue of cholecystokinin and the type A cholecystokinin receptor using photoaffinity labeling.

    PubMed

    Ji, Z; Hadac, E M; Henne, R M; Patel, S A; Lybrand, T P; Miller, L J

    1997-09-26

    Mechanisms of ligand binding and activation of G protein-coupled receptors are particularly important, due to their ubiquitous expression and potential as drug targets. Molecular interactions between ligands and these receptors are best defined for small molecule ligands that bind within the transmembrane helices. Extracellular domains seem to be more important for peptide ligands, based largely on effects of receptor mutagenesis, where interference with binding or activity can reflect allosteric as well as direct effects. We now take the more direct approach of photoaffinity labeling the active site of the cholecystokinin (CCK) receptor, using a photolabile analogue of CCK having a blocked amino terminus. This probe, 125I-desaminotyrosyl-Gly-[Nle28,31, pNO2-Phe33]CCK-(26-33), binds specifically, saturably, and with high affinity (Ki = 3.3 nM) and has full agonist activity. This makes likely its being sited in a natural position within the receptor. As substrate, we used CHO-CCK receptor cells overexpressing functional recombinant rat type A CCK receptor. Covalent labeling of the appropriate Mr = 85,000-95,000 plasma membrane glycoprotein with core of Mr = 42,000 was established by SDS-polyacrylamide gel electrophoresis and autoradiography. A single domain adjacent to transmembrane 1 was labeled, as established by cyanogen bromide cleavage and separation by gel and/or high pressure liquid chromatography. The site of interaction was further defined by additional proteolysis with trypsin, with purification of the labeled fragment, followed by manual Edman degradation and radiochemical sequencing. This demonstrated that Trp39 was specifically labeled and likely resides proximate to the carboxyl-terminal pNO2-Phe33 residue of the probe. A model of this ligand-bound receptor has been constructed and will be used to plan future experiments to refine our understanding of this interaction. PMID:9305898

  9. Residues in the alpha helix 7 of the bacterial maltose binding protein which are important in interactions with the Mal FGK2 complex.

    PubMed

    Szmelcman, S; Sassoon, N; Hofnung, M

    1997-03-01

    The periplasmic maltose binding protein, MalE, is a major element in maltose transport and in chemotaxis towards this sugar. Previous genetic analysis of the MalE protein revealed functional domains involved in transport and chemotactic functions. Among them the surface located alpha helix 7, which is part of the C-lobe, one of the two lobes forming the three dimensional structure of MalE. Small deletions in this region abolished maltose transport, although maintaining wild-type affinity and specificity as well as a normal chemoreceptor function. It was suggested that alpha helix 7 may be implicated in interactions between the maltose binding protein and the membrane-bound protein complex (Duplay P, Szmelcman S. 1987. Silent and functional changes in the periplasmic maltose binding protein of Escherichia coli K12. II. Chemotaxis towards maltose. J Mol Biol 194:675-678: Duplay P, Szmelcman S, Bedouelle H, Hofnung M. 1987. Silent and functional changes in the periplasmic maltose binding protein of Escherichia coli K12. I: Transport of maltose. J Mol Biol 194:663-673). In this study, we submitted a region of 14 residues--Asp 207 to Gly 220--encompassing alpha helix 7, to genetic analysis by oligonucleotide mediated random mutagenesis. Out of 127 identified mutations, twelve single and five double mutants with normal affinities towards maltose were selected for further investigation. Two types of mutations were characterized, silent mutations that did not affect maltose transport and mutations that heavily impaired transport kinetics, even thought the maltose binding capacity of the mutant proteins remained normal. Three substitutions at Tyr 210 (Y210S, Y210L, Y210N) drastically reduced maltose transport. One substitution at Ala 213 (A213I) and one substitution at Glu 214 (E214K) also impaired transport. These three identified residues, Tyr 210, Ala 213, and Glu 214, which are constituents of alpha helix 7, therefore seem to play some important role in maltose

  10. Observational Data Analysis and Numerical Model Assessment of the Seafloor Interaction and Mobility of Sand and Weathered Oil Agglomerates (Surface Residual Balls) in the Surf Zone

    NASA Astrophysics Data System (ADS)

    Dalyander, S.; Long, J.; Plant, N. G.; Penko, A.; Calantoni, J.; Thompson, D.; Mclaughlin, M. K.

    2014-12-01

    When weathered oil is transported ashore, such as during the Deepwater Horizon oil spill, it can mix with suspended sediment in the surf zone to create heavier-than-water sand and oil agglomerates in the form of mats several centimeters thick and tens of meters long. Broken off pieces of these mats and smaller agglomerates formed in situ (called Surface Residual Balls, SRBs) can cause beach re-oiling months to years after the initial spill. The physical dynamics of these SRBs in the nearshore, where they are larger (cm-scale) and less dense than natural sediment, are poorly understood. In the current study, SRB mobility and seafloor interaction is investigated through a combination of laboratory and field experiments with pseudo-SRBs developed to be physically stable proxies for genuine agglomerates. Formulations for mobility prediction based on comparing estimated shear stress to the critical Shields and modified Shields parameters developed for mixed sediment beds are assessed against observations. Processes such as burial, exhumation, and interaction with bedforms (e.g., migrating ripples) are also explored. The observations suggest that incipient motion estimates based on a modified Shields parameter have some skill in predicting SRB movement, but that other forcing mechanisms such as pressure gradients may be important under some conditions. Additionally, burial and exhumation due to the relatively high mobility of sand grains are confirmed as key processes controlling SRB dynamics in the surf zone. This work has broad implications for understanding surf zone sediment transport at the short timescale associated with mobilizing sand grains and SRBs as well as at the longer timescales associated with net transport patterns, sediment budgets, and bed elevation changes.

  11. Deformed ODD-ODD nuclei: Matrix elements for the residual n-p interaction and patterns of alternating perturbations in level spacings

    SciTech Connect

    Hoff, R.W.; Jain, A.K.; Kvasil, J.; Sood, P.C.; Sheline, R.K.; Florida State Univ., Tallahassee, FL )

    1989-09-01

    The application of a simple semi-empirical model is discussed in terms of interpreting experimental nuclear structure data for twelve of the best characterized odd-odd deformed nuclei. An essential part of this modeling is to calculate values for the Gallagher-Moszkowski splittings and Newby shifts, the observables that arise from the n-p residual interaction in odd-odd nuclei. Assumptions regarding the form for this n-p force are traced historically. The predictive power of a favored form of the n-p force, one that includes a central force with short and long-range components, a tensor force, and some effects of core polarization, is examined in light of experimental data obtained since its formulation. A data set of 42 experimentally determined Newby shifts has been reviewed as to the reliability of each entry. Exceptions to a recently proposed rule for the a priori determination of the sign of Newby shift are discussed. Evidence is presented for the existence of an odd-even staggering or signature effect in the rotational spacings of many K{sup {minus}} bands (with K > 0). By use of Coriolis-coupling calculations, it has been possible to reproduce the staggering observed in some of the K{sup {minus}} rotational bands of {sup 156}Tb, {sup 168}Tm, {sup 176}Lu, {sup 182}Ta, and {sup 182}Re. 27 refs., 3 figs., 3 tabs.

  12. Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides.

    PubMed

    Beroza, P; Fredkin, D R; Okamura, M Y; Feher, G

    1991-07-01

    We used Monte Carlo methods to treat statistical problem of electrostatic interactions among many titrating amino acids and applied these methods to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides, including all titrating sites. We computed the average protonation of residues as a function of pH from an equilibrium distribution of states generated by random sampling. Electrostatic energies were calculated from a finite difference solution to the linearized Poisson-Boltzmann equation using the coordinates from solved protein structures. For most calculations we used the Metropolis algorithm to sample protonation states; for strongly coupled sites, we substantially reduced sampling errors by using a modified algorithm that allows multiple site transitions. The Monte Carlo method agreed with calculations for a small test system, lysozyme, for which the complete partition function was calculated. We also calculated the pH dependence of the free energy change associated with electron transfer from the primary to the secondary quinone in the photosynthetic reaction center. The shape of the resulting curve agreed fairly well with experiment, but the proton uptake from which the free energy was calculated agreed only to within a factor of two with the observed values. We believe that this discrepancy resulted from errors in the individual electrostatic energy calculations rather than from errors in the Monte Carlo sampling. PMID:2062860

  13. Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides.

    PubMed Central

    Beroza, P; Fredkin, D R; Okamura, M Y; Feher, G

    1991-01-01

    We used Monte Carlo methods to treat statistical problem of electrostatic interactions among many titrating amino acids and applied these methods to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides, including all titrating sites. We computed the average protonation of residues as a function of pH from an equilibrium distribution of states generated by random sampling. Electrostatic energies were calculated from a finite difference solution to the linearized Poisson-Boltzmann equation using the coordinates from solved protein structures. For most calculations we used the Metropolis algorithm to sample protonation states; for strongly coupled sites, we substantially reduced sampling errors by using a modified algorithm that allows multiple site transitions. The Monte Carlo method agreed with calculations for a small test system, lysozyme, for which the complete partition function was calculated. We also calculated the pH dependence of the free energy change associated with electron transfer from the primary to the secondary quinone in the photosynthetic reaction center. The shape of the resulting curve agreed fairly well with experiment, but the proton uptake from which the free energy was calculated agreed only to within a factor of two with the observed values. We believe that this discrepancy resulted from errors in the individual electrostatic energy calculations rather than from errors in the Monte Carlo sampling. PMID:2062860

  14. Identification of amino acid residues of a designed ankyrin repeat protein potentially involved in intermolecular interactions with CD4: analysis by molecular dynamics simulations.

    PubMed

    Nimmanpipug, Piyarat; Khampa, Chalermpon; Lee, Vannajan Sanghiran; Nangola, Sawitree; Tayapiwatana, Chatchai

    2011-11-01

    We applied molecular dynamics simulations to investigate the binding properties of a designed ankyrin repeat protein, the DARPin-CD4 complex. DARPin 23.2 has been reported to disturb the human immunodeficiency virus (HIV) viral entry process by Schweizer et al. The protein docking simulation was analysed by comparing the specific ankyrin binder (DARPin 23.2) to an irrelevant control (2JAB) in forming a composite with CD4. To determine the binding free energy of both ankyrins, the MM/PBSA and MM/GBSA protocols were used. The free energy decomposition of both complexes were analysed to explore the role of certain amino acid residues in complex configuration. Interestingly, the molecular docking analysis of DARPin 23.2 revealed a similar CD4 interaction regarding the gp120 theoretical anchoring motif. In contrast, the binding of control ankyrin to CD4 occurred at a different location. This observation suggests that there is an advantage to the molecular modification of DARPin 23.2, an enhanced affinity for CD4. PMID:21962990

  15. Hydrophobic interaction between contiguous residues in the S6 transmembrane segment acts as a stimuli integration node in the BK channel

    PubMed Central

    Carrasquel-Ursulaez, Willy; Contreras, Gustavo F.; Sepúlveda, Romina V.; Aguayo, Daniel; González-Nilo, Fernando

    2015-01-01

    Large-conductance Ca2+- and voltage-activated K+ channel (BK) open probability is enhanced by depolarization, increasing Ca2+ concentration, or both. These stimuli activate modular voltage and Ca2+ sensors that are allosterically coupled to channel gating. Here, we report a point mutation of a phenylalanine (F380A) in the S6 transmembrane helix that, in the absence of internal Ca2+, profoundly hinders channel opening while showing only minor effects on the voltage sensor active–resting equilibrium. Interpretation of these results using an allosteric model suggests that the F380A mutation greatly increases the free energy difference between open and closed states and uncouples Ca2+ binding from voltage sensor activation and voltage sensor activation from channel opening. However, the presence of a bulky and more hydrophobic amino acid in the F380 position (F380W) increases the intrinsic open–closed equilibrium, weakening the coupling between both sensors with the pore domain. Based on these functional experiments and molecular dynamics simulations, we propose that F380 interacts with another S6 hydrophobic residue (L377) in contiguous subunits. This pair forms a hydrophobic ring important in determining the open–closed equilibrium and, like an integration node, participates in the communication between sensors and between the sensors and pore. Moreover, because of its effects on open probabilities, the F380A mutant can be used for detailed voltage sensor experiments in the presence of permeant cations. PMID:25548136

  16. Identification of Amino Acid Residues in Fibroblast Growth Factor 14 (FGF14) Required for Structure-Function Interactions with Voltage-gated Sodium Channel Nav1.6.

    PubMed

    Ali, Syed R; Singh, Aditya K; Laezza, Fernanda

    2016-05-20

    The voltage-gated Na(+) (Nav) channel provides the basis for electrical excitability in the brain. This channel is regulated by a number of accessory proteins including fibroblast growth factor 14 (FGF14), a member of the intracellular FGF family. In addition to forming homodimers, FGF14 binds directly to the Nav1.6 channel C-tail, regulating channel gating and expression, properties that are required for intrinsic excitability in neurons. Seeking amino acid residues with unique roles at the protein-protein interaction interface (PPI) of FGF14·Nav1.6, we engineered model-guided mutations of FGF14 and validated their impact on the FGF14·Nav1.6 complex and the FGF14:FGF14 dimer formation using a luciferase assay. Divergence was found in the β-9 sheet of FGF14 where an alanine (Ala) mutation of Val-160 impaired binding to Nav1.6 but had no effect on FGF14:FGF14 dimer formation. Additional analysis revealed also a key role of residues Lys-74/Ile-76 at the N-terminal of FGF14 in the FGF14·Nav1.6 complex and FGF14:FGF14 dimer formation. Using whole-cell patch clamp electrophysiology, we demonstrated that either the FGF14(V160A) or the FGF14(K74A/I76A) mutation was sufficient to abolish the FGF14-dependent regulation of peak transient Na(+) currents and the voltage-dependent activation and steady-state inactivation of Nav1.6; but only V160A with a concomitant alanine mutation at Tyr-158 could impede FGF14-dependent modulation of the channel fast inactivation. Intrinsic fluorescence spectroscopy of purified proteins confirmed a stronger binding reduction of FGF14(V160A) to the Nav1.6 C-tail compared with FGF14(K74A/I76A) Altogether these studies indicate that the β-9 sheet and the N terminus of FGF14 are well positioned targets for drug development of PPI-based allosteric modulators of Nav channels. PMID:26994141

  17. Two-body, dry abrasive wear of Fe/Cr/C experimental alloys - relationship between microstructure and mechanical properties

    SciTech Connect

    Kwok, C.K.S.

    1982-01-01

    A systematic study of abrasive wear resistance of Fe/Cr/Mn based alloys has been carried out using a two body pin-on-disc wear machine. Abrasives used were silicon carbide, alumina and quartz. The objective of this study was to evaluate the abrasive wear resistance and to investigate the relationships between microstructure, mechanical properties, and abrasive wear resistance for these experimental alloys. Several commercial alloys were also tested to provide a basis for comparison. The goal of this study was to develop information so as to improve wear resistance of these experimental alloys by means of thermal treatments. Grain-refinement by double heat treatment was carried out in this research.

  18. HFOLD - A program package for calculating two-body MSSM Higgs decays at full one-loop level.

    PubMed

    Frisch, W; Eberl, H; Hluchá, H

    2011-10-01

    HFOLD (Higgs Full One Loop Decays) is a Fortran program package for calculating all MSSM Higgs two-body decay widths and the corresponding branching ratios at full one-loop level. The package is done in the SUSY Parameter Analysis convention and supports the SUSY Les Houches Accord input and output format. PROGRAM SUMMARY: Program title: HFOLD Catalogue identifier: AEJG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 340 621 No. of bytes in distributed program, including test data, etc.: 1 760 051 Distribution format: tar.gz Programming language: Fortran 77 Computer: Workstation, PC Operating system: Linux RAM: 524 288 000 Bytes Classification: 11.1 External routines: LoopTools 2.2 (http://www.feynarts.de/looptools/), SLHALib 2.2 (http://www.feynarts.de/slha/). The LoopTools code is included in the distribution package. Nature of problem: A future high-energy e+e- linear collider will be the best environment for the precise measurements of masses, cross sections, branching ratios, etc. Experimental accuracies are expected at the per-cent down to the per-mile level. These must be matched from the theoretical side. Therefore higher order calculations are mandatory. Solution method: This program package calculates all MSSM Higgs two-body decay widths and the corresponding branching ratios at full one-loop level. The renormalization is done in the DR scheme following the SUSY Parameter Analysis convention. The program supports the SUSY Les Houches Accord input and output format. Running time: The example provided takes only a few seconds to run. PMID:21969735

  19. Visual capture and the experience of having two bodies – Evidence from two different virtual reality techniques

    PubMed Central

    Heydrich, Lukas; Dodds, Trevor J.; Aspell, Jane E.; Herbelin, Bruno; Bülthoff, Heinrich H.; Mohler, Betty J.; Blanke, Olaf

    2013-01-01

    In neurology and psychiatry the detailed study of illusory own body perceptions has suggested close links between bodily processing and self-consciousness. One such illusory own body perception is heautoscopy where patients have the sensation of being reduplicated and to exist at two or even more locations. In previous experiments, using a video head-mounted display, self-location and self-identification were manipulated by applying conflicting visuo-tactile information. Yet the experienced singularity of the self was not affected, i.e., participants did not experience having multiple bodies or selves. In two experiments presented in this paper, we investigated self-location and self-identification while participants saw two virtual bodies (video-generated in study 1 and 3D computer generated in study 2) that were stroked either synchronously or asynchronously with their own body. In both experiments, we report that self-identification with two virtual bodies was stronger during synchronous stroking. Furthermore, in the video generated setup with synchronous stroking participants reported a greater feeling of having multiple bodies than in the control conditions. In study 1, but not in study 2, we report that self-location – measured by anterior posterior drift – was significantly shifted towards the two bodies in the synchronous condition only. Self-identification with two bodies, the sensation of having multiple bodies, and the changes in self-location show that the experienced singularity of the self can be studied experimentally. We discuss our data with respect to ownership for supernumerary hands and heautoscopy. We finally compare the effects of the video and 3D computer generated head-mounted display technology and discuss the possible benefits of using either technology to induce changes in illusory self-identification with a virtual body. PMID:24385970

  20. Structure-Based Network Analysis of Activation Mechanisms in the ErbB Family of Receptor Tyrosine Kinases: The Regulatory Spine Residues Are Global Mediators of Structural Stability and Allosteric Interactions

    PubMed Central

    James, Kevin A.; Verkhivker, Gennady M.

    2014-01-01

    The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced “superacceptor” activity in oncogenic EGFR dimers. We have found that kinase activation may be determined by allosteric interactions between modules of structurally stable residues that synchronize the dynamics in the nucleotide binding site and the αC-helix with the collective motions of the integrating αF-helix and the substrate binding site. The results of this study have pointed to a central role of the conserved His-Arg-Asp (HRD) motif in the catalytic loop and the Asp-Phe-Gly (DFG) motif as key mediators of structural stability and allosteric communications in the ErbB kinases. We have determined that residues that are indispensable for kinase regulation and catalysis often corresponded to the high centrality nodes within the protein structure network and could be distinguished by their unique network signatures. The optimal communication pathways are also controlled by these nodes and may ensure efficient allosteric signaling in the functional kinase state. Structure-based network analysis has quantified subtle effects of ATP binding on conformational dynamics and stability of the EGFR structures. Consistent with the NMR studies, we have found that nucleotide-induced modulation of the residue interaction networks is not limited to the

  1. A 20-residue peptide of the inner membrane protein OutC mediates interaction with two distinct sites of the outer membrane secretin OutD and is essential for the functional type II secretion system in Erwinia chrysanthemi.

    PubMed

    Login, Frédéric H; Fries, Markus; Wang, Xiaohui; Pickersgill, Richard W; Shevchik, Vladimir E

    2010-05-01

    The type II secretion system (T2SS) is widely exploited by proteobacteria to secrete enzymes and toxins involved in bacterial survival and pathogenesis. The outer membrane pore formed by the secretin OutD and the inner membrane protein OutC are two key components of the secretion complex, involved in secretion specificity. Here, we show that the periplasmic regions of OutC and OutD interact directly and map the interaction site of OutC to a 20-residue peptide named OutCsip (secretin interacting peptide, residues 139-158). This peptide interacts in vitro with two distinct sites of the periplasmic region of OutD, one located on the N0 subdomain and another overlapping the N2-N3' subdomains. The two interaction sites of OutD have different modes of binding to OutCsip. A single substitution, V143S, located within OutCsip prevents its interaction with one of the two binding sites of OutD and fully inactivates the T2SS. We show that the N0 subdomain of OutD interacts also with a second binding site within OutC located in the region proximal to the transmembrane segment. We suggest that successive interactions between these distinct regions of OutC and OutD may have functional importance in switching the secretion machine. PMID:20444086

  2. Positive charges on lysine residues of the extrinsic 18 kDa protein are important to its electrostatic interaction with spinach photosystem II membranes.

    PubMed

    Gao, Jin-Peng; Yong, Zhen-Hua; Zhang, Feng; Ruan, Kang-Cheng; Xu, Chun-He; Chen, Gen-Yun

    2005-11-01

    To determine the contribution of charged amino acids to binding with the photosystem II complex (PSII), the amino or carboxyl groups of the extrinsic 18 kDa protein were modified with N-succinimidyl propionate (NSP) or glycine methyl ester (GME) in the presence of a water-soluble carbodiimide, respectively. Based on isoelectric point shift, 4-10 and 10-14 amino groups were modified in the presence of 2 and 4 mM NSP, respectively. Similarly, 3-4 carboxyl groups were modified by reaction with 100 mM GME. Neutralization of negatively charged carboxyl groups with GME did not alter the binding activity of the extrinsic 18 kDa protein. However, the NSP-modified 18 kDa protein, in which the positively charged amino groups had been modified to uncharged methyl esters, failed to bind with the PSII membrane in the presence of the extrinsic 23 kDa protein. This defect can not be attributed to structural or conformational alterations imposed by chemical modification, as the fluorescence and circular dichroism spectra among native, GME- and NSP-modified extrinsic 18 kDa proteins were similar. Thus, we have concluded that the positive charges of lysyl residues in the extrinsic 18 kDa protein are important for its interaction with PSII membranes in the presence of the extrinsic 23 kDa protein. Furthermore, it was found that the negative charges of carboxyl groups of this protein did not participate in binding with the extrinsic 23 kDa protein associated with PSII membranes. PMID:16270152

  3. NMR studies of ligand carboxylate group interactions with arginine residues in complexes of Lactobacillus casei dihydrofolate reductase with substrates and substrate analogues.

    PubMed

    Birdsall, B; Polshakov, V I; Feeney, J

    2000-08-15

    In a series of complexes of Lactobacillus casei dihydrofolate reductase (DHFR) formed with substrates and substrate analogues, the (1)H/(15)N NMR chemical shifts for the guanidino group of the conserved Arg 57 residue were found to be sensitive to the mode of binding of their H(eta) protons to the charged oxygen atoms in ligand carboxylate groups. In all cases, Arg 57 showed four nonequivalent H(eta) signals indicating hindered rotation about the N(epsilon)-C(zeta) and C(zeta)-N(eta) bonds. The H(eta)(12) and H(eta)(22) protons have large downfield shifts as expected for a symmetrical end-on interaction with the ligand carboxylate group. The chemical shifts are essentially the same in the complexes with folate and p-aminobenzoyl-L-glutamate (PABG) and similar to those found previously for the methotrexate complex reflecting the strong and similar hydrogen bonds formed with the carboxylate oxygens. Interestingly, the rates of rotation about the N(epsilon)-C(zeta) bond for the complexes containing the weakly binding PABG fragment are almost identical to those measured in the complex with methotrexate, which binds 10(7) times more tightly. In the methotrexate complex, this rotation depends on correlated rotations about the N(epsilon)-C(zeta) bond of Arg 57 and the C(alpha)-C' bond of the ligand glutamate alpha-carboxylate group. Thus, even in a fragment such as PABG, which has a much faster off-rate, the carboxylate group binds to the enzyme in a similar way to that in a parent molecule such as folate and methotrexate with the rotation about the N(epsilon)-C(zeta) bond of Arg 57 being essentially the same in all the different complexes. PMID:10933799

  4. Classical density functional theory and the phase-field crystal method using a rational function to describe the two-body direct correlation function.

    PubMed

    Pisutha-Arnond, N; Chan, V W L; Iyer, M; Gavini, V; Thornton, K

    2013-01-01

    We introduce a new approach to represent a two-body direct correlation function (DCF) in order to alleviate the computational demand of classical density functional theory (CDFT) and enhance the predictive capability of the phase-field crystal (PFC) method. The approach utilizes a rational function fit (RFF) to approximate the two-body DCF in Fourier space. We use the RFF to show that short-wavelength contributions of the two-body DCF play an important role in determining the thermodynamic properties of materials. We further show that using the RFF to empirically parametrize the two-body DCF allows us to obtain the thermodynamic properties of solids and liquids that agree with the results of CDFT simulations with the full two-body DCF without incurring significant computational costs. In addition, the RFF can also be used to improve the representation of the two-body DCF in the PFC method. Last, the RFF allows for a real-space reformulation of the CDFT and PFC method, which enables descriptions of nonperiodic systems and the use of nonuniform and adaptive grids. PMID:23410466

  5. Crop residues

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Crop residues [e.g., corn (Zea mays) stover and small grain straw] are sometimes excluded when discussing cellulosic energy crops per se, but because of the vast area upon which they are grown and their current role in the development of cellulosic energy systems. This chapter focuses on current cor...

  6. Analysis of two-body charmed B meson decays in factorization-assisted topological-amplitude approach

    NASA Astrophysics Data System (ADS)

    Zhou, Si-Hong; Wei, Yan-Bing; Qin, Qin; Li, Ying; Yu, Fu-Sheng; Lü, Cai-Dian

    2015-11-01

    Within the factorization-assisted topological-amplitude approach, we study the two-body charmed B meson decays Bu ,d ,s→D(*)M , with M denoting a light pseudoscalar (or vector) meson. The meson decay constants and transition form factors are factorized out from the hadronic matrix element of topological diagrams. Therefore, the effect of SU(3) symmetry breaking is retained, which is different from the conventional topological diagram approach. The number of free nonperturbative parameters to be fitted from experimental data is also much less. Only four universal nonperturbative parameters χC, ϕC, χE and ϕE are introduced to describe the contribution of the color-suppressed tree and W -exchanged diagrams for all the decay channels. With the fitted parameters from 31 decay modes induced by b →c transition, we then predict the branching fractions of 120 decay modes induced by both b →c and b →u transitions. Our results are well consistent with the measured data or to be tested in the LHCb and Belle-II experiments in the future. Besides, the SU(3) symmetry breaking, isospin violation and C P asymmetry are also investigated.

  7. Global analysis of two-body D →V P decays within the framework of flavor symmetry

    NASA Astrophysics Data System (ADS)

    Cheng, Hai-Yang; Chiang, Cheng-Wei; Kuo, An-Li

    2016-06-01

    Two-body charmed meson decays D →V P are studied within the framework of the diagrammatic approach. Under flavor SU(3) symmetry, all the flavor amplitude sizes and their associated strong phases are extracted by performing a χ2 fit. Thanks to the recent measurement of Ds+→π+ρ0 , the magnitudes and the strong phases of the W -annihilation amplitudes AP ,V have been extracted for the first time. As a consequence, the branching fractions of all the D →V P decays are predicted, especially those modes that could not be predicted previously due to the unknown AP ,V. Our working assumption, the flavor SU(3) symmetry, is tested by comparing our predictions with experiment for the singly and doubly Cabibbo-suppressed decay modes based on the flavor amplitudes extracted from the Cabibbo-favored decays using the current data. The predictions for the doubly Cabibbo-suppressed channels are in good agreement with the data, while those for the singly Cabibbo-suppressed decay modes are seen to have flavor SU(3) symmetry breaking effects. We find that the inclusion of SU(3) symmetry breaking in color-allowed and color-suppressed tree amplitudes is needed in general in order to have a better agreement with experiment. Nevertheless, the exact flavor SU(3)-symmetric approach alone is adequate to provide an overall explanation for the current data.

  8. Conservative dynamics of two-body systems at the fourth post-Newtonian approximation of general relativity

    NASA Astrophysics Data System (ADS)

    Damour, Thibault; Jaranowski, Piotr; Schäfer, Gerhard

    2016-04-01

    The fourth post-Newtonian (4PN) two-body dynamics has been recently tackled by several different approaches: effective field theory, Arnowitt-Deser-Misner Hamiltonian, action-angle-Delaunay averaging, effective-one-body, gravitational self-force, first law of dynamics, and Fokker action. We review the achievements of these approaches and discuss the complementarity of their results. Our main conclusions are: (i) the results of the first complete derivation of the 4PN dynamics [T. Damour, P. Jaranowski, and G. Schäfer, Phys. Rev. D 89, 064058 (2014)] have been, piecewise, fully confirmed by several subsequent works; (ii) the results of the Delaunay-averaging technique [T. Damour, P. Jaranowski, and G. Schäfer, Phys. Rev. D 91, 084024 (2015)] have been confirmed by several independent works; and (iii) several claims in a recent harmonic-coordinates Fokker-action computation [L. Bernard et al., arXiv:1512.02876v2] are incorrect, but can be corrected by the addition of a couple of ambiguity parameters linked to subtleties in the regularization of infrared and ultraviolet divergences.

  9. Key amino acid residues involved in multi-point binding interactions between brazzein, a sweet protein, and the T1R2-T1R3 human sweet receptor

    PubMed Central

    Assadi-Porter, Fariba M.; Maillet, Emeline L.; Radek, James T.; Quijada, Jeniffer; Markley, John L.; Max, Marianna

    2010-01-01

    The sweet protein brazzein activates the human sweet receptor, a heterodimeric G-protein coupled receptor (GPCR) composed of subunits T1R2 and T1R3. In order to elucidate the key amino acid(s) responsible for this interaction, we mutated residues in brazzein and each of the two subunits of the receptor. The effects of brazzein mutations were assayed by a human taste panel and by an in vitro assay involving receptor subunits expressed recombinantly in human embryonic kidney cells; the effects of the receptor mutations were assayed by the in vitro assay. We mutated surface residues of brazzein at three putative interaction sites: Site 1 (Loop43), Site 2 (N- and C-terminus and adjacent Glu36, Loop33), and Site 3 (Loop9–19). Basic residues in Site 1 and acidic residues in Site 2 were essential for positive responses from each assay. Mutation of Y39A (Site 1) greatly reduced positive responses. A bulky side chain at position 54 (Site 2), rather than a side chain with hydrogen bonding potential, was required for positive responses as was the presence of the native disulfide bond in Loop 9–19 (Site 3). Results from mutagenesis and chimeras of the receptor indicated that brazzein interacts with both T1R2 and T1R3 and that the Venus fly trap module of T1R2 is important for brazzein agonism. With one exception, all mutations of receptor residues at putative interaction sites predicted by wedge models failed to yield the expected decrease in the brazzein response. The exception, hT1R2:R217A-hT1R3, which contained a substitution in lobe 2 at the interface between the two subunits, exhibited a small selective decrease in brazzein activity. However, because the mutation was found to increase the positive cooperativity of binding by multiple ligands proposed to bind both T1R subunits (brazzein, monellin, and sucralose) but not those that bind to a single subunit (neotame and cyclamate), we suggest that this site in involved in subunit-subunit interaction rather than direct

  10. Structure and lipid interactions of an anti-inflammatory and anti-atherogenic 10 residue Class G* Apolipoprotein J peptide using solution NMR#

    PubMed Central

    Mishra, Vinod K.; Palgunachari, Mayakonda N.; Hudson, Jason S.; Shin, Ronald; Keenum, Tamara D.; Rama Krishna, N.; Anantharamaiah, G. M.

    2010-01-01

    The surprising observation that a 10 residue class G* peptide from apolipoprotein J, [113-122]apoJ, possesses anti-inflammatory and anti-atherogenic properties prompted us to delineate its structural characteristics in the presence of normal and oxidized lipid. Towards this, we have determined high resolution structure of [113-122]apoJ in solution using nuclear magnetic resonance (NMR) spectroscopy and studied its interaction with lipids, including oxidized lipids, using a number of biophysical methods. Circular dichroism and NMR studies established that in the presence of dodecylphosphocholine (DPC) micelle this peptide adopts amphipathic α helical structure. The observed Nuclear Overhauser effects indicate that the amphipathic helical structure of the peptide is stabilized by the N-terminal acetyl and C-terminal amide blocking groups. We used isothermal titration calorimetry to measure binding enthalpy of the peptide with DPC micelle, an oxidized lipid, 1-(palmitoyl)-2-(5-keto-6-octene-dioyl) phosphatidylcholine (KOdiA-PC), and the mixture of these two lipids (5mol% KOdiA-PC in DPC micelle). We find that the peptide binding with DPC micelle is associated with an enthalpy change (-16.75±0.16 Kcal/mol) much larger than that resulting from the binding with KodiA-PC (-3.67±0.13 Kcal/mol). Incorporation of a small amount of KOdiA-PC (5mol %) in DPC micelle also results in the lowering of peptide binding enthalpy (-13.43±0.18 Kcal/mol). These results are consistent with overall negative charge and altered conformational properties of oxidized sn-2 chain of KOdiA-PC. Our results have unambiguously established the amphipathic α helical structure of [113-122]apoJ peptide in the presence of DPC micelle as well as its ability to bind oxidized lipid. These in vitro results help explain the previously observed anti-inflammatory and anti-atherosclerotic properties of this peptide. PMID:20970404

  11. The TDF System for Thermonuclear Plasma Reaction Rates, Mean Energies and Two-Body Final State Particle Spectra

    SciTech Connect

    Warshaw, S I

    2001-07-11

    The rate of thermonuclear reactions in hot plasmas as a function of local plasma temperature determines the way in which thermonuclear ignition and burning proceeds in the plasma. The conventional model approach to calculating these rates is to assume that the reacting nuclei in the plasma are in Maxwellian equilibrium at some well-defined plasma temperature, over which the statistical average of the reaction rate quantity {sigma}v is calculated, where {sigma} is the cross-section for the reaction to proceed at the relative velocity v between the reacting particles. This approach is well-understood and is the basis for much nuclear fusion and astrophysical nuclear reaction rate data. The Thermonuclear Data File (TDF) system developed at the Lawrence Livermore National Laboratory (Warshaw 1991), which is the topic of this report, contains data on the Maxwellian-averaged thermonuclear reaction rates for various light nuclear reactions and the correspondingly Maxwellian-averaged energy spectra of the particles in the final state of those reactions as well. This spectral information closely models the output particle and energy distributions in a burning plasma, and therefore leads to more accurate computational treatments of thermonuclear burn, output particle energy deposition and diagnostics, in various contexts. In this report we review and derive the theoretical basis for calculating Maxwellian-averaged thermonuclear reaction rates, mean particle energies, and output particle spectral energy distributions for these reactions in the TDF system. The treatment of the kinematics is non-relativistic. The current version of the TDF system provides exit particle energy spectrum distributions for two-body final state reactions only. In a future report we will discuss and describe how output particle energy spectra for three- and four-body final states can be developed for the TDF system. We also include in this report a description of the algorithmic implementation of the

  12. The Impact of Retained Austenite Characteristics on the Two-Body Abrasive Wear Behavior of Ultrahigh Strength Bainitic Steels

    NASA Astrophysics Data System (ADS)

    Narayanaswamy, Balaji; Hodgson, Peter; Timokhina, Ilana; Beladi, Hossein

    2016-08-01

    two-body abrasion.

  13. On tide-induced lagrangian residual current and residual transport: 1. Lagrangian residual current

    USGS Publications Warehouse

    Feng, Shizuo; Cheng, Ralph T.; Pangen, Xi

    1986-01-01

    Residual currents in tidal estuaries and coastal embayments have been recognized as fundamental factors which affect the long-term transport processes. It has been pointed out by previous studies that it is more relevant to use a Lagrangian mean velocity than an Eulerian mean velocity to determine the movements of water masses. Under weakly nonlinear approximation, the parameter k, which is the ratio of the net displacement of a labeled water mass in one tidal cycle to the tidal excursion, is assumed to be small. Solutions for tides, tidal current, and residual current have been considered for two-dimensional, barotropic estuaries and coastal seas. Particular attention has been paid to the distinction between the Lagrangian and Eulerian residual currents. When k is small, the first-order Lagrangian residual is shown to be the sum of the Eulerian residual current and the Stokes drift. The Lagrangian residual drift velocity or the second-order Lagrangian residual current has been shown to be dependent on the phase of tidal current. The Lagrangian drift velocity is induced by nonlinear interactions between tides, tidal currents, and the first-order residual currents, and it takes the form of an ellipse on a hodograph plane. Several examples are given to further demonstrate the unique properties of the Lagrangian residual current.

  14. Residual Cap

    NASA Technical Reports Server (NTRS)

    2006-01-01

    10 May 2006 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a summertime view of the south polar residual cap of Mars. In this image, mesas composed largely of solid carbon dioxide are separated from one another by irregularly-shaped depressions. The variation in brightness across this scene is a function of several factors including, but not limited to, varying proportions of dust and solid carbon dioxide, undulating topography, and differences in the roughness of the slopes versus the flat surfaces.

    Location near: 86.7oS, 343.3oW Image width: 3 km (1.9 mi) Illumination from: upper left Season: Southern Summer

  15. Identification of hormone-interacting amino acid residues within the steroid-binding domain of the glucocorticoid receptor in relation to other steroid hormone receptors

    SciTech Connect

    Carlstedt-Duke, J.; Stroemstedt, P.E.; Persson, B.; Cederlund, E.; Gustafsson, J.A.; Joernvall, H.

    1988-05-15

    Purified rat liver glucocorticoid receptor was covalently charged with (/sup 3/H)glucocorticoid by photoaffinity labeling (UV irradiation of (/sup 3/H)triamcinolone acetonide-glucocorticoid receptor) or affinity labeling (incubation with (/sup 3/H)dexamethasone mesylate). After labeling, separate samples of the denatured receptor were cleaved with trypsin (directly or after prior succinylation), chymotrypsin, and cyanogen bromide. Labeled residues in the peptides obtained were identified by radiosequence analysis. The peaks of radioactivity corresponded to Met-622 and Cys-754 after photoaffinity labeling with (/sup 3/H)triamcinolone acetonide and Cys-656 after affinity labeling with (/sup 3/H)dexamethasone mesylate. The labeled residues are all positioned within hydrophobic segments of the steroid-binding domain. The patterns of hydropathy and secondary structure for the glucocorticoid receptor are highly similar to those for the progestin receptor and similar but less so to those for the estrogen receptor and to those for c-erb A.

  16. A Mutational Analysis of Residues in Cholera Toxin A1 Necessary for Interaction with Its Substrate, the Stimulatory G Protein Gsα

    PubMed Central

    Jobling, Michael G.; Gotow, Lisa F.; Yang, Zhijie; Holmes, Randall K.

    2015-01-01

    Pathogenesis of cholera diarrhea requires cholera toxin (CT)-mediated adenosine diphosphate (ADP)-ribosylation of stimulatory G protein (Gsα) in enterocytes. CT is an AB5 toxin with an inactive CTA1 domain linked via CTA2 to a pentameric receptor-binding B subunit. Allosterically activated CTA1 fragment in complex with NAD+ and GTP-bound ADP-ribosylation factor 6 (ARF6-GTP) differs conformationally from the CTA1 domain in holotoxin. A surface-exposed knob and a short α-helix (formed, respectively, by rearranging “active-site” and “activation” loops in inactive CTA1) and an ADP ribosylating turn-turn (ARTT) motif, all located near the CTA1 catalytic site, were evaluated for possible roles in recognizing Gsα. CT variants with one, two or three alanine substitutions at surface-exposed residues within these CTA1 motifs were tested for assembly into holotoxin and ADP-ribosylating activity against Gsα and diethylamino-(benzylidineamino)-guanidine (DEABAG), a small substrate predicted to fit into the CTA1 active site). Variants with single alanine substitutions at H55, R67, L71, S78, or D109 had nearly wild-type activity with DEABAG but significantly decreased activity with Gsα, suggesting that the corresponding residues in native CTA1 participate in recognizing Gsα. As several variants with multiple substitutions at these positions retained partial activity against Gsα, other residues in CTA1 likely also participate in recognizing Gsα. PMID:25793724

  17. Spring Chinook Salmon Interactions Indices and Residual/Precocious Male Monitoring in the Upper Yakima Basin; Yakima/Klickitat Fisheries Project Monitoring and Evaluation, 2004-2005 Annual Report.

    SciTech Connect

    Pearsons, Todd N.; Johnson, Christopher L.; James, Brenda B.

    2005-05-01

    This report examines some of the factors that can influence the success of supplementation, which is currently being tested in the Yakima Basin using upper Yakima stock of spring chinook salmon. Supplementation success in the Yakima Basin is defined relative to four topic areas: natural production, genetics, ecological interactions, and harvest (Busack et al. 1997). The success of spring chinook salmon supplementation in the Yakima Basin is dependent, in part, upon fish culture practices and favorable physical and biological conditions in the natural environment (Busack et al. 1997; James et al. 1999; Pearsons et al., 2003; Pearsons et al. 2004). Shortfalls in either of these two topics (i.e., failure in culturing many fish that have high long-term fitness or environmental conditions that constrain spring chinook salmon production) will cause supplementation success to be limited. For example, inadvertent selection or propagation of spring chinook that residualize or precocially mature may hinder supplementation success. Spring chinook salmon that residualize (do not migrate during the normal migration period) may have lower survival rates than migrants and, additionally, may interact with wild fish and cause unacceptable impacts to non-target taxa. Large numbers of precocials (nonanadromous spawners) may increase competition for females and significantly skew ratios of offspring sired by nonanadromous males, which could result in more nonanadromous spring chinook in future generations. Conditions in the natural environment may also limit the success of spring chinook supplementation. For example, intra or interspecific competition may constrain spring chinook salmon production. Spring chinook salmon juveniles may compete with each other for food or space or compete with other species that have similar ecological requirements. Monitoring of spring chinook salmon residuals, precocials, prey abundance, carrying capacity, and competition will help researchers

  18. Identification of critical residues in Hepatitis E virus macro domain involved in its interaction with viral methyltransferase and ORF3 proteins

    PubMed Central

    Anang, Saumya; Subramani, Chandru; Nair, Vidya P.; Kaul, Sheetal; Kaushik, Nidhi; Sharma, Chandresh; Tiwari, Ashutosh; Ranjith-Kumar, CT; Surjit, Milan

    2016-01-01

    Hepatitis E virus (HEV) is a major cause of hepatitis in normal and organ transplant individuals. HEV open reading frame-1 encodes a polypeptide comprising of the viral nonstructural proteins as well as domains of unknown function such as the macro domain (X-domain), V, DUF3729 and Y. The macro domain proteins are ubiquitously present from prokaryotes to human and in many positive-strand RNA viruses, playing important roles in multiple cellular processes. Towards understanding the function of the HEV macro domain, we characterized its interaction partners among other HEV encoded proteins. Here, we report that the HEV X-domain directly interacts with the viral methyltransferase and the ORF3 proteins. ORF3 association with the X-domain was mediated through two independent motifs, located within its N-terminal 35aa (amino acids) and C-terminal 63-123aa. Methyltransferase interaction domain was mapped to N-terminal 30-90aa. The X-domain interacted with both ORF3 and methyltransferase through its C-terminal region, involving 66th,67th isoleucine and 101st,102nd leucine, conserved across HEV genotypes. Furthermore, ORF3 and methyltransferase competed with each other for associating with the X-domain. These findings provide molecular understanding of the interaction between the HEV macro domain, methyltransferase and ORF3, suggesting an important role of the macro domain in the life cycle of HEV. PMID:27113483

  19. Identification of critical residues in Hepatitis E virus macro domain involved in its interaction with viral methyltransferase and ORF3 proteins.

    PubMed

    Anang, Saumya; Subramani, Chandru; Nair, Vidya P; Kaul, Sheetal; Kaushik, Nidhi; Sharma, Chandresh; Tiwari, Ashutosh; Ranjith-Kumar, C T; Surjit, Milan

    2016-01-01

    Hepatitis E virus (HEV) is a major cause of hepatitis in normal and organ transplant individuals. HEV open reading frame-1 encodes a polypeptide comprising of the viral nonstructural proteins as well as domains of unknown function such as the macro domain (X-domain), V, DUF3729 and Y. The macro domain proteins are ubiquitously present from prokaryotes to human and in many positive-strand RNA viruses, playing important roles in multiple cellular processes. Towards understanding the function of the HEV macro domain, we characterized its interaction partners among other HEV encoded proteins. Here, we report that the HEV X-domain directly interacts with the viral methyltransferase and the ORF3 proteins. ORF3 association with the X-domain was mediated through two independent motifs, located within its N-terminal 35aa (amino acids) and C-terminal 63-123aa. Methyltransferase interaction domain was mapped to N-terminal 30-90aa. The X-domain interacted with both ORF3 and methyltransferase through its C-terminal region, involving 66(th),67(th) isoleucine and 101(st),102(nd) leucine, conserved across HEV genotypes. Furthermore, ORF3 and methyltransferase competed with each other for associating with the X-domain. These findings provide molecular understanding of the interaction between the HEV macro domain, methyltransferase and ORF3, suggesting an important role of the macro domain in the life cycle of HEV. PMID:27113483

  20. Structural evolution and membrane interaction of the 40-residue β amyloid peptides: differences in the initial proximity between peptides and the membrane bilayer studied by solid-state nuclear magnetic resonance spectroscopy.

    PubMed

    Qiang, Wei; Akinlolu, Rumonat D; Nam, Mimi; Shu, Nicolas

    2014-12-01

    Interactions between the β amyloid (Aβ) peptides and cellular membranes have severe consequences such as neuronal cell disruption and therefore may play important roles in Alzheimer's disease. Understanding the structural basis behind such interactions, however, is hindered by the complexity of the Aβ-membrane systems. In particular, because the Aβ peptides are partially incorporated in the membrane bilayer after enzymatic cleavage, there are multiple possibilities in terms of the initial proximity between the peptides and membranes. Structural studies using in vitro model systems with either externally added or preincorporated Aβ in membrane bilayers resulted in distinct evolution pathways. Previous work has shown that the externally added Aβ formed long and mature filaments, while preincorporated Aβ generated short and curvy fibrils. In this study, we perform detailed characterizations on the structural evolution and membrane interaction for these two pathways, using a combination of solid-state nuclear magnetic resonance spectroscopy and other techniques. For the externally added Aβ, we determined the residue-specific structural evolution during the fibrillation process. While the entire fibrillation process for the externally added Aβ was slow, the preincorporated Aβ generated Aβ-lipid complexes rapidly. Specific interactions between the lipids and peptides were observed, suggesting the colocalization of lipids and peptides within the complex. Formation of such a complex induced molecular-level changes in the lipid bilayer, which may serve as a possible mechanism of membrane disruption. PMID:25397729

  1. Modeling Latent Interactions at Level 2 in Multilevel Structural Equation Models: An Evaluation of Mean-Centered and Residual-Centered Unconstrained Approaches

    ERIC Educational Resources Information Center

    Leite, Walter L.; Zuo, Youzhen

    2011-01-01

    Among the many methods currently available for estimating latent variable interactions, the unconstrained approach is attractive to applied researchers because of its relatively easy implementation with any structural equation modeling (SEM) software. Using a Monte Carlo simulation study, we extended and evaluated the unconstrained approach to…

  2. Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin; Yakima/Klickitat Fisheries Project Monitoring and Evaluation Report 5 of 7, 2003-2004 Annual Report.

    SciTech Connect

    Pearsons, Todd N.; Johnson, Christopher L.; James, Brenda B.

    2004-05-01

    This report examines some of the factors that can influence the success of supplementation, which is currently being tested in the Yakima Basin using upper Yakima stock of spring chinook salmon. Supplementation success in the Yakima Basin is defined relative to four topic areas: natural production, genetics, ecological interactions, and harvest (Busack et al. 1997). The success of spring chinook salmon supplementation in the Yakima Basin is dependent, in part, upon fish culture practices and favorable physical and biological conditions in the natural environment (Busack et al. 1997; James et al. 1999; Pearsons et al., 2003). Shortfalls in either of these two topics (i.e., failure in culturing many fish that have high long-term fitness or environmental conditions that constrain spring chinook salmon production) will cause supplementation success to be limited. For example, inadvertent selection or propagation of spring chinook that residualize or precocially mature may hinder supplementation success. Spring chinook salmon that residualize (do not migrate during the normal migration period) may have lower survival rates than migrants and, additionally, may interact with wild fish and cause unacceptable impacts to non-target taxa. Large numbers of precocials (nonanadromous spawners) may increase competition for females and significantly skew ratios of offspring sired by nonanadromous males, which could result in more nonanadromous spring chinook in future generations. Conditions in the natural environment may also limit the success of spring chinook supplementation. For example, intra or interspecific competition may constrain spring chinook salmon production. Spring chinook salmon juveniles may compete with each other for food or space or compete with other species that have similar ecological requirements. Monitoring of spring chinook salmon residuals, precocials, prey abundance, carrying capacity, and competition will help researchers interpret why supplementation

  3. Preferential interaction of the his pause RNA hairpin with RNA polymerase β subunit residues 904–950 correlates with strong transcriptional pausing

    PubMed Central

    Wang, Daguang; Severinov, Konstantin; Landick, Robert

    1997-01-01

    RNA secondary structures (hairpins) that form as the nascent RNA emerges from RNA polymerase are important components of many signals that regulate transcription, including some pause sites, all ρ-independent terminators, and some antiterminators. At the his leader pause site, a 5-bp-stem, 8-nt-loop pause RNA hairpin forms 11 nt from the RNA 3′ end and stabilizes a transcription complex conformation slow to react with NTP substrate. This stabilization appears to depend at least in part on an interaction with RNA polymerase. We tested for RNA hairpin interaction with the paused polymerase by crosslinking 5-iodoUMP positioned specifically in the hairpin loop. In the paused conformation, strong and unusual crosslinking of the pause hairpin to β904–950 replaced crosslinking to β′ and to other parts of β that occurred in nonpaused complexes prior to hairpin formation. These changes in nascent RNA interactions may inhibit reactive alignment of the RNA 3′ end in the paused complex and be related to events at ρ-independent terminators. PMID:9237994

  4. Residue management: Back to the roots

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Addressing the issues of climate change and sustainable biomass feedstocks have soil as a common theme. Managing crop residues is directly related to soil management. Understanding how soil and crop residue management interact provides insight on how to assure agricultural soil can serve as a carbon...

  5. Deciphering Mode of Action of Functionally Important Regions in the Intrinsically Disordered Paxillin (Residues 1-313) Using Its Interaction with FAT (Focal Adhesion Targeting Domain of Focal Adhesion Kinase)

    PubMed Central

    Neerathilingam, Muniasamy; Bairy, Sneha G.; Mysore, Sumukh

    2016-01-01

    Intrinsically disordered proteins (IDPs) play a major role in various cellular functions ranging from transcription to cell migration. Mutations/modifications in such IDPs are shown to be associated with various diseases. Current strategies to study the mode of action and regulatory mechanisms of disordered proteins at the structural level are time consuming and challenging. Therefore, using simple and swift strategies for identifying functionally important regions in unstructured segments and understanding their underlying mechanisms is critical for many applications. Here we propose a simple strategy that employs dissection of human paxillin (residues 1–313) that comprises intrinsically disordered regions, followed by its interaction study using FAT (Focal adhesion targeting domain of focal adhesion kinase) as its binding partner to retrace structural behavior. Our findings show that the paxillin interaction with FAT exhibits a masking and unmasking effect by a putative intra-molecular regulatory region. This phenomenon suggests how cancer associated mutations in paxillin affect its interactions with Focal Adhesion Kinase (FAK). The strategy could be used to decipher the mode of regulations and identify functionally relevant constructs for other studies. PMID:26928467

  6. Solvable light-front model of the electromagnetic form factor of the relativistic two-body bound state in 1+1 dimensions

    SciTech Connect

    Mankiewicz, L. ); Sawicki, M. )

    1989-11-15

    Within a relativistically correct yet analytically solvable model of light-front quantum mechanics we construct the electromagnetic form factor of the two-body bound state and we study the validity of the static approximation to the full form factor. Upon comparison of full form factors calculated for different values of binding energy we observe an unexpected effect that for very strongly bound states further increase in binding leads to an increase in the size of the bound system. A similar effect is found for another quantum-mechanical model of relativistic dynamics.

  7. Two-body recombination in a quantum-mechanical lattice gas: Entropy generation and probing of short-range magnetic correlations

    SciTech Connect

    Baur, Stefan K.; Mueller, Erich J.

    2010-08-15

    We study entropy generation in a one-dimensional (1D) model of bosons in an optical lattice experiencing two-particle losses. Such heating is a major impediment to observing exotic low temperature states, and 'simulating' condensed matter systems. Developing intuition through numerical simulations, we present a simple empirical model for the entropy produced in this 1D setting. We also explore the time evolution of one- and two-particle correlation functions, showing that they are robust against two-particle loss. Because of this robustness, induced two-body losses can be used as a probe of short-range magnetic correlations.

  8. Two-body recombination in a quantum-mechanical lattice gas: Entropy generation and probing of short-range magnetic correlations

    NASA Astrophysics Data System (ADS)

    Baur, Stefan K.; Mueller, Erich J.

    2010-08-01

    We study entropy generation in a one-dimensional (1D) model of bosons in an optical lattice experiencing two-particle losses. Such heating is a major impediment to observing exotic low temperature states, and “simulating” condensed matter systems. Developing intuition through numerical simulations, we present a simple empirical model for the entropy produced in this 1D setting. We also explore the time evolution of one- and two-particle correlation functions, showing that they are robust against two-particle loss. Because of this robustness, induced two-body losses can be used as a probe of short-range magnetic correlations.

  9. PIC: Protein Interactions Calculator.

    PubMed

    Tina, K G; Bhadra, R; Srinivasan, N

    2007-07-01

    Interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. There are several weak and strong interactions that render stability to a protein structure or an assembly. Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulphur interactions and cation-pi interactions within a protein or between proteins in a complex. Interactions are calculated on the basis of standard, published criteria. The identified interactions between residues can be visualized using a RasMol and Jmol interface. The advantage with PIC server is the easy availability of inter-residue interaction calculations in a single site. It also determines the accessible surface area and residue-depth, which is the distance of a residue from the surface of the protein. User can also recognize specific kind of interactions, such as apolar-apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside. PMID:17584791

  10. Theoretical analysis of the astrophysical S-factor for the capture reaction α + d → {sup 6}Li + γ in the two-body model

    SciTech Connect

    Tursunov, E. M. Turakulov, S. A.; Descouvemont, P.

    2015-03-15

    Theoretical estimates for the astrophysical S-factor and the rate of the reaction d(α, γ){sup 6}Li were obtained on the basis of the two-body model involving an α−d potential that has a simple Gaussian form and which describes correctly S-, P-, and D-wave phase shifts, the binding energy, and the asymptotic normalization coefficient for the S-wave bound state. The wave functions for the bound and continuum channels were calculated with the aid of the highly precise Numerov algorithm. The results for the contributions of the E1 and E2 transition components reveal a good convergence as the upper limit in the effective integrals increases up to 40 fm. The results obtained for the astrophysical S-factor and the rate of the reaction d(α, γ){sup 6}Li in the temperature range of 10{sup 6}K ≤ T ≤ 10{sup 10} K agree well with the results of the calculations performed by A.M. Mukhamedzhanov and his coauthors [Phys. Rev. C 83, 055805 (2011)] by using the known asymptotic form of the wave function at low energies and a complicated two-body potential at higher energies.

  11. Machine-learning approach for one- and two-body corrections to density functional theory: Applications to molecular and condensed water

    NASA Astrophysics Data System (ADS)

    Bartók, Albert P.; Gillan, Michael J.; Manby, Frederick R.; Csányi, Gábor

    2013-08-01

    We show how machine learning techniques based on Bayesian inference can be used to enhance the computer simulation of molecular materials, focusing here on water. We train our machine-learning algorithm using accurate, correlated quantum chemistry, and predict energies and forces in molecular aggregates ranging from clusters to solid and liquid phases. The widely used electronic-structure methods based on density functional theory (DFT) by themselves give poor accuracy for molecular materials like water, and we show how our techniques can be used to generate systematically improvable one- and two-body corrections to DFT with modest extra resources. The resulting corrected DFT scheme is considerably more accurate than uncorrected DFT for the relative energies of small water clusters and different ice structures and significantly improves the description of the structure and dynamics of liquid water. However, our results for ice structures and the liquid indicate that beyond-two-body DFT errors cannot be ignored, and we suggest how our machine-learning methods can be further developed to correct these errors.

  12. Exploring Beta-Amyloid Protein Transmembrane Insertion Behavior and Residue-Specific Lipid Interactions in Lipid Bilayers Using Multiscale MD Simulations

    NASA Astrophysics Data System (ADS)

    Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

    2013-03-01

    Beta-amyloid (Abeta) interactions with neurons are linked to Alzheimer's. Using a multiscale MD simulation strategy that combines the high efficiency of phase space sampling of coarse-grained MD (CGD) and the high spatial resolution of Atomistic MD (AMD) simulations, we studied the Abeta insertion dynamics in cholesterol-enriched and -depleted lipid bilayers that mimic the neuronal membranes domains. Forward (AMD-CGD) and reverse (CGD-AMD) mappings were used. At the atomistic level, cholesterol promoted insertion of Abeta with high (folded) or low (unfolded) helical contents of the lipid insertion domain (Lys28-Ala42), and the insertions were stabilized by the Lys28 snorkeling and Ala42-anchoring to the polar lipid groups of the bilayer up to 200ns. After the forward mapping, the folded inserted state switched to a new extended inserted state with the Lys28 descended to the middle of the bilayer while the unfolded inserted state migrated to the membrane surface up to 4000ns. The two new states remained stable for 200ns at the atomistic scale after the reverse mapping. Our results suggested that different Abeta membrane-orientation states separated by free energy barriers can be explored by the multiscale MD more effectively than by Atomistic MD simulations alone. NIH RC1-GM090897-02

  13. Predicting stabilizing mutations in proteins using Poisson-Boltzmann based models: study of unfolded state ensemble models and development of a successful binary classifier based on residue interaction energies.

    PubMed

    Estrada, Jorge; Echenique, Pablo; Sancho, Javier

    2015-12-14

    In many cases the stability of a protein has to be increased to permit its biotechnological use. Rational methods of protein stabilization based on optimizing electrostatic interactions have provided some fine successful predictions. However, the precise calculation of stabilization energies remains challenging, one reason being that the electrostatic effects on the unfolded state are often neglected. We have explored here the feasibility of incorporating Poisson-Boltzmann model electrostatic calculations performed on representations of the unfolded state as large ensembles of geometrically optimized conformations calculated using the ProtSA server. Using a data set of 80 electrostatic mutations experimentally tested in two-state proteins, the predictive performance of several such models has been compared to that of a simple one that considers an unfolded structure of non-interacting residues. The unfolded ensemble models, while showing correlation between the predicted stabilization values and the experimental ones, are worse than the simple model, suggesting that the ensembles do not capture well the energetics of the unfolded state. A more attainable goal is classifying potential mutations as either stabilizing or non-stabilizing, rather than accurately calculating their stabilization energies. To implement a fast classification method that can assist in selecting stabilizing mutations, we have used a much simpler electrostatic model based only on the native structure and have determined its precision using different stabilizing energy thresholds. The binary classifier developed finds 7 true stabilizing mutants out of every 10 proposed candidates and can be used as a robust tool to propose stabilizing mutations. PMID:26530878

  14. Optimized Bose-Einstein-condensate production in a dipole trap based on a 1070-nm multifrequency laser: Influence of enhanced two-body loss on the evaporation process

    SciTech Connect

    Lauber, T.; Kueber, J.; Wille, O.; Birkl, G.

    2011-10-15

    We present an optimized strategy for the production of tightly confined Bose-Einstein condensates (BEC) of {sup 87}Rb in a crossed dipole trap with direct loading from a magneto-optical trap. The dipole trap is created with light of a multifrequency fiber laser with a center wavelength of 1070 nm. Evaporative cooling is performed by ramping down the laser power only. A comparison of the resulting atom number in an almost pure BEC to the initial atom number and the value for the gain in phase space density per atom lost confirm that this straightforward strategy is very efficient. We observe that the temporal characteristics of evaporation sequence are strongly influenced by power-dependent two-body losses resulting from enhanced optical pumping to the higher-energy hyperfine state. We characterize these losses and compare them to results obtained with a single-frequency laser at 1030 nm.

  15. Optimized Bose-Einstein-condensate production in a dipole trap based on a 1070-nm multifrequency laser: Influence of enhanced two-body loss on the evaporation process

    NASA Astrophysics Data System (ADS)

    Lauber, T.; Küber, J.; Wille, O.; Birkl, G.

    2011-10-01

    We present an optimized strategy for the production of tightly confined Bose-Einstein condensates (BEC) of 87Rb in a crossed dipole trap with direct loading from a magneto-optical trap. The dipole trap is created with light of a multifrequency fiber laser with a center wavelength of 1070 nm. Evaporative cooling is performed by ramping down the laser power only. A comparison of the resulting atom number in an almost pure BEC to the initial atom number and the value for the gain in phase space density per atom lost confirm that this straightforward strategy is very efficient. We observe that the temporal characteristics of evaporation sequence are strongly influenced by power-dependent two-body losses resulting from enhanced optical pumping to the higher-energy hyperfine state. We characterize these losses and compare them to results obtained with a single-frequency laser at 1030 nm.

  16. Nonleptonic two-body decays of the B{sub c} meson in the light-front quark model and the QCD factorization approach

    SciTech Connect

    Choi, Ho-Meoyng; Ji, Chueng-Ryong

    2009-12-01

    We study exclusive nonleptonic two-body B{sub c}{yields}(D{sub (s)},{eta}{sub c},B{sub (s)})+F decays with F (pseudoscalar or vector mesons) factored out in the QCD factorization approach. The nonleptonic decay amplitudes are related to the product of meson decay constants and the form factors for semileptonic B{sub c} decays. As inputs in obtaining the branching ratios for a large set of nonleptonic B{sub c} decays, we use the weak form factors for the semileptonic B{sub c}{yields}(D{sub (s)},{eta}{sub c},B{sub (s)}) decays in the whole kinematical region and the unmeasured meson decay constants obtained from our previous light-front quark model. We compare our results for the branching ratios with those of other theoretical studies.

  17. Further characterization of the interaction of histidine-rich glycoprotein with heparin: evidence for the binding of two molecules of histidine-rich glycoprotein by high molecular weight heparin and for the involvement of histidine residues in heparin binding

    SciTech Connect

    Burch, M.K.; Blackburn, M.N.; Morgan, W.T.

    1987-11-17

    Rabbit histidine-rich glycoprotein (HRG, 94 kDa) binds heparin with high affinity (apparent K/sub d/ 60-110 nM). Eosin Y (1 equiv) bound to HRG was used as a reporter group to monitor associations of HRG with heparins of molecular mass 10, 17.5, and 30 kDa. The stoichiometries of the heparin- (/sup 125/I) HRG complexes were determined by fluorescence and absorbance measurements as well as by analytical ultracentrifugation. Two types of complex form: complexes of 1 heparin: 1 HRG and of 1 heparin:2 HRG. The 1:2 complex formation requires a minimum heparin chain length since 17.5-kDa but not 10-kDa heparin binds two HRG molecules. The formation of the 1:2 complexes of the larger heparin fractions is enhanced by divalent copper or zinc (1-10 equiv) bound to HRG. However, metal is not required for complex formation since all sizes of heparin examined interact tightly with HRG in the presence of ethylenediaminetetraacetic acid. Between 0.1 and 0.3 M ionic strength, both 1:1 and 1:2 complexes of heparin with HRG are progressively destabilized. No heparin-HRG complex is found at ionic strengths of 0.5 M. Between pH 8.5 and pH 6.5 both 1:2 and 1:1 complexes are found with 17.5-kDa heparin, but at pH 5.5 only 1:1 complexes are formed. The heparin-HRG interaction is progressively decreased by modification of the histidine residues of HRG, whereas modification of 22 of the 33 lysine residues of HRG has little effect. Supporting the role of histidine in heparin binding, a histidine-proline-glycine-rich peptide (molecular mass 28 kDa) derived from HRG and intact HRG binds to heparin-Sepharose at pH 6.8, but only HRG binds to the affinity medium at pH 7.4.

  18. SFOLD — A program package for calculating two-body sfermion decays at full one-loop level in the MSSM

    NASA Astrophysics Data System (ADS)

    Hluchá, H.; Eberl, H.; Frisch, W.

    2012-10-01

    SFOLD (Sfermion Full One-Loop Decays) is a Fortran program package for calculating all sfermion two-body decay widths and the corresponding branching ratios at full one-loop level within the MSSM. The package adopts the SUSY Parameter Analysis convention and supports the SUSY Les Houches Accord input and output format. With the SFOLD package we found non-negligible electroweak corrections in bosonic decays of b˜,t˜ and τ˜. Program summaryProgram title: SFOLD Catalogue identifier: AEMZ_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 263346 No. of bytes in distributed program, including test data, etc.: 1481697 Distribution format: tar.gz Programming language: Fortran 77. Computer: Workstation, PC. Operating system: Linux. RAM: approx. 500 Mbytes Classification: 11.1. External routines: LoopTools 2.6 (http://www.feynarts.de/looptools/), SLHALib 2.2 (http://www.feynarts.de/slha/) Nature of problem: If the MSSM is realized in nature, LHC will produce supersymmetric particles copiously. The best environment for a precise determination of the model parameters would be a high energy e+e- linear collider. Experimental accuracies are expected at the per-cent down to the per-mill level. These must be matched from the theoretical side. Therefore loop calculations are mandatory. Solution method: This program package calculates all sfermion two-body decay widths and the corresponding branching ratios at full one-loop level within the MSSM. The renormalization is done in the DR¯ scheme following the SUSY Parameter Analysis convention. The program supports the SUSY Les Houches Accord input and output format. Running time: The test provided just takes a few seconds to run.

  19. Evaluation of energies of interaction correlated with observed stabilities and rheological properties of asphalt-aggregate mixtures of western shale-oil residue as a modifier to petroleum asphalt

    SciTech Connect

    Tauer, J.E.; Ensley, E.K.; Harnsberger, P.M.; Robertson, R.E.

    1993-02-01

    The objective of this study was to perform a preliminary evaluation of improving bonding and aging characteristics using a distillation residue from the Green River Formation (western) shale oil as a modifier to a petroleum asphalt for use as a crack and joint filler material in portland cement concrete and asphaltic pavements. This study was to examine the differences in moisture damage resistance and adhesion properties, as measured by bonding energy, of shale-oil modified asphalts compared with non-modified asphalts. The shale-oil modified asphalts mechanical properties were not expected to match those of the rubberized asphalt. A commercially available rubberized asphalt crack and joint filler material was also tested only for comparison of mechanical properties. Portland cement concrete briquets prepared with an asphalt material sandwiched between two concrete wafers were tested in a stress-relaxation type of experiment to evaluate the relaxation and recovery properties of the sealant materials. Energy of interaction (bonding energy) measurements were performed on asphalt materials with portland cement concrete, two silicate aggregates, and a limestone aggregate to evaluate the compatibility of the asphalt materials with various aggregates. The results show that the shale-oil modified petroleum asphalt improved the relaxation time, percent recovery, and bonding energy compared with the petroleum asphalt.

  20. Exact two-body quantum dynamics of an electron-hole pair in semiconductor coupled quantum wells: A time-dependent approach

    NASA Astrophysics Data System (ADS)

    Grasselli, Federico; Bertoni, Andrea; Goldoni, Guido

    2016-05-01

    We simulate the time-dependent coherent dynamics of a spatially indirect exciton—an electron-hole pair with the two particles confined in different layers—in a GaAs coupled quantum well system. We use a unitary wave-packet propagation method taking into account in full the four degrees of freedom of the two particles in a two-dimensional system, including both the long-range Coulomb attraction and arbitrary two-dimensional electrostatic potentials affecting the electron and/or the hole separately. The method has been implemented for massively parallel architectures to cope with the huge numerical problem, showing good scaling properties and allowing evolution for tens of picoseconds. We have investigated both transient time phenomena and asymptotic time transmission and reflection coefficients for potential profiles consisting of (i) extended barriers and wells and (ii) a single-slit geometry. We found clear signatures of the internal two-body dynamics, with transient phenomena in the picosecond time scale which might be revealed by optical spectroscopy. Exact results have been compared with mean-field approaches which, neglecting dynamical correlations by construction, turn out to be inadequate to describe the electron-hole pair evolution in realistic experimental conditions.

  1. Measurement of branching fractions and search for CP-violating charge asymmetries in charmless two-body B decays into pions and kaons.

    PubMed

    Aubert, B; Boutigny, D; Gaillard, J M; Hicheur, A; Karyotakis, Y; Lees, J P; Robbe, P; Tisserand, V; Palano, A; Chen, G P; Chen, J C; Qi, N D; Rong, G; Wang, P; Zhu, Y S; Eigen, G; Reinertsen, P L; Stugu, B; Abbott, B; Abrams, G S; Borgland, A W; Breon, A B; Brown, D N; Button-Shafer, J; Cahn, R N; Clark, A R; Fan, Q; Gill, M S; Gowdy, S J; Gritsan, A; Groysman, Y; Jacobsen, R G; Kadel, R W; Kadyk, J; Kerth, L T; Kluth, S; Kolomensky, Y G; Kral, J F; LeClerc, C; Levi, M E; Liu, T; Lynch, G; Meyer, A B; Momayezi, M; Oddone, P J; Perazzo, A; Pripstein, M; Roe, N A; Romosan, A; Ronan, M T; Shelkov, V G; Telnov, A V; Wenzel, W A; Bright-Thomas, P G; Harrison, T J; Hawkes, C M; Kirk, A; Knowles, D J; O'Neale, S W; Penny, R C; Watson, A T; Watson, N K; Deppermann, T; Koch, H; Krug, J; Kunze, M; Lewandowski, B; Peters, K; Schmuecker, H; Steinke, M; Andress, J C; Barlow, N R; Bhimji, W; Chevalier, N; Clark, P J; Cottingham, W N; De Groot, N; Dyce, N; Foster, B; Mass, A; McFall, J D; Wallom, D; Wilson, F F; Abe, K; Hearty, C; Mattison, T S; McKenna, J A; Thiessen, D; Camanzi, B; Jolly, S; McKemey, A K; Tinslay, J; Blinov, V E; Bukin, A D; Bukin, D A; Buzykaev, A R; Dubrovin, M S; Golubev, V B; Ivanchenko, V N; Korol, A A; Kravchenko, E A; Onuchin, A P; Salnikov, A A; Serednyakov, S I; Skovpen, Y I; Telnov, V I; Yushkov, A N; Lankford, A J; Mandelkern, M; McMahon, S; Stoker, D P; Ahsan, A; Arisaka, K; Buchanan, C; Chun, S; Branson, J G; MacFarlane, D B; Prell, S; Rahatlou, S; Raven, G; Sharma, V; Campagnari, C; Dahmes, B; Hart, P A; Kuznetsova, N; Levy, S L; Long, O; Lu, A; Richman, J D; Verkerke, W; Witherell, M; Yellin, S; Beringer, J; Dorfan, D E; Eisner, A M; Frey, A; Grillo, A A; Grothe, M; Heusch, C A; Johnson, R P; Kroeger, W; Lockman, W S; Pulliam, T; Sadrozinski, H; Schalk, T; Schmitz, R E; Schumm, B A; Seiden, A; Turri, M; Walkowiak, W; Williams, D C; Wilson, M G; Chen, E; Dubois-Felsmann, G P; Dvoretskii, A; Hitlin, D G; Metzler, S; Oyang, J; Porter, F C; Ryd, A; Samuel, A; Weaver, M; Yang, S; Zhu, R Y; Devmal, S; Geld, T L; Jayatilleke, S; Mancinelli, G; Meadows, B T; Sokoloff, M D; Bloom, P; Fahey, S; Ford, W T; Gaede, F; Johnson, D R; Michael, A K; Nauenberg, U; Olivas, A; Park, H; Rankin, P; Roy, J; Sen, S; Smith, J G; van Hoek, W C; Wagner, D L; Blouw, J; Harton, J L; Krishnamurthy, M; Soffer, A; Toki, W H; Wilson, R J; Zhang, J; Brandt, T; Brose, J; Colberg, T; Dahlinger, G; Dickopp, M; Dubitzky, R S; Maly, E; Müller-Pfefferkorn, R; Otto, S; Schubert, K R; Schwierz, R; Spaan, B; Wilden, L; Behr, L; Bernard, D; Bonneaud, G R; Brochard, F; Cohen-Tanugi, J; Ferrag, S; Roussot, E; T'Jampens, S; Thiebaux, C; Vasileiadis, G; Verderi, M; Anjomshoaa, A; Bernet, R; Khan, A; Muheim, F; Playfer, S; Swain, J E; Falbo, M; Bozzi, C; Dittongo, S; Folegani, M; Piemontese, L; Treadwell, E; Anulli, F; Baldini-Ferroli, R; Calcaterra, A; de Sangro, R; Falciai, D; Finocchiaro, G; Patteri, P; Peruzzi, I M; Piccolo, M; Xie, Y; Zallo, A; Bagnasco, S; Buzzo, A; Contri, R; Crosetti, G; Fabbricatore, P; Farinon, S; Lo Vetere, M; Macri, M; Monge, M R; Musenich, R; Pallavicini, M; Parodi, R; Passaggio, S; Pastore, F C; Patrignani, C; Pia, M G; Priano, C; Robutti, E; Santroni, A; Morii, M; Bartoldus, R; Dignan, T; Hamilton, R; Mallik, U; Cochran, J; Crawley, H B; Fischer, P A; Lamsa, J; Meyer, W T; Rosenberg, E I; Benkebil, M; Grosdidier, G; Hast, C; Höcker, A; Lacker, H M; LePeltier, V; Lutz, A M; Plaszczynski, S; Schune, M H; Trincaz-Duvoid, S; Valassi, A; Wormser, G; Bionta, R M; Brigljevic, V; Fackler, O; Fujino, D; Lange, D J; Mugge, M; Shi, X; van Bibber, K; Wenaus, T J; Wright, D M; Wuest, C R; Carroll, M; Fry, J R; Gabathuler, E; Gamet, R; George, M; Kay, M; Payne, D J; Sloane, R J; Touramanis, C; Aspinwall, M L; Bowerman, D A; Dauncey, P D; Egede, U; Eschrich, I; Gunawardane, N J; Martin, R; Nash, J A; Sanders, P; Smith, D; Azzopardi, D E; Back, J J; Dixon, P; Harrison, P F; Potter, R J; Shorthouse, H W; Strother, P; Vidal, P B; Williams, M I; Cowan, G; George, S; Green, M G; Kurup, A; Marker, C E; McGrath, P; McMahon, T R; Ricciardi, S; Salvatore, F; Scott, I; Vaitsas, G; Brown, D; Davis, C L; Allison, J; Barlow, R J; Boyd, J T; Forti, A; Fullwood, J; Jackson, F; Lafferty, G D; Savvas, N; Simopoulos, E T; Weatherall, J H; Farbin, A; Jawahery, A; Lillard, V; Olsen, J; Roberts, D A; Schieck, J R; Blaylock, G; Dallapiccola, C; Flood, K T; Hertzbach, S S; Kofler, R; Lin, C S; Moore, T B; Staengle, H; Willocq, S; Wittlin, J; Brau, B; Cowan, R; Sciolla, G; Taylor, F; Yamamoto, R K; Britton, D I; Milek, M; Patel, P M; Trischuk, J; Lanni, F; Palombo, F; Bauer, J M; Booke, M; Cremaldi, L; Eschenburg, V; Kroeger, R; Reidy, J; Sanders, D A; Summers, D J; Martin, J P; Nief, J Y; Seitz, R; Taras, P; Zacek, V; Nicholson, H; Sutton, C S; Cartaro, C; Cavallo, N; De Nardo, G; Fabozzi, F; Gatto, C; Lista, L; Paolucci, P; Piccolo, D; Sciacca, C; LoSecco, J M; Alsmiller, J R; Gabriel, T A; Handler, T; Brau, J; Frey, R; Iwasaki, M; Sinev, N B; Strom, D; Colecchia, F; Dal Corso, F; Dorigo, A; Galeazzi, F; Margoni, M; Michelon, G; Morandin, M; Posocco, M; Rotondo, M; Simonetto, F; Stroili, R; Torassa, E; Voci, C; Benayoun, M; Briand, H; Chauveau, J; David, P; De La Vaissière, C; Del Buono, L; Hamon, O; Le Diberder, F; Leruste, P; Lory, J; Roos, L; Stark, J; Versillé, S; Manfredi, P F; Re, V; Speziali, V; Frank, E D; Gladney, L; Guo, Q H; Panetta, J H; Angelini, C; Batignani, G; Bettarini, S; Bondioli, M; Carpinelli, M; Forti, F; Giorgi, M A; Lusiani, A; Martinez-Vidal, F; Morganti, M; Neri, N; Paoloni, E; Rama, M; Rizzo, G; Sandrelli, F; Simi, G; Triggiani, G; Walsh, J; Haire, M; Judd, D; Paick, K; Turnbull, L; Wagoner, D E; Albert, J; Bula, C; Lu, C; McDonald, K T; Miftakov, V; Schaffner, S F; Smith, A J; Tumanov, A; Varnes, E W; Cavoto, G; del Re, D; Faccini, R; Ferrarotto, F; Ferroni, F; Fratini, K; Lamanna, E; Leonardi, E; Mazzoni, M A; Morganti, S; Pierini, M; Piredda, G; Safai Tehrani, F; Serra, M; Voena, C; Christ, S; Waldi, R; Adye, T; Franek, B; Geddes, N I; Gopal, G P; Xella, S M; Aleksan, R; De Domenico, G; Emery, S; Gaidot, A; Ganzhur, S F; Giraud, P F; Hamel De Monchenault, G; Kozanecki, W; Langer, M; London, G W; Mayer, B; Serfass, B; Vasseur, G; Yeche, C; Zito, M; Copty, N; Purohit, M V; Singh, H; Yumiceva, F X; Adam, I; Anthony, P L; Aston, D; Baird, K; Bartelt, J; Bloom, E; Boyarski, A M; Bulos, F; Calderini, G; Claus, R; Convery, M R; Coupal, D P; Coward, D H; Dorfan, J; Doser, M; Dunwoodie, W; Field, R C; Glanzman, T; Godfrey, G L; Grosso, P; Himel, T; Huffer, M E; Innes, W R; Jessop, C P; Kelsey, M H; Kim, P; Kocian, M L; Langenegger, U; Leith, D W; Luitz, S; Luth, V; Lynch, H L; Manzin, G; Marsiske, H; Menke, S; Messner, R; Moffeit, K C; Mount, R; Muller, D R; O'Grady, C P; Petrak, S; Quinn, H; Ratcliff, B N; Robertson, S H; Rochester, L S; Roodman, A; Schietinger, T; Schindler, R H; Schwiening, J; Serbo, V V; Snyder, A; Soha, A; Spanier, S M; Stahl, A; Stelzer, J; Su, D; Sullivan, M K; Talby, M; Tanaka, H A; Trunov, A; Va'vra, J; Wagner, S R; Weinstein, A J; Wisniewski, W J; Young, C C; Burchat, P R; Cheng, C H; Kirkby, D; Meyer, T I; Roat, C; De Silva, A; Henderson, R; Bugg, W; Cohn, H; Hart, E; Weidemann, A W; Benninger, T; Izen, J M; Kitayama, I; Lou, X C; Turcotte, M; Bianchi, F; Bona, M; Di Girolamo, B; Gamba, D; Smol, A; Zanin, D; Bosisio, L; Della Ricca, G; Lanceri, L; Pompili, A; Poropat, P; Prest, M; Vallazza, E; Vuagnin, G; Panvini, R S; Brown, C M; Kowalewski, R; Roney, J M; Band, H R; Charles, E; Dasu, S; Elmer, P; Hu, H; Johnson, J R; Liu, R; Nielsen, J; Orejudos, W; Pan, Y; Prepost, R; Scott, I J; Sekula, S J; von Wimmersperg-Toeller, J H; Wu, S L; Yu, Z; Zobering, H; Kordich, T M; Neal, H

    2001-10-01

    We present measurements, based on a sample of approximately 23x10(6) BB pairs, of the branching fractions and a search for CP-violating charge asymmetries in charmless hadronic decays of B mesons into two-body final states of kaons and pions. We find the branching fractions B(B0-->pi(+)pi(-)) = (4.1+/-1.0+/-0.7)x10(-6), B(B0-->K+pi(-)) = (16.7+/-1.6+/-1.3)x10(-6), B(B+-->K+pi(0)) = (10.8(+2.1)(-1.9)+/-1.0)x10(-6), B(B+-->K0pi(+)) = (18.2(+3.3)(-3.0)+/-2.0)x10(-6), B(B0-->K0pi(0)) = (8.2(+3.1)(-2.7)+/-1.2)x10(-6). We also report 90% confidence level upper limits for B meson decays to the pi(+)pi(0), K+K-, and K0K+ final states. In addition, charge asymmetries have been found to be consistent with zero, where the statistical precision is in the range of +/-0.10 to +/-0.18, depending on the decay mode. PMID:11580691

  2. Co-simulation for performance prediction of integrated building and HVAC systems - An analysis of solution characteristics using a two-body system

    SciTech Connect

    Trcka, Marija; L.M. Hensena, Jan; Wetter, Michael

    2010-06-21

    Integrated performance simulation of buildings and heating, ventilation and airconditioning (HVAC) systems can help reducing energy consumption and increasing occupant comfort. However, no single building performance simulation (BPS) tool offers suffcient capabilities and flexibilities to analyze integrated building systems and to enable rapid prototyping of innovative building and system technologies. One way to alleviate this problem is to use co-simulation to integrate different BPS tools. Co-simulation approach represents a particular case of simulation scenario where at least two simulators solve coupled differential-algebraic systems of equations and exchange data that couples these equations during the time integration. This article analyzes how co-simulation influences consistency, stability and accuracy of the numerical approximation to the solution. Consistency and zero-stability are studied for a general class of the problem, while a detailed consistency and absolute stability analysis is given for a simple two-body problem. Since the accuracy of the numerical approximation to the solution is reduced in co-simulation, the article concludes by discussing ways for how to improve accuracy.

  3. Predictive CP violating relations for charmless two-body decays of beauty baryons Ξb-,0 and Λb0 with flavor SU (3) symmetry

    NASA Astrophysics Data System (ADS)

    He, Xiao-Gang; Li, Guan-Nan

    2015-11-01

    Several baryons containing a heavy b-quark have been discovered. The decays of these states provide new platform for testing the standard model (SM). We study CP violation in SM for charmless two-body decays of the flavor SU (3) anti-triplet beauty baryon (b-baryon) B = (Ξb-, Ξb0, Λb0) in a model independent way. We found, in the flavor SU (3) symmetry limit, a set of new predictive relations among the branching ratio Br and CP asymmetry ACP for B decays, such as ACP (Ξb- →K0Ξ-) /ACP (Ξb- →Kbar0Σ-) = - Br (Ξb- →Kbar0Σ-) / Br (Ξb- →K0Σ-), ACP (Λb0 →π- p) /ACP (Ξb0 →K-Σ+) = - Br (Ξb0 →K-Σ+)τ Λb0 / Br (Λb0 →π- p)τ Ξb0, and ACP (Λb0 →K- p) /ACP (Ξb0 →π-Σ+) = - Br (Ξb0 →π-Σ+)τ Λb0 / Br (Λb0 →K- p)τ Ξb0. Future data from LHCb can test these relations and also other relations found.

  4. Measurement of Branching Fractions and Search for CP-Violating Charge Asymmetries in Charmless Two-Body B Decays into Pions and Kaons

    NASA Astrophysics Data System (ADS)

    Aubert, B.; Boutigny, D.; Gaillard, J.-M.; Hicheur, A.; Karyotakis, Y.; Lees, J. P.; Robbe, P.; Tisserand, V.; Palano, A.; Chen, G. P.; Chen, J. C.; Qi, N. D.; Rong, G.; Wang, P.; Zhu, Y. S.; Eigen, G.; Reinertsen, P. L.; Stugu, B.; Abbott, B.; Abrams, G. S.; Borgland, A. W.; Breon, A. B.; Brown, D. N.; Button-Shafer, J.; Cahn, R. N.; Clark, A. R.; Fan, Q.; Gill, M. S.; Gowdy, S. J.; Gritsan, A.; Groysman, Y.; Jacobsen, R. G.; Kadel, R. W.; Kadyk, J.; Kerth, L. T.; Kluth, S.; Kolomensky, Yu. G.; Kral, J. F.; Leclerc, C.; Levi, M. E.; Liu, T.; Lynch, G.; Meyer, A. B.; Momayezi, M.; Oddone, P. J.; Perazzo, A.; Pripstein, M.; Roe, N. A.; Romosan, A.; Ronan, M. T.; Shelkov, V. G.; Telnov, A. V.; Wenzel, W. A.; Bright-Thomas, P. G.; Harrison, T. J.; Hawkes, C. M.; Kirk, A.; Knowles, D. J.; O'Neale, S. W.; Penny, R. C.; Watson, A. T.; Watson, N. K.; Deppermann, T.; Koch, H.; Krug, J.; Kunze, M.; Lewandowski, B.; Peters, K.; Schmuecker, H.; Steinke, M.; Andress, J. C.; Barlow, N. R.; Bhimji, W.; Chevalier, N.; Clark, P. J.; Cottingham, W. N.; de Groot, N.; Dyce, N.; Foster, B.; Mass, A.; McFall, J. D.; Wallom, D.; Wilson, F. F.; Abe, K.; Hearty, C.; Mattison, T. S.; McKenna, J. A.; Thiessen, D.; Camanzi, B.; Jolly, S.; McKemey, A. K.; Tinslay, J.; Blinov, V. E.; Bukin, A. D.; Bukin, D. A.; Buzykaev, A. R.; Dubrovin, M. S.; Golubev, V. B.; Ivanchenko, V. N.; Korol, A. A.; Kravchenko, E. A.; Onuchin, A. P.; Salnikov, A. A.; Serednyakov, S. I.; Skovpen, Yu. I.; Telnov, V. I.; Yushkov, A. N.; Lankford, A. J.; Mandelkern, M.; McMahon, S.; Stoker, D. P.; Ahsan, A.; Arisaka, K.; Buchanan, C.; Chun, S.; Branson, J. G.; Macfarlane, D. B.; Prell, S.; Rahatlou, Sh.; Raven, G.; Sharma, V.; Campagnari, C.; Dahmes, B.; Hart, P. A.; Kuznetsova, N.; Levy, S. L.; Long, O.; Lu, A.; Richman, J. D.; Verkerke, W.; Witherell, M.; Yellin, S.; Beringer, J.; Dorfan, D. E.; Eisner, A. M.; Frey, A.; Grillo, A. A.; Grothe, M.; Heusch, C. A.; Johnson, R. P.; Kroeger, W.; Lockman, W. S.; Pulliam, T.; Sadrozinski, H.; Schalk, T.; Schmitz, R. E.; Schumm, B. A.; Seiden, A.; Turri, M.; Walkowiak, W.; Williams, D. C.; Wilson, M. G.; Chen, E.; Dubois-Felsmann, G. P.; Dvoretskii, A.; Hitlin, D. G.; Metzler, S.; Oyang, J.; Porter, F. C.; Ryd, A.; Samuel, A.; Weaver, M.; Yang, S.; Zhu, R. Y.; Devmal, S.; Geld, T. L.; Jayatilleke, S.; Mancinelli, G.; Meadows, B. T.; Sokoloff, M. D.; Bloom, P.; Fahey, S.; Ford, W. T.; Gaede, F.; Johnson, D. R.; Michael, A. K.; Nauenberg, U.; Olivas, A.; Park, H.; Rankin, P.; Roy, J.; Sen, S.; Smith, J. G.; van Hoek, W. C.; Wagner, D. L.; Blouw, J.; Harton, J. L.; Krishnamurthy, M.; Soffer, A.; Toki, W. H.; Wilson, R. J.; Zhang, J.; Brandt, T.; Brose, J.; Colberg, T.; Dahlinger, G.; Dickopp, M.; Dubitzky, R. S.; Maly, E.; Müller-Pfefferkorn, R.; Otto, S.; Schubert, K. R.; Schwierz, R.; Spaan, B.; Wilden, L.; Behr, L.; Bernard, D.; Bonneaud, G. R.; Brochard, F.; Cohen-Tanugi, J.; Ferrag, S.; Roussot, E.; T'jampens, S.; Thiebaux, C.; Vasileiadis, G.; Verderi, M.; Anjomshoaa, A.; Bernet, R.; Khan, A.; Muheim, F.; Playfer, S.; Swain, J. E.; Falbo, M.; Bozzi, C.; Dittongo, S.; Folegani, M.; Piemontese, L.; Treadwell, E.; Anulli, F.; Baldini-Ferroli, R.; Calcaterra, A.; de Sangro, R.; Falciai, D.; Finocchiaro, G.; Patteri, P.; Peruzzi, I. M.; Piccolo, M.; Xie, Y.; Zallo, A.; Bagnasco, S.; Buzzo, A.; Contri, R.; Crosetti, G.; Fabbricatore, P.; Farinon, S.; Lo Vetere, M.; Macri, M.; Monge, M. R.; Musenich, R.; Pallavicini, M.; Parodi, R.; Passaggio, S.; Pastore, F. C.; Patrignani, C.; Pia, M. G.; Priano, C.; Robutti, E.; Santroni, A.; Morii, M.; Bartoldus, R.; Dignan, T.; Hamilton, R.; Mallik, U.; Cochran, J.; Crawley, H. B.; Fischer, P.-A.; Lamsa, J.; Meyer, W. T.; Rosenberg, E. I.; Benkebil, M.; Grosdidier, G.; Hast, C.; Höcker, A.; Lacker, H. M.; Lepeltier, V.; Lutz, A. M.; Plaszczynski, S.; Schune, M. H.; Trincaz-Duvoid, S.; Valassi, A.; Wormser, G.; Bionta, R. M.; Brigljević, V.; Fackler, O.; Fujino, D.; Lange, D. J.; Mugge, M.; Shi, X.; van Bibber, K.; Wenaus, T. J.; Wright, D. M.; Wuest, C. R.; Carroll, M.; Fry, J. R.; Gabathuler, E.; Gamet, R.; George, M.; Kay, M.; Payne, D. J.; Sloane, R. J.; Touramanis, C.; Aspinwall, M. L.; Bowerman, D. A.; Dauncey, P. D.; Egede, U.; Eschrich, I.; Gunawardane, N. J.; Martin, R.; Nash, J. A.; Sanders, P.; Smith, D.; Azzopardi, D. E.; Back, J. J.; Dixon, P.; Harrison, P. F.; Potter, R. J.; Shorthouse, H. W.; Strother, P.; Vidal, P. B.; Williams, M. I.; Cowan, G.; George, S.; Green, M. G.; Kurup, A.; Marker, C. E.; McGrath, P.; McMahon, T. R.; Ricciardi, S.; Salvatore, F.; Scott, I.; Vaitsas, G.; Brown, D.; Davis, C. L.; Allison, J.; Barlow, R. J.; Boyd, J. T.; Forti, A.; Fullwood, J.; Jackson, F.; Lafferty, G. D.; Savvas, N.; Simopoulos, E. T.; Weatherall, J. H.

    2001-10-01

    We present measurements, based on a sample of approximately 23×106 BBbar pairs, of the branching fractions and a search for CP-violating charge asymmetries in charmless hadronic decays of B mesons into two-body final states of kaons and pions. We find the branching fractions B(B0-->π+π-) = (4.1+/-1.0+/-0.7)×10-6, B(B0-->K+π-) = (16.7+/-1.6+/-1.3)×10-6, B(B+-->K+π0) = (10.8+2.1-1.9+/-1.0)×10-6, B(B+-->K0π+) = (18.2+3.3-3.0+/-2.0)×10-6, B(B0-->K0π0) = (8.2+3.1-2.7+/-1.2)×10-6. We also report 90% confidence level upper limits for B meson decays to the π+π0, K+K-, and Kbar0K+ final states. In addition, charge asymmetries have been found to be consistent with zero, where the statistical precision is in the range of +/-0.10 to +/-0.18, depending on the decay mode.

  5. Measurements of branching fractions and CP-violating asymmetries in B meson decays to charmless two-body states containing a K(0).

    PubMed

    Aubert, B; Barate, R; Boutigny, D; Couderc, F; Gaillard, J-M; Hicheur, A; Karyotakis, Y; Lees, J P; Robbe, P; Tisserand, V; Zghiche, A; Palano, A; Pompili, A; Chen, J C; Qi, N D; Rong, G; Wang, P; Zhu, Y S; Eigen, G; Ofte, I; Stugu, B; Abrams, G S; Borgland, A W; Breon, A B; Brown, D N; Button-Shafer, J; Cahn, R N; Charles, E; Day, C T; Gill, M S; Gritsan, A V; Groysman, Y; Jacobsen, R G; Kadel, R W; Kadyk, J; Kerth, L T; Kolomensky, Yu G; Kukartsev, G; LeClerc, C; Levi, M E; Lynch, G; Mir, L M; Oddone, P J; Orimoto, T J; Pripstein, M; Roe, N A; Romosan, A; Ronan, M T; Shelkov, V G; Telnov, A V; Wenzel, W A; Ford, K; Harrison, T J; Hawkes, C M; Knowles, D J; Morgan, S E; Penny, R C; Watson, A T; Watson, N K; Goetzen, K; Held, T; Koch, H; Lewandowski, B; Pelizaeus, M; Peters, K; Schmuecker, H; Steinke, M; Boyd, J T; Chevalier, N; Cottingham, W N; Kelly, M P; Latham, T E; Mackay, C; Wilson, F F; Abe, K; Cuhadar-Donszelmann, T; Hearty, C; Mattison, T S; McKenna, J A; Thiessen, D; Kyberd, P; McKemey, A K; Teodorescu, L; Blinov, V E; Bukin, A D; Golubev, V B; Ivanchenko, V N; Kravchenko, E A; Onuchin, A P; Serednyakov, S I; Skovpen, Yu I; Solodov, E P; Yushkov, A N; Best, D; Bruinsma, M; Chao, M; Eschrich, I; Kirkby, D; Lankford, A J; Mandelkern, M; Mommsen, R K; Roethel, W; Stoker, D P; Buchanan, C; Hartfiel, B L; Gary, J W; Layter, J; Shen, B C; Wang, K; del Re, D; Hadavand, H K; Hill, E J; MacFarlane, D B; Paar, H P; Rahatlou, Sh; Sharma, V; Berryhill, J W; Campagnari, C; Dahmes, B; Levy, S L; Long, O; Lu, A; Mazur, M A; Richman, J D; Verkerke, W; Beck, T W; Beringer, J; Eisner, A M; Heusch, C A; Lockman, W S; Schalk, T; Schmitz, R E; Schumm, B A; Seiden, A; Spradlin, P; Turri, M; Walkowiak, W; Williams, D C; Wilson, M G; Albert, J; Chen, E; Dubois-Felsmann, G P; Dvoretskii, A; Erwin, R J; Hitlin, D G; Narsky, I; Piatenko, T; Porter, F C; Ryd, A; Samuel, A; Yang, S; Jayatilleke, S; Mancinelli, G; Meadows, B T; Sokoloff, M D; Abe, T; Blanc, F; Bloom, P; Chen, S; Clark, P J; Ford, W T; Nauenberg, U; Olivas, A; Rankin, P; Roy, J; Smith, J G; van Hoek, W C; Zhang, L; Harton, J L; Hu, T; Soffer, A; Toki, W H; Wilson, R J; Zhang, J; Aleksan, R; Emery, S; Gaidot, A; Ganzhur, S F; Giraud, P-F; Hamelde Monchenault, G; Kozanecki, W; Langer, M; Legendre, M; London, G W; Mayer, B; Schott, G; Vasseur, G; Yeche, Ch; Zito, M; Altenburg, D; Brandt, T; Brose, J; Colberg, T; Dickopp, M; Hauke, A; Lacker, H M; Maly, E; Müller-Pfefferkorn, R; Nogowski, R; Otto, S; Schubert, J; Schubert, K R; Schwierz, R; Spaan, B; Wilden, L; Bernard, D; Bonneaud, G R; Brochard, F; Cohen-Tanugi, J; Grenier, P; Thiebaux, Ch; Vasileiadis, G; Verderi, M; Khan, A; Lavin, D; Muheim, F; Playfer, S; Swain, J E; Andreotti, M; Azzolini, V; Bettoni, D; Bozzi, C; Calabrese, R; Cibinetto, G; Luppi, E; Negrini, M; Piemontese, L; Sarti, A; Treadwell, E; Anulli, F; Baldini-Ferroli, R; Calcaterra, A; De Sangro, R; Falciai, D; Finocchiaro, G; Patteri, P; Peruzzi, I M; Piccolo, M; Zallo, A; Buzzo, A; Capra, R; Contri, R; Crosetti, G; Lo Vetere, M; Macri, M; Monge, M R; Passaggio, S; Patrignani, C; Robutti, E; Santroni, A; Tosi, S; Bailey, S; Morii, M; Won, E; Dubitzky, R S; Bhimji, W; Bowerman, D A; Dauncey, P D; Egede, U; Gaillard, J R; Morton, G W; Nash, J A; Taylor, G P; Grenier, G J; Lee, S-J; Mallik, U; Cochran, J; Crawley, H B; Lamsa, J; Meyer, W T; Prell, S; Rosenberg, E I; Yi, J; Biasini, M; Pioppi, M; Davier, M; Grosdidier, G; Höcker, A; Laplace, S; Diberder, F Le; Lepeltier, V; Lutz, A M; Petersen, T C; Plaszczynski, S; Schune, M H; Tantot, L; Wormser, G; Brigljević, V; Cheng, C H; Lange, D J; Simani, M C; Wright, D M; Bevan, A J; Coleman, J P; Fry, J R; Gabathuler, E; Gamet, R; Kay, M; Parry, R J; Payne, D J; Sloane, R J; Touramanis, C; Back, J J; Cormack, C M; Harrison, P F; Shorthouse, H W; Vidal, P B; Brown, C L; Cowan, G; Flack, R L; Flaecher, H U; George, S; Green, M G; Kurup, A; Marker, C E; McMahon, T R; Ricciardi, S; Salvatore, F; Vaitsas, G; Winter, M A; Brown, D; Davis, C L; Allison, J; Barlow, N R; Barlow, R J; Hart, P A; Hodgkinson, M C; Jackson, F; Lafferty, G D; Lyon, A J; Weatherall, J H; Williams, J C; Farbin, A; Hulsbergen, W D; Jawahery, A; Kovalskyi, D; Lae, C K; Lillard, V; Roberts, D A; Blaylock, G; Dallapiccola, C; Flood, K T; Hertzbach, S S; Kofler, R; Koptchev, V B; Moore, T B; Saremi, S; Staengle, H; Willocq, S; Cowan, R; Sciolla, G; Taylor, F; Yamamoto, R K; Mangeol, D J J; Patel, P M; Robertson, S H; Lazzaro, A; Palombo, F; Bauer, J M; Cremaldi, L; Eschenburg, V; Godang, R; Kroeger, R; Reidy, J; Sanders, D A; Summers, D J; Zhao, H W; Brunet, S; Cote-Ahern, D; Taras, P; Nicholson, H; Raven, G; Cartaro, C; Cavallo, N; De Nardo, G; Fabozzi, F; Gatto, C; Lista, L; Paolucci, P; Piccolo, D; Sciacca, C; Jessop, C P; LoSecco, J M; Gabriel, T A; Brau, B; Gan, K K; Honscheid, K; Hufnagel, D; Kagan, H; Kass, R; Pulliam, T; Ter-Antonyan, R; Wong, Q K; Brau, J; Frey, R; Igonkina, O; Potter, C T; Sinev, N B; Strom, D; Torrence, E; Colecchia, F; Dorigo, A; Galeazzi, F; Margoni, M; Morandin, M; Posocco, M; Rotondo, M; Simonetto, F; Stroili, R; Tiozzo, G; Voci, C; Benayoun, M; Briand, H; Chauveau, J; David, P; De la Vaissière, Ch; Del Buono, L; Hamon, O; John, M J J; Leruste, Ph; Ocariz, J; Pivk, M; Roos, L; Stark, J; T'Jampens, S; Therin, G; Manfredi, P F; Re, V; Behera, P K; Gladney, L; Guo, Q H; Panetta, J; Angelini, C; Batignani, G; Bettarini, S; Bondioli, M; Bucci, F; Calderini, G; Carpinelli, M; Del Gamba, V; Forti, F; Giorgi, M A; Lusiani, A; Marchiori, G; Martinez-Vidal, F; Morganti, M; Neri, N; Paoloni, E; Rama, M; Rizzo, G; Sandrelli, F; Walsh, J; Haire, M; Judd, D; Paick, K; Wagoner, D E; Cavoto, G; Danielson, N; Elmer, P; Lu, C; Miftakov, V; Olsen, J; Smith, A J S; Bellini, F; Faccini, R; Ferrarotto, F; Ferroni, F; Gaspero, M; Mazzoni, M A; Morganti, S; Pierini, M; Piredda, G; Safai Tehrani, F; Voena, C; Christ, S; Wagner, G; Waldi, R; Adye, T; De Groot, N; Franek, B; Geddes, N I; Gopal, G P; Olaiya, E O; Xella, S M; Purohit, M V; Weidemann, A W; Yumiceva, F X; Aston, D; Bartoldus, R; Berger, N; Boyarski, A M; Buchmueller, O L; Convery, M R; Cristinziani, M; Dong, D; Dorfan, J; Dujmic, D; Dunwoodie, W; Elsen, E E; Field, R C; Glanzman, T; Gowdy, S J; Hadig, T; Halyo, V; Hryn'ova, T; Innes, W R; Kelsey, M H; Kim, P; Kocian, M L; Langenegger, U; Leith, D W G S; Libby, J; Luitz, S; Luth, V; Lynch, H L; Marsiske, H; Messner, R; Muller, D R; O'Grady, C P; Ozcan, V E; Perazzo, A; Perl, M; Petrak, S; Ratcliff, B N; Roodman, A; Salnikov, A A; Schindler, R H; Schwiening, J; Simi, G; Snyder, A; Soha, A; Stelzer, J; Su, D; Sullivan, M K; Va'vra, J; Wagner, S R; Weaver, M; Weinstein, A J R; Wisniewski, W J; Wright, D H; Young, C C; Burchat, P R; Edwards, A J; Meyer, T I; Petersen, B A; Roat, C; Ahmed, M; Ahmed, S; Alam, M S; Ernst, J A; Saeed, M A; Saleem, M; Wappler, F R; Bugg, W; Krishnamurthy, M; Spanier, S M; Eckmann, R; Kim, H; Ritchie, J L; Satpathy, A; Schwitters, R F; Izen, J M; Kitayama, I; Lou, X C; Ye, S; Bianchi, F; Bona, M; Gallo, F; Gamba, D; Borean, C; Bosisio, L; Della Ricca, G; Dittongo, S; Grancagnolo, S; Lanceri, L; Poropat, P; Vitale, L; Vuagnin, G; Panvini, R S; Banerjee, Sw; Brown, C M; Fortin, D; Jackson, P D; Kowalewski, R; Roney, J M; Band, H R; Dasu, S; Datta, M; Eichenbaum, A M; Johnson, J R; Kutter, P E; Li, H; Liu, R; Lodovico, F Di; Mihalyi, A; Mohapatra, A K; Pan, Y; Prepost, R; Sekula, S J; von Wimmersperg-Toeller, J H; Wu, J; Wu, S L; Yu, Z; Neal, H

    2004-05-21

    We present measurements of branching fractions and CP-violating asymmetries in decays of B mesons to two-body final states containing a K0. The results are based on a data sample of approximately 88 x 10(6) Upsilon(4S)-->BB decays collected with the BABAR detector at the PEP-II asymmetric-energy B Factory at SLAC. We measure B(B+-->K(0)pi(+))=(22.3+/-1.7+/-1.1)x10(-6), B(B0-->K(0)pi(0)=(11.4+/-1.7+/-0.8)x10(-6), B(B+-->K(0)K+)<2.5 x 10(-6), and B(B0-->K(0)K(0)<1.8 x 10(-6), where the first uncertainty is statistical and the second is systematic, and the upper limits are at the 90% confidence level. In addition, the following CP-violating asymmetries have been measured: A(CP)(B+-->K(0)pi(+))=-0.05+/-0.08+/-0.01 and A(CP)(B0-->K(0)pi(0)=0.03+/-0.36+/-0.11. PMID:15169340

  6. Method and apparatus for modeling interactions

    DOEpatents

    Xavier, Patrick G.

    2002-01-01

    The present invention provides a method and apparatus for modeling interactions that overcomes drawbacks. The method of the present invention comprises representing two bodies undergoing translations by two swept volume representations. Interactions such as nearest approach and collision can be modeled based on the swept body representations. The present invention is more robust and allows faster modeling than previous methods.

  7. Extracting sea level residual in tidally dominated estuarine environments

    NASA Astrophysics Data System (ADS)

    Brown, Jennifer M.; Bolaños, Rodolfo; Howarth, Michael J.; Souza, Alejandro J.

    2012-07-01

    Sea level comprises a mean level, tidal elevation and a residual elevation. Knowledge of what causes maximum water levels is often key in coastal management. However, different methods to extract deviations in water level (residuals) from modelled and observed elevation can give different results. The Dee Estuary, northwest England is a macrotidal estuary that undergoes periodic stratification. It is used here to demonstrate methods to extract the residual water level in response to the following interactive processes: tidal, river-induced stratification and flow, meteorology and waves. Using modelling techniques, the interaction and contribution of different physical processes are investigated. Classical harmonic tidal analysis, model simulations and filtering techniques have been used to "de-tide" the total elevation for short-term (approximately month long) records. Each technique gives a different result highlighting the need to select the correct method for a required study. Analysis of the residual components demonstrates that all processes inducing residuals interact with the tide generating a semi-diurnal residual component. It is suggested that modelling methods enable the full effect of tidal interaction to remain in the residual, whilst harmonic tidal analysis (partly) modify and filtering methods (fully) remove this component of the residual. The analysis methods presented and their influences on the resultant residual are applicable to other study sites. However, when applied specifically to the mouth of the Dee Estuary, the external surge is found to be the main contributor to the total residual, whilst local wind and stratification effects are of secondary importance.

  8. Demonstration of a direct interaction between residue 22 in the carboxyl-terminal half of secretin and the amino-terminal tail of the secretin receptor using photoaffinity labeling.

    PubMed

    Dong, M; Wang, Y; Pinon, D I; Hadac, E M; Miller, L J

    1999-01-01

    An understanding of the molecular basis of hormonal activation of receptors provides important insights for drug design. Toward this end, intrinsic photoaffinity labeling is a powerful tool to directly identify the ligand-binding domain. We have developed a new radioiodinatable agonist ligand of the secretin receptor that incorporates a photolabile p-benzoyl-L-phenylalanine (Bpa) into the position of Leu22 and have utilized this to identify the adjacent receptor domain. The rat [Tyr10,Bpa22]secretin-27 probe was a fully efficacious agonist, with a potency to stimulate cAMP accumulation by Chinese hamster ovary SecR cells similar to that of natural secretin (EC50 = 68 +/- 22 pM analogue and 95 +/- 25 pM secretin). It bound specifically and with high affinity (Ki = 5.0 +/- 1.1 nM) and covalently labeled the Mr = 57,000-62,000 secretin receptor. Cyanogen bromide cleavage of the receptor yielded a major labeled fragment of apparent Mr = 19,000 that shifted to Mr = 9,000 after deglycosylation. This was most consistent with either of two glycosylated domains within the amino-terminal tail of the receptor. Immunoprecipitation with antibody directed to epitope tags incorporated into each of the candidate domains established that the fragment at the amino terminus of the receptor was the site of labeling. This was further localized to the amino-terminal 30 residues of the receptor by additional proteolysis of this fragment with endoproteinase Lys-C. This provides the first direct demonstration of a contact between a secretin-like agonist and its receptor and will contribute a useful constraint to the modeling of this interaction. PMID:9873030

  9. Microstructure, Mechanical Properties, and Two-Body Abrasive Wear Behavior of Cold-Sprayed 20 vol.% Cubic BN-NiCrAl Nanocomposite Coating

    NASA Astrophysics Data System (ADS)

    Luo, Xiao-Tao; Yang, Er-Juan; Shang, Fu-Lin; Yang, Guan-Jun; Li, Chen-Xin; Li, Chang-Jiu

    2014-10-01

    20 vol.% cubic boron nitride (cBN) dispersoid reinforced NiCrAl matrix nanocomposite coating was prepared by cold spray using mechanically alloyed nanostructured composite powders. The as-sprayed nanocomposite coating was annealed at a temperature of 750 °C to enhance the inter-particle bonding. Microstructure of spray powders and coatings was characterized. Vickers microhardness of the coatings was measured. Two-body abrasive wear behavior of the coatings was examined on a pin-on-disk test. It was found that, in mechanically alloyed composite powders, nano-sized and submicro-sized cBN particles are uniformly distributed in nanocrystalline NiCrAl matrix. Dense coating was deposited by cold spray at a gas temperature of 650 °C with the same phases and grain size as those of the starting powder. Vickers hardness test yielded a hardness of 1063 HV for the as-sprayed 20 vol.% cBN-NiCrAl coating. After annealed at 750 °C for 5 h, unbonded inter-particle boundaries were partially healed and evident grain growth of nanocrystalline NiCrAl was avoided. Wear resistance of the as-sprayed 20 vol.% cBN-NiCrAl nanocomposite coating was comparable to the HVOF-sprayed WC-12Co coating. Annealing of the nanocomposite coating resulted in the improvement of wear resistance by a factor of ~33% owing to the enhanced inter-particle bonding. Main material removal mechanisms during the abrasive wear are also discussed.

  10. Interfacial residual thermal strain

    NASA Astrophysics Data System (ADS)

    Kasen, M.; Santoyo, R.

    A method has been developed for assessing the influence of polymer chemical composition and of processing parameters on the magnitude of residual stress developed in glass-fibre-reinforced composites subjected to various cure cycles and subsequently cooled to cryogenic temperatures. The test method was applied to nine resin types, including epoxy, vinyl ester, polyester, cyanate ester and phenolic formulations. Results suggest that polyester resin develops substantially less overall residual strain than do the other resin systems.

  11. Hartree-Fock Mean-Field Models Using Separable Interactions

    SciTech Connect

    Stevenson, P.; Stone, J.R.; Strayer, M.R.

    1999-06-28

    An effective two-body nuclear interaction is presented which is a sum of terms separable in coordinate space. Calculations are made using this interaction of some doubly closed-shell spherical nuclei using many-body perturbation theory with the Hartree-Fock state as a reference state. It is demonstrated that the interaction gives good bulk properties in finite nuclei.

  12. RESIDUAL ENERGY SPECTRUM OF SOLAR WIND TURBULENCE

    SciTech Connect

    Chen, C. H. K.; Bale, S. D.; Salem, C. S.; Maruca, B. A.

    2013-06-20

    It has long been known that the energy in velocity and magnetic field fluctuations in the solar wind is not in equipartition. In this paper, we present an analysis of 5 yr of Wind data at 1 AU to investigate the reason for this. The residual energy (difference between energy in velocity and magnetic field fluctuations) was calculated using both the standard magnetohydrodynamic (MHD) normalization for the magnetic field and a kinetic version, which includes temperature anisotropies and drifts between particle species. It was found that with the kinetic normalization, the fluctuations are closer to equipartition, with a mean normalized residual energy of {sigma}{sub r} = -0.19 and mean Alfven ratio of r{sub A} = 0.71. The spectrum of residual energy, in the kinetic normalization, was found to be steeper than both the velocity and magnetic field spectra, consistent with some recent MHD turbulence predictions and numerical simulations, having a spectral index close to -1.9. The local properties of residual energy and cross helicity were also investigated, showing that globally balanced intervals with small residual energy contain local patches of larger imbalance and larger residual energy at all scales, as expected for nonlinear turbulent interactions.

  13. Close proximity gunshot residues.

    PubMed

    Thornton, J I

    1986-04-01

    Intuitively, a hand held in close proximity to a firearm at the instant of discharge will intercept a significant amount of gunshot residue, even though the hand did not actually come into contact with the weapon. There is, however, little information specifically described in the forensic science literature concerning the residue levels which might be encountered in such an instance. The present work confirms that antimony levels consistent with an individual having fired or handled a firearm may be intercepted by a hand held in close proximity. PMID:3711843

  14. CROP-RESIDUE MANAGEMENT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Our agricultural production system is under increasing pressure to provide low cost, high quality food, fiber and biofuels while maintaining and preserving the environment. Increased interest in crop residues for production system sustainability is related to the recognition that the soil, water and...

  15. Residual stresses in material processing

    SciTech Connect

    Kozaczek, K.J.; Watkins, T.R.; Hubbard, C.R.; Wang, Xun-Li; Spooner, S.

    1994-09-01

    Material manufacturing processes often introduce residual stresses into the product. The residual stresses affect the properties of the material and often are detrimental. Therefore, the distribution and magnitude of residual stresses in the final product are usually an important factor in manufacturing process optimization or component life prediction. The present paper briefly discusses the causes of residual stresses. It then adresses the direct, nondestructive methods of residual stress measurement by X-ray and neutron diffraction. Examples are presented to demonstrate the importance of residual stress measurement in machining and joining operations.

  16. SRC Residual fuel oils

    DOEpatents

    Tewari, Krishna C.; Foster, Edward P.

    1985-01-01

    Coal solids (SRC) and distillate oils are combined to afford single-phase blends of residual oils which have utility as fuel oils substitutes. The components are combined on the basis of their respective polarities, that is, on the basis of their heteroatom content, to assure complete solubilization of SRC. The resulting composition is a fuel oil blend which retains its stability and homogeneity over the long term.

  17. Residual Neuromuscular Blockade.

    PubMed

    Plummer-Roberts, Anna L; Trost, Christina; Collins, Shawn; Hewer, Ian

    2016-02-01

    This article provides an update on residual neuromuscular blockade for nurse anesthetists. The neuromuscular junction, pharmacology for producing and reversing neuromuscular blockade, monitoring sites and methods, and patient implications relating to incomplete reversal of neuromuscular blockade are reviewed. Overall recommendations include using multiple settings when employing a peripheral nerve stimulator for monitoring return of neuromuscular function and administering pharmacologic reversal when the train-of-four ratio is below 0.9. PMID:26939390

  18. Energy from rice residues

    SciTech Connect

    Mahin, D.B.

    1990-03-01

    Developing countries produce millions of tons of rice husks and straw as a byproduct of harvesting rice. Although some of these rice residues are used for fuel or other purposes, most are burned for disposal or just dumped. However, since the mid- 1980's, industrial plants for rice residue utilization have been installed in several countries and are planned in a number of others. The report provides information on systems to produce energy from rice residues that are commercially available in the United States, Europe, and various developing countries, with an emphasis on those currently used or sold on an international level. Specifically reviewed are the use of rice husks to produce: (1) industrial process heat either directly from furnaces or by generating low pressure steam in boilers; (2) mechanical and electrical power for rice milling via steam engine systems, steam turbine/generator systems, and gasifier/engine systems; and (3) electric power for the grid. The outlook for producing energy from rice straw is also assessed. In addition, the prospects for the use of energy from husks or straw in the processing of rice bran are reviewed.

  19. Bifunctional phosphoramidite reagents for the introduction of histidyl and dihistidyl residues into oligonucleotides.

    PubMed

    Smith, T H; LaTour, J V; Bochkariov, D; Chaga, G; Nelson, P S

    1999-01-01

    The synthesis and characterization of reagents for the incorporation of histidyl residues into oligonucleotides by automated chemical synthesis is described. Automated oligonucleotide synthesis utilizing a bifunctional reagent for the incorporation of a dihistidyl residue into oligonucleotides is described. Oligonucleotides incorporating one to three dihistidyl residues were prepared and characterized. The interaction of these oligonucleotides with a metal chelating IMAC matrix was explored. PMID:10411463

  20. Lignin biochemistry and soil N determine crop residue decomposition and soil priming

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cropping history can affect soil properties, including available N, but little is known about the interactive effects of residue biochemistry, temperature and cropping history on residue decomposition. A laboratory incubation examined the role of residue biochemistry and temperature on the decomposi...

  1. Ideal architecture of residue packing and its observation in protein structures.

    PubMed Central

    Raghunathan, G.; Jernigan, R. L.

    1997-01-01

    A simple model of sphere packing has been investigated as an ideal model for long-range interactions for the packing of non-bonded residues in protein structures. By superposing all residues, the geometry of packing around a central residue is investigated. It is found that all residues conform almost perfectly to this lattice model for sphere packing when a radius of 6.5 A is used to define non-bonded (virtual) interacting residues. Side-chain positions with respect to sequential backbone segments are relatively regular as well. This lattice can readily be used in conformation simulations to reduce the conformational space. PMID:9336831

  2. The residual caries dilemma.

    PubMed

    Weerheijm, K L; Groen, H J

    1999-12-01

    Restorative dentistry is based on the assumption that bacterial infection of demineralized dentine should prompt operative intervention. One of the concepts of practical dentistry is to create a favourable environment for caries arrest with minimal operative intervention. The progress of remaining primary caries is key to any discussion of this concept. This discussion is important for the atraumatic restorative treatment (ART) approach, since the removal of all carious dentine is sometimes difficult using hand instruments only. In this paper the results of possible measures to guard against the effects of residual carious and its consequences are reviewed, in order to obtain an impression of the justification for (in)complete excavation of occlusal dentinal caries. Three types of measure are considered: isolating the caries process from the oral environment, excavating the carious dentine, and using a cariostatic filling material. Each of these measures contributes to the arrest of the caries process. However, none of these measures can arrest this process by itself. A combination of all three seems necessary. It is concluded that although residual caries does not seem to be the criterion for rerestoration, one has to strive for as complete caries removal as possible. If this cannot be fulfilled the sealing capacities of the filling material seem to be more important than its cariostatic properties. PMID:10600078

  3. Measurements of CP asymmetries and branching fractions of two-body charmless decays of B^0 and B^0_s mesons

    SciTech Connect

    Morello, Michael Joseph; /Pisa, Scuola Normale Superiore

    2007-12-01

    The thesis is organized as follows: Chapter 1 describes the theoretical framework of non-leptonic B{sub (s)}{sup 0} {yields} H{sup +}h{prime}{sup -} decays, with a simple overview of the CP violation mechanism within the Standard Model and of the most used phenomenological approaches in the evaluation of strong interaction contributions. The chapter contains also a review of the theoretical expectations and the current experimental measurements along with a discussion about the importance of studying such decays. Chapter 2 contains a general description of the Tevatron collider and of the CDF II detector. Chapter 3 is devoted to the description of the data sample used for the measurement and the method used in extracting the signal from the background. Particular attention is dedicated to the on-line trigger selection, which is crucial to collect a sample enriched in B{sub (s)}{sup 0} {yields} h{sup +}h{prime}{sup -} decays. Chapter 4 shows how the information from kinematics and particle identification was used to achieve a statistical discrimination amongst modes to extract individual measurements. The available resolutions in mass or in particle identification are separately insufficient for an event-by-event separation of B{sub (s)}{sup 0} {yields} h{sup +}h{prime}{sup -} modes. The choice of observables and the technique used to combine them is an important and innovative aspect of the analysis described in this thesis. Chapter 5 is devoted to the accurate determination of the invariant mass lineshape. This is a crucial ingredient for resolving overlapping mass peaks. This chapter details all resolution effects with particular attention at the tails due to the emission of low-energy photons from charged kaons and pions in the final state (FSR). For the first time the effect of FSR has been accurately accounted for in a CDF analysis. Chapter 6 describes how kinematic and PID information, discussed in chap. 4 and chap. 5 were combined in a maximum Likelihood fit

  4. Residual gas analyzer calibration

    NASA Technical Reports Server (NTRS)

    Lilienkamp, R. H.

    1972-01-01

    A technique which employs known gas mixtures to calibrate the residual gas analyzer (RGA) is described. The mass spectra from the RGA are recorded for each gas mixture. This mass spectra data and the mixture composition data each form a matrix. From the two matrices the calibration matrix may be computed. The matrix mathematics requires the number of calibration gas mixtures be equal to or greater than the number of gases included in the calibration. This technique was evaluated using a mathematical model of an RGA to generate the mass spectra. This model included shot noise errors in the mass spectra. Errors in the gas concentrations were also included in the valuation. The effects of these errors was studied by varying their magnitudes and comparing the resulting calibrations. Several methods of evaluating an actual calibration are presented. The effects of the number of gases in then, the composition of the calibration mixture, and the number of mixtures used are discussed.

  5. Low-field magnetoacoustic residual stress measurement in steel

    NASA Technical Reports Server (NTRS)

    Namkung, M.; Utrata, D.; Heyman, J. S.; Allison, S. G.

    1987-01-01

    Much of the recent development of the magnetoacoustic technique has been devoted to refine this technique as a reliable and practical tool for measuring bulk residual stress in steel components. For this, the effects of structural and metallurgical properties on the magnetoacoustic interaction have been studied for various types of steel samples. Also, progress is being made to obtain quantitative residual stress measurements in railroad wheels. This paper reviews the physical basis and the experimental results of the magnetoacoustic stress measurements in steels.

  6. The Gatekeeper Residue and Beyond

    PubMed Central

    Choi, Ryan; Song, Yifan; Fox, Anna M.W.; Hillesland, Heidi K.; Zhang, Zhongsheng; Vidadala, RamaSubbaRao; Merritt, Ethan A.; Lau, Audrey O.T.; Maly, Dustin J.; Fan, Erkang; Barrett, Lynn K.; Van Voorhis, Wesley C.; Ojo, Kayode K.

    2015-01-01

    SUMMARY Specific roles of individual CDPKs vary, but in general, they mediate essential biological functions necessary for parasite's survival. A comparative analysis of the structural-activity relationships (SAR) of Neospora caninum, Eimeria tenella and Babesia bovis Calcium-dependent Protein kinases (CDPKs) together with those of Plasmodium falciparum, Cryptosporidium parvum, and Toxoplasma gondii was performed by screening against 333 Bumped kinase inhibitors (BKIs). Structural modeling and experimental data revealed that residues other than the gatekeeper influence compound-protein interactions resulting in distinct sensitivity profiles. We subsequently defined potential amino-acid structural influences within the ATP binding cavity for each orthologue necessary for consideration in the development of broad-spectrum apicomplexan CDPK inhibitors. Although the BKI library was developed for specific inhibition of glycine gatekeeper CDPKs combined with low inhibition of threonine gatekeeper human SRC kinase; some library compounds exhibit activity against serine or threonine containing CDPKs. Divergent BKI sensitivity of CDPK homologs could be explained on the basis of differences in the size and orientation of the hydrophobic pocket and specific variation at other amino-acid positions within the ATP binding cavity. In particular, BbCDPK4 and PfCDPK1 are sensitive to a larger fraction of compounds than EtCDPK1 despite the presence of threonine gatekeeper in all the three CDPKs. PMID:24927073

  7. Involvement of hydrophobic amino acid residues in C7-C8 loop of Aspergillus oryzae hydrophobin RolA in hydrophobic interaction between RolA and a polyester.

    PubMed

    Tanaka, Takumi; Tanabe, Hiroki; Uehara, Kenji; Takahashi, Toru; Abe, Keietsu

    2014-01-01

    Hydrophobins are amphipathic secretory proteins with eight conserved cysteine residues and are ubiquitous among filamentous fungi. The Cys3-Cys4 and Cys7-Cys8 loops of hydrophobins are thought to form hydrophobic segments involved in adsorption of hydrophobins on hydrophobic surfaces. When the fungus Aspergillus oryzae is grown in a liquid medium containing the polyester polybutylene succinate-co-adipate (PBSA), A. oryzae produces hydrophobin RolA, which attaches to PBSA. Here, we analyzed the kinetics of RolA adsorption on PBSA by using a PBSA pull-down assay and a quartz crystal microbalance (QCM) with PBSA-coated electrodes. We constructed RolA mutants in which hydrophobic amino acids in the two loops were replaced with serine, and we examined the kinetics of mutant adsorption on PBSA. QCM analysis revealed that mutants with replacements in the Cys7-Cys8 loop had lower affinity than wild-type RolA for PBSA, suggesting that this loop is involved in RolA adsorption on PBSA. PMID:25273133

  8. Materials recovery from shredder residues

    SciTech Connect

    Daniels, E. J.; Jody, B. J.; Pomykala, J., Jr.

    2000-07-24

    Each year, about five (5) million ton of shredder residues are landfilled in the US. Similar quantities are landfilled in Europe and the Pacific Rim. Landfilling of these residues results in a cost to the existing recycling industry and also represents a loss of material resources that are otherwise recyclable. In this paper, the authors outline the resources recoverable from typical shredder residues and describe technology that they have developed to recover these resources.

  9. Caspase-3 binds diverse P4 residues in peptides as revealed by crystallography and structural modeling.

    SciTech Connect

    Fang, Bin; Fu, Guoxing; Agniswamy, Johnson; Harrison, Robert W.; Weber, Irene T.

    2009-03-31

    Caspase-3 recognition of various P4 residues in its numerous protein substrates was investigated by crystallography, kinetics, and calculations on model complexes. Asp is the most frequent P4 residue in peptide substrates, although a wide variety of P4 residues are found in the cellular proteins cleaved by caspase-3. The binding of peptidic inhibitors with hydrophobic P4 residues, or no P4 residue, is illustrated by crystal structures of caspase-3 complexes with Ac-IEPD-Cho, Ac-WEHD-Cho, Ac-YVAD-Cho, and Boc-D(OMe)-Fmk at resolutions of 1.9-2.6 {angstrom}. The P4 residues formed favorable hydrophobic interactions in two separate hydrophobic regions of the binding site. The side chains of P4 Ile and Tyr form hydrophobic interactions with caspase-3 residues Trp206 and Trp214 within a non-polar pocket of the S4 subsite, while P4 Trp interacts with Phe250 and Phe252 that can also form the S5 subsite. These interactions of hydrophobic P4 residues are distinct from those for polar P4 Asp, which indicates the adaptability of caspase-3 for binding diverse P4 residues. The predicted trends in peptide binding from molecular models had high correlation with experimental values for peptide inhibitors. Analysis of structural models for the binding of 20 different amino acids at P4 in the aldehyde peptide Ac-XEVD-Cho suggested that the majority of hydrophilic P4 residues interact with Phe250, while hydrophobic residues interact with Trp206, Phe250, and Trp214. Overall, the S4 pocket of caspase-3 exhibits flexible adaptation for different residues and the new structures and models, especially for hydrophobic P4 residues, will be helpful for the design of caspase-3 based drugs.

  10. Microwave emission and crop residues

    NASA Technical Reports Server (NTRS)

    Jackson, Thomas J.; O'Neill, Peggy E.

    1991-01-01

    A series of controlled experiments were conducted to determine the significance of crop residues or stubble in estimating the emission of the underlying soil. Observations using truck-mounted L and C band passive microwave radiometers showed that for dry wheat and soybeans the dry residue caused negligible attenuation of the background emission. Green residues, with water contents typical of standing crops, did have a significant effect on the background emission. Results for these green residues also indicated that extremes in plant structure, as created using parallel and perpendicular stalk orientations, can cause very large differences in the degree of attenuation.

  11. Separation of two bodies in space

    NASA Technical Reports Server (NTRS)

    Chamberlain, R. G.; Mack, T. H.; Silsby, W.

    1970-01-01

    Computer program analyzes the motion of two rigid bodies in space, separating as a result of any one, or a combination of, the following mechanisms - springs with ball ends, springs with one end guided, pyrotechnics, rockets, cold-gas jets, air pistons, and Coulomb drag.

  12. Evaluating Higher Education's Two-Body Problem

    ERIC Educational Resources Information Center

    Woolstenhulme, Jared Lynn

    2013-01-01

    Academic couples make up a significant portion of the academic labor market. Unlike other dual-career households, academic couples must not only find employment in the same region, but often in the same institution. Previous work has not considered how outcomes may be different when dual career households work for the same employer. In the first…

  13. High Energy Two-Body Deuteron Photodisintegration

    SciTech Connect

    Terburg, Bart

    1999-07-31

    The differential cross section for two­body deuteron photodisintegration was measured at photon energies between 0.8 and 4.0 GeV and center­of­mass angles theta_cm =37deg, 53deg, 70deg, and 90deg as part of CEBAF experiment E89­012. Constituent counting rules predict a scaling of this cross section at asymptotic energies. In previous experiments this scaling has surprisingly been observed at energies between 1.4 and 2.8 GeV at 90deg. The results from this experiment are in reasonable agreement with previous measurements at lower energies. The data at 70deg and 90deg show a constituent counting rule behavior up to 4.0 GeV photon energy. The 37deg and 53deg data do not agree with the constituent counting rule prediction. The new data are compared with a variety of theoretical models inspired by quantum chromodynamics (QCD) and traditional hadronic nuclear physics.

  14. Impact of Corn Residue Removal on Crop and Soil Productivity

    NASA Astrophysics Data System (ADS)

    Johnson, J. M.; Wilhelm, W. W.; Hatfield, J. L.; Voorhees, W. B.; Linden, D.

    2003-12-01

    Over-reliance on imported fuels, increasing atmospheric levels of greenhouses and sustaining food production for a growing population are three of the most important problems facing society in the mid-term. The US Department of Energy and private enterprise are developing technology necessary to use high cellulose feedstock, such as crop residues, for ethanol production. Based on production levels, corn (Zea mays L.) residue has potential as a biofuel feedstock. Crop residues are a renewable and domestic fuel source, which can reduce the rate of fossil fuel use (both imported and domestic) and provide an additional farm commodity. Crop residues protect the soil from wind and water erosion, provide inputs to form soil organic matter (a critical component determining soil quality) and play a role in nutrient cycling. Crop residues impact radiation balance and energy fluxes and reduce evaporation. Therefore, the benefits of using crop residues as fuel, which removes crop residues from the field, must be balanced against negative environmental impacts (e.g. soil erosion), maintaining soil organic matter levels, and preserving or enhancing productivity. All ramifications of new management practices and crop uses must be explored and evaluated fully before an industry is established. There are limited numbers of long-term studies with soil and crop responses to residue removal that range from negative to negligible. The range of crop and soil responses to crop residue removal was attributed to interactions with climate, management and soil type. Within limits, corn residue can be harvested for ethanol production to provide a renewable, domestic source of energy feedstock that reduces greenhouse gases. Removal rates must vary based on regional yield, climatic conditions and cultural practices. Agronomists are challenged to develop a protocol (tool) for recommending maximum permissible removal rates that ensure sustained soil productivity.

  15. Effective Electromagnetic Interaction Potential in Flat and Curved Spacetimes

    SciTech Connect

    Caicedo, Jose Alexander; Urrutia, Luis F.

    2010-07-12

    We present a summary of the main steps in the construction of the effective relativistic interaction potential between two charged Dirac particles in the presence of a background weak gravitational field, by extending a procedure previously used for electrodynamics in Minkowski space. We consider the full two-body problem and apply the method to the hydrogen atom.

  16. Higgs particles interacting via a scalar Dark Matter field

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Yajnavalkya; Darewych, Jurij

    2016-07-01

    We study a system of two Higgs particles, interacting via a scalar Dark Matter mediating field. The variational method in the Hamiltonian formalism of QFT is used to derive relativistic wave equations for the two-Higgs system, using a truncated Fock-space trial state. Approximate solutions of the two-body equations are used to examine the existence of Higgs bound states.

  17. Universality in Protein Residue Networks

    PubMed Central

    Estrada, Ernesto

    2010-01-01

    Abstract Residue networks representing 595 nonhomologous proteins are studied. These networks exhibit universal topological characteristics as they belong to the topological class of modular networks formed by several highly interconnected clusters separated by topological cavities. There are some networks that tend to deviate from this universality. These networks represent small-size proteins having <200 residues. This article explains such differences in terms of the domain structure of these proteins. On the other hand, the topological cavities characterizing proteins residue networks match very well with protein binding sites. This study investigates the effect of the cutoff value used in building the residue network. For small cutoff values, <5 Å, the cavities found are very large corresponding almost to the whole protein surface. On the contrary, for large cutoff value, >10.0 Å, only very large cavities are detected and the networks look very homogeneous. These findings are useful for practical purposes as well as for identifying protein-like complex networks. Finally, this article shows that the main topological class of residue networks is not reproduced by random networks growing according to Erdös-Rényi model or the preferential attachment method of Barabási-Albert. However, the Watts-Strogatz model reproduces very well the topological class as well as other topological properties of residue network. A more biologically appealing modification of the Watts-Strogatz model to describe residue networks is proposed. PMID:20197043

  18. Preliminary evaluation of the persistence of organic gunshot residue.

    PubMed

    Arndt, James; Bell, Suzanne; Crookshanks, Lindsey; Lovejoy, Marco; Oleska, Casey; Tulley, Tanya; Wolfe, Drew

    2012-10-10

    The organic components of gunshot residue (OGSR, also called firearms discharge residue (FDR) or cartridge discharge residue (CDR)) have been studied and discussed in the literature. These residues, consisting of particulates such as burned and unburned powder as well as molecular compounds, are rarely used in casework except for purposes such as shooting reconstructions. Molecular compounds that survive the firing event or that are created as a result of the firing event could, with focused research and development, open a new avenue for forensic gunshot residue analysis. In this study, the persistence of organic gunshot residue was evaluated using diphenylamine (DPA) as a target analyte and ion mobility spectrometry (IMS) as the detection system. Samples were collected from hands using a solvent swabbing technique and the swab was analyzed using direct thermal desorption for sample introduction into the IMS. OGSR was found to persist for at least 4 h. Although DPA is a widely used industrial compound, analysis of numerous blank and background samples (n∼100) did not show any significant response for DPA using this detector. Variations were noted among individuals and as such, the data set does not support estimation of a half-life as has been done for traditional primer residues. No secondary transfers were observed, suggesting the possibility of skin adhesion via interactions between the lipophilic organic compounds and skin lipids. IMS proved valuable as a means of generating patterns for forensic pattern matching and shows promise as a screening tool applied to firearms discharge. PMID:22682933

  19. Charm nonleptonic decays and final state interactions

    NASA Astrophysics Data System (ADS)

    Buccella, F.; Lusignoli, M.; Pugliese, A.

    1996-02-01

    A global previous analysis of two-body nonleptonic decays of D mesons has been extended to the decays involving light scalar mesons. The allowance for final state interaction also in nonresonant channels provides a fit of much improved quality and with less symmetry breaking in the axial charges. We give predictions for about 50 decay branching ratios yet to be measured. We also discuss long distance contributions to the difference ΔΓ between the DS and DL widths.

  20. Safety assessment of drug residues

    SciTech Connect

    Jackson, B.A.

    1980-05-15

    The safety assessment of drug residues is part of the process for defining the conditions for the safe use of drugs in food-producing animals. The information needed to assess the safety of drug residues is provided by chemical and toxicity tests. Toxicity tests are conducted to identify the type of effect produced and to determine the exposure concentrations that would be expected not to produce the effect. These tests include acute, subacute, and chronic toxicity tests, as well as reproduction studies and other special tests. The results are used to find an acceptable daily intake for drug residues that can be used to set a tolerance.

  1. A residual flexibility approach to multibody dynamics

    NASA Technical Reports Server (NTRS)

    Blelloch, Paul A.; Antal, Gregory W.

    1993-01-01

    Many complex systems can be modeled as a collection of interacting bodies, where the relative motion of the bodies may be large. The dynamics of such systems are simulated using multibody dynamic formulations. Many of these treat each body as a rigid component, but recently the flexibility of the components has been incorporated. This paper presents a residual flexibility formulation of the multibody dynamics problem. The formulation is very simple and offers great computational efficiency since it treats each body as a free structure in space, interacting with other bodies only through interface forces. Each body's accelerations can be solved independently, as can each set of interface forces. We have applied the technique successfully to several special applications, and the initial implementation in a general mechanisms code has given excellent results in comparison to a direct finite element representation of flexibility.

  2. The role of interaction vertices in bound state calculations

    SciTech Connect

    Cetin Savkli; Franz Gross; John Tjon

    2001-02-01

    In recent studies of the one and two-body problem for scalar interactions it was shown that crossed ladder and ''crossed rainbow'' (for the one-body case) exchanges play a crucial role in nonperturbative dynamics. In this letter we use exact analytical and numerical results to show that the contribution of vertex dressings to the two-body bound state mass for scalar QED are canceled by the wavefunction normalization. This proves, for the first time, that the mass of a two-body bound state given by the full theory can be obtained by summing only ladder and crossed ladder diagrams using a bare vertex and a constant dressed mass. We also discuss the implications of the remarkable cancellation between rainbow and crossed rainbow diagrams that is a feature of one-body calculations.

  3. Residual stresses and vector hysteresis modeling

    NASA Astrophysics Data System (ADS)

    Ktena, Aphrodite

    2016-04-01

    Residual stresses in magnetic materials, whether the result of processing or intentional loading, leave their footprint on macroscopic data, such hysteresis loops and differential permeability measurements. A Preisach-type vector model is used to reproduce the phenomenology observed based on assumptions deduced from the data: internal stresses lead to smaller and misaligned grains, hence increased domain wall pinning and angular dispersion of local easy axes, favouring rotation as a magnetization reversal mechanism; misaligned grains contribute to magnetostatic fields opposing the direction of the applied field. The model is using a vector operator which accounts for both reversible and irreversible processes; the Preisach concept for interactions for the role of stress related demagnetizing fields; and a characteristic probability density function which is constructed as a weighed sum of constituent functions: the material is modeled as consisting of various subsystems, e.g. reversal mechanisms or areas subject to strong/weak long range interactions and each subsystem is represented by a constituent probability density function. Our assumptions are validated since the model reproduces the hysteresis loops and differential permeability curves observed experimentally and calculations involving rotating inputs at various residual stress levels are consistent and in agreement with experimental evidence.

  4. Americium recovery from reduction residues

    DOEpatents

    Conner, W.V.; Proctor, S.G.

    1973-12-25

    A process for separation and recovery of americium values from container or bomb'' reduction residues comprising dissolving the residues in a suitable acid, adjusting the hydrogen ion concentration to a desired level by adding a base, precipitating the americium as americium oxalate by adding oxalic acid, digesting the solution, separating the precipitate, and thereafter calcining the americium oxalate precipitate to form americium oxide. (Official Gazette)

  5. DISSOLUTION OF NEPTUNIUM OXIDE RESIDUES

    SciTech Connect

    Kyser, E

    2009-01-12

    This report describes the development of a dissolution flowsheet for neptunium (Np) oxide (NpO{sub 2}) residues (i.e., various NpO{sub 2} sources, HB-Line glovebox sweepings, and Savannah River National Laboratory (SRNL) thermogravimetric analysis samples). Samples of each type of materials proposed for processing were dissolved in a closed laboratory apparatus and the rate and total quantity of off-gas were measured. Samples of the off-gas were also analyzed. The quantity and type of solids remaining (when visible) were determined after post-dissolution filtration of the solution. Recommended conditions for dissolution of the NpO{sub 2} residues are: Solution Matrix and Loading: {approx}50 g Np/L (750 g Np in 15 L of dissolver solution), using 8 M nitric acid (HNO{sub 3}), 0.025 M potassium fluoride (KF) at greater than 100 C for at least 3 hours. Off-gas: Analysis of the off-gas indicated nitric oxide (NO), nitrogen dioxide (NO{sub 2}) and nitrous oxide (N{sub 2}O) as the only identified components. No hydrogen (H{sub 2}) was detected. The molar ratio of off-gas produced per mole of Np dissolved ranged from 0.25 to 0.4 moles of gas per mole of Np dissolved. A peak off-gas rate of {approx}0.1 scfm/kg bulk oxide was observed. Residual Solids: Pure NpO{sub 2} dissolved with little or no residue with the proposed flowsheet but the NpCo and both sweepings samples left visible solid residue after dissolution. For the NpCo and Part II Sweepings samples the residue amounted to {approx}1% of the initial material, but for the Part I Sweepings sample, the residue amounted to {approx}8 % of the initial material. These residues contained primarily aluminum (Al) and silicon (Si) compounds that did not completely dissolve under the flowsheet conditions. The residues from both sweepings samples contained minor amounts of plutonium (Pu) particles. Overall, the undissolved Np and Pu particles in the residues were a very small fraction of the total solids.

  6. Residual-QSAR. Implications for genotoxic carcinogenesis

    PubMed Central

    2011-01-01

    Introduction Both main types of carcinogenesis, genotoxic and epigenetic, were examined in the context of non-congenericity and similarity, respectively, for the structure of ligand molecules, emphasizing the role of quantitative structure-activity relationship ((Q)SAR) studies in accordance with OECD (Organization for Economic and Cooperation Development) regulations. The main purpose of this report involves electrophilic theory and the need for meaningful physicochemical parameters to describe genotoxicity by a general mechanism. Residual-QSAR Method The double or looping multiple linear correlation was examined by comparing the direct and residual structural information against the observed activity. A self-consistent equation of observed-computed activity was assumed to give maximum correlation efficiency for those situations in which the direct correlations gave non-significant statistical information. Alternatively, it was also suited to describe slow and apparently non-noticeable cancer phenomenology, with special application to non-congeneric molecules involved in genotoxic carcinogenesis. Application and Discussions The QSAR principles were systematically applied to a given pool of molecules with genotoxic activity in rats to elucidate their carcinogenic mechanisms. Once defined, the endpoint associated with ligand-DNA interaction was used to select variables that retained the main Hansch physicochemical parameters of hydrophobicity, polarizability and stericity, computed by the custom PM3 semiempirical quantum method. The trial and test sets of working molecules were established by implementing the normal Gaussian principle of activities that applies when the applicability domain is not restrained to the congeneric compounds, as in the present study. The application of the residual, self-consistent QSAR method and the factor (or average) method yielded results characterized by extremely high and low correlations, respectively, with the latter resembling

  7. Disorder and residual helicity alter p53-Mdm2 binding affinity and signaling in cells.

    PubMed

    Borcherds, Wade; Theillet, François-Xavier; Katzer, Andrea; Finzel, Ana; Mishall, Katie M; Powell, Anne T; Wu, Hongwei; Manieri, Wanda; Dieterich, Christoph; Selenko, Philipp; Loewer, Alexander; Daughdrill, Gary W

    2014-12-01

    Levels of residual structure in disordered interaction domains determine in vitro binding affinities, but whether they exert similar roles in cells is not known. Here, we show that increasing residual p53 helicity results in stronger Mdm2 binding, altered p53 dynamics, impaired target gene expression and failure to induce cell cycle arrest upon DNA damage. These results establish that residual structure is an important determinant of signaling fidelity in cells. PMID:25362358

  8. Residual stresses in welded plates

    NASA Technical Reports Server (NTRS)

    Bernstein, Edward L.

    1994-01-01

    The purpose of this project was to develop a simple model which could be used to study residual stress. The mechanism that results in residual stresses in the welding process starts with the deposition of molten weld metal which heats the immediately adjacent material. After solidification of weld material, normal thermal shrinkage is resisted by the adjacent, cooler material. When the thermal strain exceeds the elastic strain corresponding to the yield point stress, the stress level is limited by this value, which decreases with increasing temperature. Cooling then causes elastic unloading which is restrained by the adjoining material. Permanent plastic strain occurs, and tension is caused in the region immediately adjacent to the weld material. Compression arises in the metal farther from the weld in order to maintain overall static equilibrium. Subsequent repair welds may add to the level of residual stresses. The level of residual stress is related to the onset of fracture during welding. Thus, it is of great importance to be able to predict the level of residual stresses remaining after a weld procedure, and to determine the factors, such as weld speed, temperature, direction, and number of passes, which may affect the magnitude of remaining residual stress. It was hoped to use traditional analytical modeling techniques so that it would be easier to comprehend the effect of these variables on the resulting stress. This approach was chosen in place of finite element methods so as to facilitate the understanding of the physical processes. The accuracy of the results was checked with some existing experimental studies giving residual stress levels found from x-ray diffraction measurements.

  9. Residual deformations in ocular tissues

    PubMed Central

    Wang, Ruoya; Raykin, Julia; Gleason, Rudolph L.; Ethier, C. Ross

    2015-01-01

    Residual deformations strongly influence the local biomechanical environment in a number of connective tissues. The sclera is known to be biomechanically important in healthy and diseased eyes, such as in glaucoma. Here, we study the residual deformations of the sclera, as well as the adjacent choroid and retina. Using freshly harvested porcine eyes, we developed two approaches of quantifying residual deformations in the spherically shaped tissues of interest. The first consisted of punching discs from the posterior wall of the eye and quantifying the changes in the area and eccentricity of these samples. The second consisted of cutting a ring from the equatorial sclera and making stress-relieving cuts in it. Measurements of curvature were made before and after the stress-relieving cuts. Using the first approach, we observed a 42% areal contraction of the choroid, but only modest contractions of the sclera and retina. The observed contractions were asymmetric. In the second approach, we observed an opening of the scleral rings (approx. 10% decrease in curvature). We conclude that residual bending deformations are present in the sclera, which we speculate may be due to radially heterogeneous growth and remodelling of the tissue during normal development. Further, residual areal deformations present in the choroid may be due to the network of elastic fibres in this tissue and residual deformations in the constituent vascular bed. Future studies of ocular biomechanics should attempt to include effects of these residual deformations into mechanical models in order to gain a better understanding of the biomechanics of the ocular wall. PMID:25740853

  10. Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida

    SciTech Connect

    Brodkin, Heather R.; Novak, Walter R.P.; Milne, Amy C.; D’Aquino, J. Alejandro; Karabacak, N.M.; Goldberg, Ilana G.; Agar, Jeffrey N.; Payne, Mark S.; Petsko, Gregory A.; Ondrechen, Mary Jo; Ringe, Dagmar

    2011-09-28

    Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell and these in turn interact with residues in a third shell. These residues in the second and third layers may have distinct roles in maintaining the essential chemical properties of the first-shell catalytic residues, particularly their spatial arrangement relative to the substrate binding pocket, and their electrostatic and dynamic properties. The extent to which these remote residues participate in catalysis and precisely how they affect first-shell residues remains unexplored. To improve our understanding of the roles of second- and third-shell residues in catalysis, we used THEMATICS to identify residues in the second and third shells of the Co-type nitrile hydratase from Pseudomonas putida (ppNHase) that may be important for catalysis. Five of these predicted residues, and three additional, conserved residues that were not predicted, have been conservatively mutated, and their effects have been studied both kinetically and structurally. The eight residues have no direct contact with the active site metal ion or bound substrate. These results demonstrate that three of the predicted second-shell residues ({alpha}-Asp164, {beta}-Glu56, and {beta}-His147) and one predicted third-shell residue ({beta}-His71) have significant effects on the catalytic efficiency of the enzyme. One of the predicted residues ({alpha}-Glu168) and the three residues not predicted ({alpha}-Arg170, {alpha}-Tyr171, and {beta}-Tyr215) do not have any significant effects on the catalytic efficiency of the enzyme.

  11. Evidence for Participation of Remote Residues in the Catalytic Activity of Co-type Nitrile Hydratase from Pseudomonas putida†

    PubMed Central

    Brodkin, Heather R.; Novak, Walter R. P.; Milne, Amy C.; D’Aquino, J. Alejandro; Karabacak, N. M.; Agar, Jeffrey N.; Payne, Mark S.; Petsko, Gregory A.; Ondrechen, Mary Jo; Ringe, Dagmar

    2012-01-01

    Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell, and these in turn interact with residues in a third shell. These residues in the second and third layers may have distinct roles in maintaining the essential chemical properties of the first-shell catalytic residues, particularly their spatial arrangement relative to the substrate binding pocket, and their electrostatic and dynamic properties. The extent to which these remote residues participate in catalysis and precisely how they affect first-shell residues remains unexplored. In order to better understand the roles of second- and third-shell residues in catalysis, we used THEMATICS to identify residues in the second- and third-shells of the Co-type nitrile hydratase from Pseudomonas putida (ppNHase) that may be important for catalysis. Five of these predicted residues, plus three additional, conserved residues that were not predicted, have been conservatively mutated, and their effects studied both kinetically and structurally. All of these eight residues have no direct contact with the active site metal ion or bound substrate. These results demonstrate that three of the predicted second-shell residues, α-Asp164, β-Glu56, and β-His147, and one predicted third-shell residue β-His71, have significant effects on the catalytic efficiency of the enzyme. One of the predicted residues, α-Glu168, and the three residues not predicted, α-Arg170, α-Tyr171, and β-Tyr215, do not show any significant effects on the catalytic efficiency of the enzyme. PMID:21473592

  12. SRide: a server for identifying stabilizing residues in proteins

    PubMed Central

    Magyar, Csaba; Gromiha, M. Michael; Pujadas, Gerard; Tusnády, Gábor E.; Simon, István

    2005-01-01

    Residues expected to play key roles in the stabilization of proteins [stabilizing residues (SRs)] are selected by combining several methods based mainly on the interactions of a given residue with its spatial, rather than its sequential neighborhood and by considering the evolutionary conservation of the residues. A residue is selected as a stabilizing residue if it has high surrounding hydrophobicity, high long-range order, high conservation score and if it belongs to a stabilization center. The definition of all these parameters and the thresholds used to identify the SRs are discussed in detail. The algorithm for identifying SRs was originally developed for TIM-barrel proteins [M. M. Gromiha, G. Pujadas, C. Magyar, S. Selvaraj, and I. Simon (2004), Proteins, 55, 316–329] and is now generalized for all proteins of known 3D structure. SRs could be applied in protein engineering and homology modeling and could also help to explain certain folds with significant stability. The SRide server is located at . PMID:15980477

  13. SRide: a server for identifying stabilizing residues in proteins.

    PubMed

    Magyar, Csaba; Gromiha, M Michael; Pujadas, Gerard; Tusnády, Gábor E; Simon, István

    2005-07-01

    Residues expected to play key roles in the stabilization of proteins [stabilizing residues (SRs)] are selected by combining several methods based mainly on the interactions of a given residue with its spatial, rather than its sequential neighborhood and by considering the evolutionary conservation of the residues. A residue is selected as a stabilizing residue if it has high surrounding hydrophobicity, high long-range order, high conservation score and if it belongs to a stabilization center. The definition of all these parameters and the thresholds used to identify the SRs are discussed in detail. The algorithm for identifying SRs was originally developed for TIM-barrel proteins [M. M. Gromiha, G. Pujadas, C. Magyar, S. Selvaraj, and I. Simon (2004), Proteins, 55, 316-329] and is now generalized for all proteins of known 3D structure. SRs could be applied in protein engineering and homology modeling and could also help to explain certain folds with significant stability. The SRide server is located at http://sride.enzim.hu. PMID:15980477

  14. Dry fermentation of agricultural residues

    NASA Astrophysics Data System (ADS)

    Jewell, W. J.; Chandler, J. A.; Dellorto, S.; Fanfoni, K. J.; Fast, S.; Jackson, D.; Kabrick, R. M.

    1981-09-01

    A dry fermentation process is discussed which converts agricultural residues to methane, using the residues in their as produced state. The process appears to simplify and enhance the possibilities for using crop residues as an energy source. The major process variables investigated include temperature, the amount and type of inoculum, buffer requirements, compaction, and pretreatment to control the initial available organic components that create pH problems. A pilot-scale reactor operation on corn stover at a temperature of 550 C, with 25 percent initial total solids, a seed-to-feed ratio of 2.5 percent, and a buffer-to-feed ratio of 8 percent achieved 33 percent total volatile solids destruction in 60 days. Volumetric biogas yields from this unit were greater than 1 vol/vol day for 12 days, and greater than 0.5 vol/vol day for 32 days, at a substrate density of 169 kg/m (3).

  15. Bogolubov-Hartree-Fock Theory for Strongly Interacting Fermions in the Low Density Limit

    NASA Astrophysics Data System (ADS)

    Bräunlich, Gerhard; Hainzl, Christian; Seiringer, Robert

    2016-06-01

    We consider the Bogolubov-Hartree-Fock functional for a fermionic many-body system with two-body interactions. For suitable interaction potentials that have a strong enough attractive tail in order to allow for two-body bound states, but are otherwise sufficiently repulsive to guarantee stability of the system, we show that in the low-density limit the ground state of this model consists of a Bose-Einstein condensate of fermion pairs. The latter can be described by means of the Gross-Pitaevskii energy functional.

  16. Chemistry of combined residual chlorination

    SciTech Connect

    Leao, S.F.; Selleck, R.E.

    1982-01-01

    The decay of the combined chlorine residual was investigated in this work. Recent concerns about the formation of undesirable compounds such as chloroform with free residual chlorination have focused attention on the alternative use of combined residual chlorination. This work investigates the applicability of reactions proposed to describe the transformations and decay of the combined residual with time. Sodium hypochlorite was added to buffered solutions of ammonia with the chlorine residual being monitored over periods extending up to 10 days. The reaction was studied at four initial concentrations of hypochlorite of 100, 50, 25 and 10 mg/L as Cl/sub 2/ with molar application ratios of chlorine to ammonia, defined herein as M ratios, of 0.90, 0.50, 0.25 and 0.05 at each hypochlorite dose. Sixty-eight experiments were conducted at the pH of 6.6 and 7.2. The conclusions are: (1) in the absence of free chlorine, the concentration of NH/sub 3/ does not seem to affect the rate of disappearance of the residual other than through the formation of NHCl/sub 2/ by NH/sub 2/Cl hydrolysis; (2) the reaction between NHCl/sub 2/ and NH/sub 4//sup +/ to form NH/sub 2/Cl is either much slower than reported by Gray et. al. or the mechanism is different with a rate limiting step not involving NH/sub 3/ or NH/sub 4//sup +/; (3) a redox reaction in addition to the first-order decomposition of NHCl/sub 2/ appears necessary. Model simulation results indicated that a reaction of the type NH/sub 2/Cl + NHCl/sub 2/ ..-->.. P added to the first-order NHCl/sub 2/ decomposition can explain the results observed except at the higher chlorine doses.

  17. 40 CFR 1065.705 - Residual and intermediate residual fuel.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... specifications for fuels meeting the definition of residual fuel in 40 CFR 80.2, including fuels marketed as... 991.0 1010.0 ISO 3675 or ISO 12185 (see also ISO 8217). Kinematic viscosity at 50 °C, max cSt 30.0...

  18. On methylene-bridged cysteine and lysine residues in proteins.

    PubMed

    Ruszkowski, Milosz; Dauter, Zbigniew

    2016-09-01

    Cysteine residues ubiquitously stabilize tertiary and quaternary protein structure by formation of disulfide bridges. Here we investigate another linking interaction that involves sulfhydryl groups of cysteines, namely intra- and intermolecular methylene-bridges between cysteine and lysine residues. A number of crystal structures possessing such a linkage were identified in the Protein Data Bank. Inspection of the electron density maps and re-refinement of the nominated structures unequivocally confirmed the presence of Lys-CH2 -Cys bonds in several cases. PMID:27261771

  19. Collection of sugarcane crop residue for energy

    SciTech Connect

    Eiland, B.R.; Clayton, J.E.

    1982-12-01

    Crop residue left after sugarcane harvesting was recovered using a forage harvester and a large round baler. The quantity, bulk density and moisture content of the crop residue was determined in four fields. Crop residue from 7 ha was burned in boilers at a sugar mill. Samples of this residue were tested by a laboratory and compared to sugarcane bagasse.

  20. Residual Structures in Latent Growth Curve Modeling

    ERIC Educational Resources Information Center

    Grimm, Kevin J.; Widaman, Keith F.

    2010-01-01

    Several alternatives are available for specifying the residual structure in latent growth curve modeling. Two specifications involve uncorrelated residuals and represent the most commonly used residual structures. The first, building on repeated measures analysis of variance and common specifications in multilevel models, forces residual variances…

  1. Preferential antagonism of the interactions of the integrin alpha IIb beta 3 with immobilized glycoprotein ligands by snake-venom RGD (Arg-Gly-Asp) proteins. Evidence supporting a functional role for the amino acid residues flanking the tripeptide RGD in determining the inhibitory properties of snake-venom RGD proteins.

    PubMed Central

    Lu, X; Williams, J A; Deadman, J J; Salmon, G P; Kakkar, V V; Wilkinson, J M; Baruch, D; Authi, K S; Rahman, S

    1994-01-01

    The inhibitory properties of a panel of snake-venom-derived RGD (Arg-Gly-Asp) proteins, including the disintegrins kistrin, elegantin and albolabrin, and the neurotoxin homologue dendroaspin, were investigated in a platelet-adhesion assay using three immobilized ligands of the glycoprotein IIb-IIIa complex (alpha IIb beta 3), namely fibrinogen, fibronectin and von Willebrand factor (vWF). The snake-venom proteins preferentially inhibited the adhesion of ADP-treated platelets to one or more of the immobilized ligands. Kistrin and dendroaspin exhibited similar inhibitory characteristics, abrogating platelet adhesion to fibrinogen and vWF at nanomolar concentrations, but poorly inhibiting adhesion to fibronectin. Kistrin and dendroaspin share little overall amino-acid-sequence identity, but a considerable level of sequence similarity exists around the RGD tripeptide. Synthetic cyclic peptides corresponding to these regions of kistrin and dendroaspin inhibited platelet adhesion to both fibrinogen and fibronectin with approximately equal potency, but were 100-fold weaker antagonists of the interactions of the alpha IIb beta 3 complex with fibrinogen than their parent proteins. The disintegrins elegantin and albolabrin, which share approx. 60% overall amino-acid-sequence similarity with kistrin but have different residues around the RGD tripeptide, exhibited different antagonistic preferences. Elegantin inhibited platelet adhesion to immobilized vWF and fibronectin, but was significantly less effective at disrupting adhesion to fibrinogen. Albolabrin selectively inhibited platelet adhesion to immobilized vWF and was less effective with fibrinogen and fibronectin as adhesive ligands. In contrast with the behaviour of these venom proteins, the adhesion of ADP-treated platelets to immobilized fibrinogen, fibronectin and vWF was inhibited non-selectively by a range of monoclonal antibodies with specificity for the alpha IIb beta 3 complex. These observations, therefore

  2. Bose Polarons in the Strongly Interacting Regime.

    PubMed

    Hu, Ming-Guang; Van de Graaff, Michael J; Kedar, Dhruv; Corson, John P; Cornell, Eric A; Jin, Deborah S

    2016-07-29

    When an impurity is immersed in a Bose-Einstein condensate, impurity-boson interactions are expected to dress the impurity into a quasiparticle, the Bose polaron. We superimpose an ultracold atomic gas of ^{87}Rb with a much lower density gas of fermionic ^{40}K impurities. Through the use of a Feshbach resonance and radio-frequency spectroscopy, we characterize the energy, spectral width, and lifetime of the resultant polaron on both the attractive and the repulsive branches in the strongly interacting regime. The width of the polaron in the attractive branch is narrow compared to its binding energy, even as the two-body scattering length diverges. PMID:27517776

  3. Bose Polarons in the Strongly Interacting Regime

    NASA Astrophysics Data System (ADS)

    Hu, Ming-Guang; Van de Graaff, Michael J.; Kedar, Dhruv; Corson, John P.; Cornell, Eric A.; Jin, Deborah S.

    2016-07-01

    When an impurity is immersed in a Bose-Einstein condensate, impurity-boson interactions are expected to dress the impurity into a quasiparticle, the Bose polaron. We superimpose an ultracold atomic gas of 87Rb with a much lower density gas of fermionic 40 impurities. Through the use of a Feshbach resonance and radio-frequency spectroscopy, we characterize the energy, spectral width, and lifetime of the resultant polaron on both the attractive and the repulsive branches in the strongly interacting regime. The width of the polaron in the attractive branch is narrow compared to its binding energy, even as the two-body scattering length diverges.

  4. Classification of explosive residues on organic substrates using laser induced breakdown spectroscopy.

    PubMed

    De Lucia, Frank C; Gottfried, Jennifer L

    2012-03-01

    Standoff laser induced breakdown spectroscopy (LIBS) has previously been used to classify trace residues as either hazardous (explosives, biological, etc.) or benign. Correct classification can become more difficult depending on the surface/substrate underneath the residue due to variations in the laser-material interaction. In addition, classification can become problematic if the substrate material has a similar elemental composition to the residue. We have evaluated coupling multivariate analysis with standoff LIBS to determine the effectiveness of classifying thin explosive residue layers on painted surfaces. Good classification results were obtained despite the fact that the painted surface contributes to the LIBS emission signal. PMID:22410930

  5. IMPROVED TECHNIQUES FOR RESIDUAL OZONE

    EPA Science Inventory

    Eight analytical methods for the determination of residual ozone in water are evaluated. Four are iodometric methods based on the reduction of ozone by iodide ion: the iodometric method, the amperometric method, the arsenic (III) back titration method, and the N, N-diethyl-p-phen...

  6. Leptogenesis and residual CP symmetry

    NASA Astrophysics Data System (ADS)

    Chen, Peng; Ding, Gui-Jun; King, Stephen F.

    2016-03-01

    We discuss flavour dependent leptogenesis in the framework of lepton flavour models based on discrete flavour and CP symmetries applied to the type-I seesaw model. Working in the flavour basis, we analyse the case of two general residual CP symmetries in the neutrino sector, which corresponds to all possible semi-direct models based on a preserved Z 2 in the neutrino sector, together with a CP symmetry, which constrains the PMNS matrix up to a single free parameter which may be fixed by the reactor angle. We systematically study and classify this case for all possible residual CP symmetries, and show that the R-matrix is tightly constrained up to a single free parameter, with only certain forms being consistent with successful leptogenesis, leading to possible connections between leptogenesis and PMNS parameters. The formalism is completely general in the sense that the two residual CP symmetries could result from any high energy discrete flavour theory which respects any CP symmetry. As a simple example, we apply the formalism to a high energy S 4 flavour symmetry with a generalized CP symmetry, broken to two residual CP symmetries in the neutrino sector, recovering familiar results for PMNS predictions, together with new results for flavour dependent leptogenesis.

  7. Pyrotechnic reaction residue particle analysis.

    PubMed

    Kosanke, Kenneth L; Dujay, Richard C; Kosanke, Bonnie J

    2006-03-01

    Pyrotechnic reaction residue particle (PRRP) production, sampling and analysis are all very similar to that for primer gunshot residue. In both cases, the preferred method of analysis uses scanning electron microscopy to locate suspect particles and then uses energy dispersive x-ray spectroscopy to characterize the particle's constituent chemical elements. There are relatively few times when standard micro-analytical chemistry performed on pyrotechnic residues may not provide sufficient information for forensic investigators. However, on those occasions, PRRP analysis provides a greatly improved ability to discriminate between materials of pyrotechnic origin and other unrelated substances also present. The greater specificity of PRRP analysis is the result of its analyzing a large number of individual micron-sized particles, rather than producing only a single integrated result such as produced using standard micro-analytical chemistry. For example, PRRP analyses are used to demonstrate its ability to successfully (1) discriminate between pyrotechnic residues and unrelated background contamination, (2) identify that two different pyrotechnic compositions had previously been exploded within the same device, and (3) establish the chronology of an incident involving two separate and closely occurring explosions. PMID:16566762

  8. Three-body interactions between slow light Rydberg polaritons

    NASA Astrophysics Data System (ADS)

    Jachymski, Krzysztof; Bienias, Przemyslaw; Büchler, Hans Peter

    2016-05-01

    Rydberg polaritons have recently emerged as a promising platform for nonlinear optics and photonic quantum simulation. They are created in an atomic medium using electromagnetically induced transparency (EIT) scheme involving a Rydberg excitation. Cavity photons can be used in this context to create long-lived, coherent samples consisting of several polaritons. We show that in addition to effective two-body interaction potential inherited from the Rydberg states, the polaritons also exhibit effective three-body interactions. For attractive two-body forces, the three-body term induces short-range repulsion. We analyze the impact of this interaction on the three-body photonic bound states in one-dimensional geometry and discuss the prospects for engineering novel quantum states.

  9. Insights into the role of the aromatic residue in galactose-binding sites: MP2/6-311G++** study on galactose- and glucose-aromatic residue analogue complexes.

    PubMed

    Sujatha, Mannargudi S; Sasidhar, Yellamraju U; Balaji, Petety V

    2005-06-14

    The presence of an aromatic residue (Trp, Phe, Tyr) facing the nonpolar face of galactose is a common feature of galactose-specific lectins. The interactions such as those between the C-H groups of galactose and the pi-electron cloud of aromatic residues have been characterized as weak hydrogen bonds between soft acids and soft bases, largely governed by dispersive and charge transfer interactions. An analysis of the binding sites of several galactose-specific lectins revealed that the spatial position-orientation of galactose relative to the binding site aromatic residue varies substantially. The effect of variations in position-orientations of galactose on the interaction energies of galactose-aromatic residue complexes has not been determined so far. In view of this, MP2/6-311G++** calculations were performed on galactose- and glucose-aromatic residue analogue complexes in eight position-orientations. The results show that the strength of the C-H...pi interactions in galactose-aromatic residue complexes is comparable to that of a hydrogen bond. Rather than the type of aromatic residue, the position-orientation of the saccharide appears to be more critical in determining the strength of their interactions. Earlier studies have found the binding site aromatic residue to be critical, but its role was not clear. This study shows that the aromatic residue is important for discriminating galactose from glucose, in addition to its contribution to binding energy. PMID:15938646

  10. Thermogravimetric investigation of the co-combustion between the pyrolysis oil distillation residue and lignite.

    PubMed

    Li, Hao; Xia, Shuqian; Ma, Peisheng

    2016-10-01

    Co-combustion of lignite with distillation residue derived from rice straw pyrolysis oil was investigated by non-isothermal thermogravimetric analysis (TGA). The addition of distillation residue improved the reactivity and combustion efficiency of lignite, such as increasing the weight loss rate at peak temperature and decreasing the burnout temperature and the total burnout. With increasing distillation residue content in the blended fuels, the synergistic interactions between distillation residue and lignite firstly increased and then decreased during co-combustion stage. Results of XRF, FTIR, (13)C NMR and SEM analysis indicated that chemical structure, mineral components and morphology of samples have great influence on the synergistic interactions. The combustion mechanisms and kinetic parameters were calculated by the Coats Redfern model, suggesting that the lowest apparent activation energy (120.19kJ/mol) for the blended fuels was obtained by blending 60wt.% distillation residue during main co-combustion stage. PMID:27416511

  11. Creation of residual flows in a partially stratified estuary

    USGS Publications Warehouse

    Stacey, M.T.; Burau, J.R.; Monismith, Stephen G.

    2001-01-01

    The creation of residual flows in estuaries is examined using acoustic Doppler current profiler data sets from northern San Francisco Bay. The data sets are analyzed using principal component analysis to examine the temporal variability of the flows which create the residual circulation. It is seen that in this periodically and partially stratified estuary the residual flows are created through a series of pulses with strong variability at the 24-hour timescale, through the interaction of shear, stratification and mixing. This interaction is captured through the use of a dimensionless number, the horizontal Richardson number (Rix), which is developed to examine the local balance between the stratifying and destratifying forces at the tidal timescale. It is seen that Rix is a valuable parameter in predicting the onset of the residual-creating events, with a threshold value of ??? 3 on ebb tides. This critical value is argued to be a threshold, above which the stratification and shear flow create a feedback effect, each further intensifying the other. This feedback results in a highly variable exchange flow which creates the estuarine residual in intermittent pulses rather than as a steady flow. Although typically attributed to baroclinic forcing, an argument is made that these pulses of residual-creating exchange flow could be created by barotropic forcing in the presence of variable stratification which is asymmetric between flood and ebb tides. This result poses a great challenge for turbulence modeling, as the timing and magnitude of stratification and shear must be correctly simulated on the tidal timescale in order to reproduce the effects seen in the data sets presented. Copyright 2001 by the American Geophysical Union.

  12. Controls on monthly estuarine residuals: Eulerian circulation and elevation

    NASA Astrophysics Data System (ADS)

    Brown, Jennifer M.; Bolaños, Rodolfo; Souza, Alejandro J.

    2014-04-01

    The Dee Estuary, at the NW English-Welsh border, is a major asset, supporting: one of the largest wildlife habitats in Europe, industrial importance along the Welsh coastline and residential and recreational usage along the English coast. Understanding of the residual elevation is important to determine the total water levels that inundate intertidal banks, especially during storms. Whereas, improved knowledge of the 3D residual circulation is important in determining particle transport pathways to manage water quality and morphological change. Using mooring data obtained in February-March 2008, a 3D modelling system has been previously validated against in situ salinity, velocity, elevation and wave observations, to investigate the barotropic-baroclinic wave interaction within this estuary under full realistic forcing. The system consists of a coupled circulation-wave-turbulence model (POLCOMS-WAM-GOTM). Using this modelling system the contribution of different processes and their interactions to the monthly residuals in both elevation and circulation is now assessed. By studying a tidally dominated estuary under wave influence, it is found that baroclinicity induced by a weak river flow has greater importance in generating a residual circulation than the waves, even at the estuary mouth. Although the monthly residual circulation is dominated by tidal and baroclinic processes, the residual estuarine surface elevation is primarily influenced by the seasonal external forcing to the region, with secondary influence from the local wind conditions. During storm conditions, 3D radiation stress becomes important for both elevation and circulation at the event scale but is found here to have little impact over monthly time scales.

  13. Accessibility and mobility of lysine residues in. beta. -lactoglobulin

    SciTech Connect

    Brown, E.M.; Pfeffer, P.E.; Kumosinski, T.F.; Greenberg, R.

    1988-07-26

    N/sup epsilon/-(/sup 2/H/sub 6/)Isopropyllysyl-..beta..-lactoglobulin was prepared by reductive alkylation of ..beta..-lactoglobulin with (/sup 2/H/sub 6/)acetone and NaBH/sub 4/ to provide a /sup 2/H (NMR) probe for the study of lysine involvement in lipid-protein interactions. Amino acid analysis showed 80% of the protein's 15 lysine residues to be labeled. Unmodified lysine residues were located through peptide maps produced from CNBr, tryptic, and chymotryptic digests of the labeled protein. Average correlation times calculated from /sup 2/H NMR spectra were 20 and 320 ps for 8.7 and 3.3 residues, respectively, in 6 M guanidine hydrochloride; in nondenaturing solution, values of 70 and 320 ps were obtained for 6.5 and 3.2 residues, respectively, with the remaining 2.3 modified residues not observed, suggesting that side chains of lysine residues in unordered or flexible regions were more mobile than those in stable periodic structures. /sup 2/H NMR spectra of the protein complexed with dipalmitoylphosphatidylcholine confirmed the extrinsic membrane protein type behavior of ..beta..-lactoglobulin previously reported from /sup 31/P NMR studies of the phospholipids complexed with ..beta..-lactoglobulin. Although no physiological function has yet been identified, comparison of these results with the X-ray structure supports the hypothesis that residues not accessible for modification may help to stabilize the cone-shaped ..beta..-barrel thought to contain binding sites for small lipid-soluble molecules.

  14. Method and apparatus for modeling interactions

    DOEpatents

    Xavier, Patrick G.

    2000-08-08

    A method and apparatus for modeling interactions between bodies. The method comprises representing two bodies undergoing translations and rotations by two hierarchical swept volume representations. Interactions such as nearest approach and collision can be modeled based on the swept body representations. The present invention can serve as a practical tool in motion planning, CAD systems, simulation systems, safety analysis, and applications that require modeling time-based interactions. A body can be represented in the present invention by a union of convex polygons and convex polyhedra. As used generally herein, polyhedron includes polygon, and polyhedra includes polygons. The body undergoing translation can be represented by a swept body representation, where the swept body representation comprises a hierarchical bounding volume representation whose leaves each contain a representation of the region swept by a section of the body during the translation, and where the union of the regions is a superset of the region swept by the surface of the body during translation. Interactions between two bodies thus represented can be modeled by modeling interactions between the convex hulls of the finite sets of discrete points in the swept body representations.

  15. Folding simulations of alanine-based peptides with lysine residues.

    PubMed Central

    Sung, S S

    1995-01-01

    The folding of short alanine-based peptides with different numbers of lysine residues is simulated at constant temperature (274 K) using the rigid-element Monte Carlo method. The solvent-referenced potential has prevented the multiple-minima problem in helix folding. From various initial structures, the peptides with three lysine residues fold into helix-dominated conformations with the calculated average helicity in the range of 60-80%. The peptide with six lysine residues shows only 8-14% helicity. These results agree well with experimental observations. The intramolecular electrostatic interaction of the charged lysine side chains and their electrostatic hydration destabilize the helical conformations of the peptide with six lysine residues, whereas these effects on the peptides with three lysine residues are small. The simulations provide insight into the helix-folding mechanism, including the beta-bend intermediate in helix initiation, the (i, i + 3) hydrogen bonds, the asymmetrical helix propagation, and the asymmetrical helicities in the N- and C-terminal regions. These findings are consistent with previous studies. PMID:7756550

  16. Final State Interactions in GENIE

    NASA Astrophysics Data System (ADS)

    Dytman, S. A.; Meyer, A. S.

    2011-11-01

    Final state interactions (FSI) are an important part of all neutrino event generators because modern detectors are made of nuclei to maximize count rate. The incident neutrino will interact with one (or two) nucleons but the final state can be quite different because the hadrons will have further interactions in the residual nucleus. This has historically been one of the major differences between event generators. GENIE will now have 2 FSI codes which allow interesting comparisons for the first time.

  17. Protein thermal denaturation is modulated by central residues in the protein structure network.

    PubMed

    Souza, Valquiria P; Ikegami, Cecília M; Arantes, Guilherme M; Marana, Sandro R

    2016-03-01

    Network structural analysis, known as residue interaction networks or graphs (RIN or RIG, respectively) or protein structural networks or graphs (PSN or PSG, respectively), comprises a useful tool for detecting important residues for protein function, stability, folding and allostery. In RIN, the tertiary structure is represented by a network in which residues (nodes) are connected by interactions (edges). Such structural networks have consistently presented a few central residues that are important for shortening the pathways linking any two residues in a protein structure. To experimentally demonstrate that central residues effectively participate in protein properties, mutations were directed to seven central residues of the β-glucosidase Sfβgly (β-d-glucoside glucohydrolase; EC 3.2.1.21). These mutations reduced the thermal stability of the enzyme, as evaluated by changes in transition temperature (Tm ) and the denaturation rate at 45 °C. Moreover, mutations directed to the vicinity of a central residue also caused significant decreases in the Tm of Sfβgly and clearly increased the unfolding rate constant at 45 °C. However, mutations at noncentral residues or at surrounding residues did not affect the thermal stability of Sfβgly. Therefore, the data reported in the present study suggest that the perturbation of the central residues reduced the stability of the native structure of Sfβgly. These results are in agreement with previous findings showing that networks are robust, whereas attacks on central nodes cause network failure. Finally, the present study demonstrates that central residues underlie the functional properties of proteins. PMID:26785700

  18. Residual Resistivity of Dilute Alloys

    NASA Astrophysics Data System (ADS)

    Vora, Aditya M.

    The residual resistivity for 156 dilute alloys of 19 hosts of different groups of the periodic table has been studied on the basis of the single parametric model potential formalism. Ashcroft's empty core model (EMC) potential is explored for the first time with five different local field correction functions, viz, Hartree (H), Taylor (T), Ichimaru-Utsumi (IU), Farid et al. (F), and Sarkar et al. (S) to investigate the effect of the exchange and correlation on the aforesaid properties. The comparison of the presently computed outcomes with the available theoretical and experimental data is highly encouraging. The investigation of residual resistivity is found to be quite sensitive to the selection of local field correction function, showing a significant variation with the change in the function.

  19. Primer residues deposited by handguns.

    PubMed

    Cooper, R; Guileyardo, J M; Stone, I C; Hall, V; Fletcher, L

    1994-12-01

    There is much anecdotal information being disseminated, even offered in expert witness testimony, concerning the deposit of primer residues on the hands of persons in front of the muzzle of handguns. We present data for 9 mm and 380 Auto pistols and for a 38 caliber revolver depicting the procedure for obtaining wipings taken from targets representing the hands of a gunshot victim. These wipings from pork tissue were then analyzed for the primer residue metals antimony, barium, and lead. The data show that the two primary metals, antimony and barium, are deposited on the targets out to 4 feet for the pistols and out to three feet for the 38-caliber revolver. Testing will continue in actual cases with the gun and ammunition involved in the shooting. PMID:7879775

  20. Catalytic combustion of residual fuels

    NASA Technical Reports Server (NTRS)

    Bulzan, D. L.; Tacina, R. R.

    1981-01-01

    A noble metal catalytic reactor was tested using two grades of petroleum derived residual fuels at specified inlet air temperatures, pressures, and reference velocities. Combustion efficiencies greater than 99.5 percent were obtained. Steady state operation of the catalytic reactor required inlet air temperatures of at least 800 K. At lower inlet air temperatures, upstream burning in the premixing zone occurred which was probably caused by fuel deposition and accumulation on the premixing zone walls. Increasing the inlet air temperature prevented this occurrence. Both residual fuels contained about 0.5 percent nitrogen by weight. NO sub x emissions ranged from 50 to 110 ppm by volume at 15 percent excess O2. Conversion of fuel-bound nitrogen to NO sub x ranged from 25 to 50 percent.

  1. Limits of adaptation, residual interferences

    NASA Technical Reports Server (NTRS)

    Mokry, Miroslav (Editor); Erickson, J. C., Jr.; Goodyer, Michael J.; Mignosi, Andre; Russo, Giuseppe P.; Smith, J.; Wedemeyer, Erich H.; Newman, Perry A.

    1990-01-01

    Methods of determining linear residual wall interference appear to be well established theoretically; however they need to be validated, for example by comparative studies of test data on the same model in different adaptive-wall wind tunnels as well as in passive, ventilated-wall tunnels. The GARTEur CAST 7 and the CAST 10/DOA 2 investigations are excellent examples of such comparative studies. Results to date in both one-variable and two-variable methods for nonlinear wall interference indicate that a great deal more research and validation are required. The status in 2D flow is advanced over that in 3D flow as is the case generally with adaptive-wall development. Nevertheless, it is now well established that for transonic testing with extensive supercritical flow present, significant wall interference is likely to exist in conventional ventilated test sections. Consequently, residual correction procedures require further development hand-in-hand with further adaptive-wall development.

  2. Vitrification of NAC process residue

    SciTech Connect

    Merrill, R.A.; Whittington, K.F.; Peters, R.D.

    1995-12-31

    Vitrification tests have been performed with simulated waste compositions formulated to represent the residue which would be obtained from the treatment of low-level, nitrate wastes from Hanford and Oak Ridge by the nitrate to ammonia and ceramic (NAC) process. The tests were designed to demonstrate the feasibility of vitrifying NAC residue and to quantify the impact of the NAC process on the volume of vitrified waste. The residue from NAC treatment of low-level nitrate wastes consists primarily of oxides of aluminum and sodium. High alumina glasses were formulated to maximize the waste loading of the NAC product. Transparent glasses with up to 35 wt% alumina, and even higher contents in opaque glasses, were obtained at melting temperatures of 1,200 C to 1,400 C. A modified TCLP leach test showed the high alumina glasses to have good chemical durability, leaching significantly less than either the ARM-1 or the DWPF-EA high-level waste reference glasses. A significant increase in the final waste volume would be a major result of the NAC process on LLW vitrification. For Hanford wastes, NAC-treatment of nitrate wastes followed by vitrification of the residue will increase the final volume of vitrified waste by 50% to 90%; for Melton Valley waste from Oak Ridge, the increase in final glass volume will be 260% to 280%. The increase in volume is relative to direct vitrification of the waste in a 20 wt% Na{sub 2}O glass formulation. The increase in waste volume directly affects not only disposal costs, but also operating and/or capital costs. Larger plant size, longer operating time, and additional energy and additive costs are direct results of increases in waste volume. Such increases may be balanced by beneficial impacts on the vitrification process; however, those effects are outside the scope of this report.

  3. Vitrification of NAC process residue

    SciTech Connect

    Merrill, R.A.; Whittington, K.F.; Peters, R.D.

    1995-09-01

    Vitrification tests have been performed with simulated waste compositions formulated to represent the residue which would be obtained from the treatment of low-level, nitrate wastes from Hanford and Oak Ridge by the nitrate to ammonia and ceramic (NAC) process. The tests were designed to demonstrate the feasibility of vitrifying NAC residue and to quantify the impact of the NAC process on the volume of vitrified waste. The residue from NAC treatment of low-level nitrate wastes consists primarily of oxides of aluminum and sodium. High alumina glasses were formulated to maximize the waste loading of the NAC product. Transparent glasses with up to 35 wt% alumina, and even higher contents in opaque glasses, were obtained at melting temperatures of 1200{degrees}C to 1400{degrees}C. A modified TCLP leach test showed the high alumina glasses to have good chemical durability, leaching significantly less than either the ARM-1 or the DWPF-EA high-level waste reference glasses. A significant increase in the final waste volume would be a major result of the NAC process on LLW vitrification. For Hanford wastes, NAC-treatment of nitrate wastes followed by vitrification of the residue will increase the final volume of vitrified waste by 50% to 90%; for Melton Valley waste from Oak Ridge, the increase in final glass volume will be 260% to 280%. The increase in volume is relative to direct vitrification of the waste in a 20 wt% Na{sub 2}O glass formulation. The increase in waste volume directly affects not only disposal costs, but also operating and/or capital costs. Larger plant size, longer operating time, and additional energy and additive costs are direct results of increases in waste volume. Such increases may be balanced by beneficial impacts on the vitrification process; however, those effects are outside the scope of this report.

  4. Residue management at Rocky Flats

    SciTech Connect

    Olencz, J.

    1995-12-31

    Past plutonium production and manufacturing operations conducted at the Rocky Flats Environmental Technology Site (RFETS) produced a variety of plutonium-contaminated by-product materials. Residues are a category of these materials and were categorized as {open_quotes}materials in-process{close_quotes} to be recovered due to their inherent plutonium concentrations. In 1989 all RFETS plutonium production and manufacturing operations were curtailed. This report describes the management of plutonium bearing liquid and solid wastes.

  5. Evaluation of residue drum storage safety risks

    SciTech Connect

    Conner, W.V.

    1994-06-17

    A study was conducted to determine if any potential safety problems exist in the residue drum backlog at the Rocky Flats Plant. Plutonium residues stored in 55-gallon drums were packaged for short-term storage until the residues could be processed for plutonium recovery. These residues have now been determined by the Department of Energy to be waste materials, and the residues will remain in storage until plans for disposal of the material can be developed. The packaging configurations which were safe for short-term storage may not be safe for long-term storage. Interviews with Rocky Flats personnel involved with packaging the residues reveal that more than one packaging configuration was used for some of the residues. A tabulation of packaging configurations was developed based on the information obtained from the interviews. A number of potential safety problems were identified during this study, including hydrogen generation from some residues and residue packaging materials, contamination containment loss, metal residue packaging container corrosion, and pyrophoric plutonium compound formation. Risk factors were developed for evaluating the risk potential of the various residue categories, and the residues in storage at Rocky Flats were ranked by risk potential. Preliminary drum head space gas sampling studies have demonstrated the potential for formation of flammable hydrogen-oxygen mixtures in some residue drums.

  6. Atomic structure of recombinant thaumatin II reveals flexible conformations in two residues critical for sweetness and three consecutive glycine residues.

    PubMed

    Masuda, Tetsuya; Mikami, Bunzo; Tani, Fumito

    2014-11-01

    Thaumatin, an intensely sweet-tasting protein used as a sweetener, elicits a sweet taste at 50 nM. Although two major variants designated thaumatin I and thaumatin II exist in plants, there have been few dedicated thaumatin II structural studies and, to date, data beyond atomic resolution had not been obtained. To identify the detailed structural properties explaining why thaumatin elicits a sweet taste, the structure of recombinant thaumatin II was determined at the resolution of 0.99 Å. Atomic resolution structural analysis with riding hydrogen atoms illustrated the differences in the direction of the side-chains more precisely and the electron density maps of the C-terminal regions were markedly improved. Though it had been suggested that the three consecutive glycine residues (G142-G143-G144) have highly flexible conformations, G143, the central glycine residue was successfully modelled in two conformations for the first time. Furthermore, the side chain r.m.s.d. values for two residues (R67 and R82) critical for sweetness exhibited substantially higher values, suggesting that these residues are highly disordered. These results demonstrated that the flexible conformations in two critical residues favoring their interaction with sweet taste receptors are prominent features of the intensely sweet taste of thaumatin. PMID:25066915

  7. Residual Stresses Modeled in Thermal Barrier Coatings

    NASA Technical Reports Server (NTRS)

    Freborg, A. M.; Ferguson, B. L.; Petrus, G. J.; Brindley, W. J.

    1998-01-01

    Thermal barrier coating (TBC) applications continue to increase as the need for greater engine efficiency in aircraft and land-based gas turbines increases. However, durability and reliability issues limit the benefits that can be derived from TBC's. A thorough understanding of the mechanisms that cause TBC failure is a key to increasing, as well as predicting, TBC durability. Oxidation of the bond coat has been repeatedly identified as one of the major factors affecting the durability of the ceramic top coat during service. However, the mechanisms by which oxidation facilitates TBC failure are poorly understood and require further characterization. In addition, researchers have suspected that other bond coat and top coat factors might influence TBC thermal fatigue life, both separately and through interactions with the mechanism of oxidation. These other factors include the bond coat coefficient of thermal expansion, the bond coat roughness, and the creep behavior of both the ceramic and bond coat layers. Although it is difficult to design an experiment to examine these factors unambiguously, it is possible to design a computer modeling "experiment" to examine the action and interaction of these factors, as well as to determine failure drivers for TBC's. Previous computer models have examined some of these factors separately to determine their effect on coating residual stresses, but none have examined all the factors concurrently. The purpose of this research, which was performed at DCT, Inc., in contract with the NASA Lewis Research Center, was to develop an inclusive finite element model to characterize the effects of oxidation on the residual stresses within the TBC system during thermal cycling as well as to examine the interaction of oxidation with the other factors affecting TBC life. The plasma sprayed, two-layer thermal barrier coating that was modeled incorporated a superalloy substrate, a NiCrAlY bond coat, and a ZrO2-8 wt % Y2O3 ceramic top coat. We

  8. PESTICIDE RESIDUE RECOVERIES FROM SURFACE WIPES

    EPA Science Inventory

    Human exposure is a consequence of pesticide use indoors with a primary source resulting from residue deposition on household surfaces. Accurate measurements of surface residues is essential for estimating exposure from different routes. Various procedures have been developed ...

  9. 48 CFR 250.104 - Residual powers.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 3 2014-10-01 2014-10-01 false Residual powers. 250.104 Section 250.104 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT... Contractual Actions 250.104 Residual powers....

  10. 48 CFR 1850.104 - Residual powers.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 6 2014-10-01 2014-10-01 false Residual powers. 1850.104 Section 1850.104 Federal Acquisition Regulations System NATIONAL AERONAUTICS AND SPACE ADMINISTRATION... 1850.104 Residual powers....

  11. 48 CFR 250.104 - Residual powers.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 3 2011-10-01 2011-10-01 false Residual powers. 250.104 Section 250.104 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT... Contractual Actions 250.104 Residual powers....

  12. 48 CFR 1850.104 - Residual powers.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 6 2012-10-01 2012-10-01 false Residual powers. 1850.104 Section 1850.104 Federal Acquisition Regulations System NATIONAL AERONAUTICS AND SPACE ADMINISTRATION... 1850.104 Residual powers....

  13. 48 CFR 970.5001 - Residual powers.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 5 2012-10-01 2012-10-01 false Residual powers. 970.5001 Section 970.5001 Federal Acquisition Regulations System DEPARTMENT OF ENERGY AGENCY SUPPLEMENTARY....5001 Residual powers....

  14. 48 CFR 250.104 - Residual powers.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 3 2013-10-01 2013-10-01 false Residual powers. 250.104 Section 250.104 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT... Contractual Actions 250.104 Residual powers....

  15. 48 CFR 970.5001 - Residual powers.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 5 2013-10-01 2013-10-01 false Residual powers. 970.5001 Section 970.5001 Federal Acquisition Regulations System DEPARTMENT OF ENERGY AGENCY SUPPLEMENTARY....5001 Residual powers....

  16. 48 CFR 970.5001 - Residual powers.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Residual powers. 970.5001 Section 970.5001 Federal Acquisition Regulations System DEPARTMENT OF ENERGY AGENCY SUPPLEMENTARY....5001 Residual powers....

  17. 48 CFR 970.5001 - Residual powers.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false Residual powers. 970.5001 Section 970.5001 Federal Acquisition Regulations System DEPARTMENT OF ENERGY AGENCY SUPPLEMENTARY....5001 Residual powers....

  18. 48 CFR 1850.104 - Residual powers.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 6 2013-10-01 2013-10-01 false Residual powers. 1850.104 Section 1850.104 Federal Acquisition Regulations System NATIONAL AERONAUTICS AND SPACE ADMINISTRATION... 1850.104 Residual powers....

  19. 48 CFR 250.104 - Residual powers.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 3 2012-10-01 2012-10-01 false Residual powers. 250.104 Section 250.104 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT... Contractual Actions 250.104 Residual powers....

  20. 48 CFR 250.104 - Residual powers.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false Residual powers. 250.104 Section 250.104 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT... Contractual Actions 250.104 Residual powers....

  1. 48 CFR 970.5001 - Residual powers.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false Residual powers. 970.5001 Section 970.5001 Federal Acquisition Regulations System DEPARTMENT OF ENERGY AGENCY SUPPLEMENTARY....5001 Residual powers....

  2. 40 CFR 1065.705 - Residual and intermediate residual fuel.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... specifications for fuels meeting the definition of residual fuel in 40 CFR 80.2, including fuels marketed as...). Kinematic viscosity at 50 °C, max cSt 30.0 80.0 180.0 380.0 700.0 ISO 3104:1994/Cor 1:1997. Flash point, min... ISO 6245. Water, max (m3/m3)% 0.5 0.5 0.5 0.5 0.5 ISO 3733. Sulfur, max (kg/kg)% 3.50 4.00 4.50 4.50...

  3. 40 CFR 1065.705 - Residual and intermediate residual fuel.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... specifications for fuels meeting the definition of residual fuel in 40 CFR 80.2, including fuels marketed as...). Kinematic viscosity at 50 °C, max cSt 30.0 80.0 180.0 380.0 700.0 ISO 3104:1994/Cor 1:1997. Flash point, min... ISO 6245. Water, max (m3/m3)% 0.5 0.5 0.5 0.5 0.5 ISO 3733. Sulfur, max (kg/kg)% 3.50 4.00 4.50 4.50...

  4. 40 CFR 1065.705 - Residual and intermediate residual fuel.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... specifications for fuels meeting the definition of residual fuel in 40 CFR 80.2, including fuels marketed as...). Kinematic viscosity at 50 °C, max cSt 30.0 80.0 180.0 380.0 700.0 ISO 3104:1994/Cor 1:1997. Flash point, min... ISO 6245. Water, max (m3/m3)% 0.5 0.5 0.5 0.5 0.5 ISO 3733. Sulfur, max (kg/kg)% 3.50 4.00 4.50 4.50...

  5. 40 CFR 1065.705 - Residual and intermediate residual fuel.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... specifications for fuels meeting the definition of residual fuel in 40 CFR 80.2, including fuels marketed as...). Kinematic viscosity at 50 °C, max cSt 30.0 80.0 180.0 380.0 700.0 ISO 3104:1994/Cor 1:1997. Flash point, min... ISO 6245. Water, max (m3/m3)% 0.5 0.5 0.5 0.5 0.5 ISO 3733. Sulfur, max (kg/kg)% 3.50 4.00 4.50 4.50...

  6. SPECIATION OF ELEMENTS IN INCINERATION RESIDUES

    EPA Science Inventory

    Knowledge as to the speciation of elements in incineration residues is important for the successful management and utilization of the residues and for modelling and predicting their leaching behavior. s part of a larger research effort on speciation in combustion residues, ESP as...

  7. COMPOSITION AND DECOMPOSITION OF PEANUT RESIDUES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Limited information exists on the mineralizable nitrogen (N) content of peanut (Arachis hypogaea L.) residue. The objective of this study was to determine the N contribution of pre- and post harvest peanut residue on two soil types. Aboveground peanut residue (cv. Georgia Green) was collected prio...

  8. 9 CFR 311.39 - Biological residues.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 9 Animals and Animal Products 2 2014-01-01 2014-01-01 false Biological residues. 311.39 Section... Biological residues. Carcasses, organs, or other parts of carcasses of livestock shall be condemned if it is determined that they are adulterated because of the presence of any biological residues....

  9. 9 CFR 311.39 - Biological residues.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 9 Animals and Animal Products 2 2012-01-01 2012-01-01 false Biological residues. 311.39 Section... Biological residues. Carcasses, organs, or other parts of carcasses of livestock shall be condemned if it is determined that they are adulterated because of the presence of any biological residues....

  10. 9 CFR 311.39 - Biological residues.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 9 Animals and Animal Products 2 2013-01-01 2013-01-01 false Biological residues. 311.39 Section... Biological residues. Carcasses, organs, or other parts of carcasses of livestock shall be condemned if it is determined that they are adulterated because of the presence of any biological residues....

  11. 9 CFR 311.39 - Biological residues.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 false Biological residues. 311.39 Section... Biological residues. Carcasses, organs, or other parts of carcasses of livestock shall be condemned if it is determined that they are adulterated because of the presence of any biological residues....

  12. 9 CFR 311.39 - Biological residues.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Biological residues. 311.39 Section... Biological residues. Carcasses, organs, or other parts of carcasses of livestock shall be condemned if it is determined that they are adulterated because of the presence of any biological residues....

  13. Management of post-harvest residue blanket

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Timely and effective residue management is essential for maximum sugar yields. Several studies were implemented in 2003 and harvested in 2004 in an effort to increase the effectiveness of residue management practices. Six studies were conducted to determine the effect of residue removal timing a...

  14. 48 CFR 50.104 - Residual powers.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 1 2013-10-01 2013-10-01 false Residual powers. 50.104... EXTRAORDINARY CONTRACTUAL ACTIONS AND THE SAFETY ACT Extraordinary Contractual Actions 50.104 Residual powers. This section prescribes standards and procedures for exercising residual powers under Pub. L....

  15. 48 CFR 50.104 - Residual powers.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 1 2011-10-01 2011-10-01 false Residual powers. 50.104... EXTRAORDINARY CONTRACTUAL ACTIONS AND THE SAFETY ACT Extraordinary Contractual Actions 50.104 Residual powers. This section prescribes standards and procedures for exercising residual powers under Pub. L....

  16. 48 CFR 50.104 - Residual powers.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Residual powers. 50.104... EXTRAORDINARY CONTRACTUAL ACTIONS AND THE SAFETY ACT Extraordinary Contractual Actions 50.104 Residual powers. This section prescribes standards and procedures for exercising residual powers under Pub. L....

  17. 48 CFR 50.104 - Residual powers.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 1 2012-10-01 2012-10-01 false Residual powers. 50.104... EXTRAORDINARY CONTRACTUAL ACTIONS AND THE SAFETY ACT Extraordinary Contractual Actions 50.104 Residual powers. This section prescribes standards and procedures for exercising residual powers under Pub. L....

  18. 48 CFR 50.104 - Residual powers.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 1 2014-10-01 2014-10-01 false Residual powers. 50.104... EXTRAORDINARY CONTRACTUAL ACTIONS AND THE SAFETY ACT Extraordinary Contractual Actions 50.104 Residual powers. This section prescribes standards and procedures for exercising residual powers under Pub. L....

  19. Microbial degradation of post-harvest residues

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Management of post-harvest residues, produced during the green cane harvesting of sugarcane in Louisiana, has become an increasingly important issue for producers, particularly in areas where burning of the residues is banned or restricted. If the residues, which range from 4-8 tonnes per hectare, ...

  20. Notes on oscillator-like interactions of various spin relativistic particles

    NASA Technical Reports Server (NTRS)

    Dvoeglazov, Valeri V.; Delsolmesa, Antonio

    1995-01-01

    The equations for various spin particles with oscillator-like interactions are discussed in this talk. Topics discussed include: (1) comment on 'The Klein-Gordon Oscillator'; (2) the Dirac oscillator in quaternion form; (3) the Dirac-Dowker oscillator; (4) the Weinberg oscillator; and (5) note on the two-body Dirac oscillator.

  1. Recent developments in neutrino-nucleus interactions in 1 GeV energy region

    SciTech Connect

    Sobczyk, Jan T.

    2015-07-15

    Neutrino interactions in 1 GeV energy region are discussed. A role of nucleon-nucleon correlations in understanding recent quasi-elastic cross section measurements on nuclear target is explained. An importance of a correct treatment of two-body current contribution to the neutrino inclusive cross section is addressed.

  2. Notes on oscillator-like interactions of various spin relativistic particles

    SciTech Connect

    Dvoeglazov, V.V.; Delsolmesa, A.

    1995-01-01

    The equations for various spin particles with oscillator-like interactions are discussed in this talk. Topics discussed include: (1) comment on `The Klein-Gordon Oscillator`; (2) the Dirac oscillator in quaternion form; (3) the Dirac-Dowker oscillator; (4) the Weinberg oscillator; and (5) note on the two-body Dirac oscillator.

  3. Wood residues: trash or treasure

    SciTech Connect

    Bolgiano, C.

    1983-12-01

    Forest residues have acquired new economic value since the growth of the wood-energy markets has prompted private woodlot owners to begin managing and harvesting their forests after nearly a century of neglect. Estimates place half the commercial forests as overstocked, with poor-quality trees and unmarketable varieties, as well as standing dead or fallen trees and slash which are aesthetically bad. Overzealous cleansing of the forest floor, however, will deplete forests soils of nutrients and expose them to erosion in addition to destroying wildlife habitat. A compromise is needed to balance the ecological and economic benefits. (DCK)

  4. Process to recycle shredder residue

    DOEpatents

    Jody, Bassam J.; Daniels, Edward J.; Bonsignore, Patrick V.

    2001-01-01

    A system and process for recycling shredder residue, in which separating any polyurethane foam materials are first separated. Then separate a fines fraction of less than about 1/4 inch leaving a plastics-rich fraction. Thereafter, the plastics rich fraction is sequentially contacted with a series of solvents beginning with one or more of hexane or an alcohol to remove automotive fluids; acetone to remove ABS; one or more of EDC, THF or a ketone having a boiling point of not greater than about 125.degree. C. to remove PVC; and one or more of xylene or toluene to remove polypropylene and polyethylene. The solvents are recovered and recycled.

  5. Organochlorine residues in starlings, 1972.

    PubMed

    Nickerson, P R; Barbehenn, K R

    1975-03-01

    During the fall of 1972 starlings were collected from 130 sites in conjunction with the National Pesticide Monitoring Program. They were analyzed for DDT and its metabolites, dieldrin, heptachlor epoxide, benzene hexachloride, polychlorinated biphenyls and, for the first time in the series, oxychlordane and HCB. Mean DDT and dieldrin residue levels have declined significantly since 1967 and a regression analysis suggests that levels of DDT and its metabolites should fall below a mean of 0.1 ppm for the 1974 starling collection. PMID:1161450

  6. 40 CFR 180.519 - Bromide ion and residual bromine; tolerances for residues.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Bromide ion and residual bromine... Tolerances § 180.519 Bromide ion and residual bromine; tolerances for residues. (a) General. The food additives, bromide ion and residual bromine, may be present in water, potable in accordance with...

  7. 40 CFR 180.519 - Bromide ion and residual bromine; tolerances for residues.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Bromide ion and residual bromine... Tolerances § 180.519 Bromide ion and residual bromine; tolerances for residues. (a) General. The food additives, bromide ion and residual bromine, may be present in water, potable in accordance with...

  8. 40 CFR 180.519 - Bromide ion and residual bromine; tolerances for residues.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Bromide ion and residual bromine... Tolerances § 180.519 Bromide ion and residual bromine; tolerances for residues. (a) General. The food additives, bromide ion and residual bromine, may be present in water, potable in accordance with...

  9. 40 CFR 180.519 - Bromide ion and residual bromine; tolerances for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Bromide ion and residual bromine... Tolerances § 180.519 Bromide ion and residual bromine; tolerances for residues. (a) General. The food additives, bromide ion and residual bromine, may be present in water, potable in accordance with...

  10. 40 CFR 180.519 - Bromide ion and residual bromine; tolerances for residues.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Bromide ion and residual bromine... Tolerances § 180.519 Bromide ion and residual bromine; tolerances for residues. (a) General. The food additives, bromide ion and residual bromine, may be present in water, potable in accordance with...

  11. Managing residual limb hyperhidrosis in wounded warriors.

    PubMed

    Pace, Sarah; Kentosh, Joshua

    2016-06-01

    Residual limb dermatologic problems are a common concern among young active traumatic amputee patients who strive to maintain an active lifestyle. Hyperhidrosis of residual limbs is a recognized inciting factor that often contributes to residual limb dermatoses and is driven by the design of the prosthetic liner covering the residual limb. Treatment of hyperhidrosis in this population presents a unique challenge. Several accepted treatments of hyperhidrosis can offer some relief but have been limited by lack of results or side-effect profiles. Microwave thermal ablation has presented an enticing potential for residual limb hyperhidrosis. PMID:27416083

  12. Fiber-optic polymer residue monitor

    SciTech Connect

    Pfeifer, K.B.; Jarecki, R.L. Jr.; Dalton, T.J.

    1998-10-01

    Semiconductor processing tools that use a plasma to etch polysilicon or oxides produce residue polymers that build up on the exposed surfaces of the processing chamber. These residues are generally stressed and with time can cause flaking onto wafers resulting in yield loss. Currently, residue buildup is not monitored, and chambers are cleaned at regular intervals resulting in excess downtime for the tool. In addition, knowledge of the residue buildup rate and index of refraction is useful in determining the state of health of the chamber process. The authors have developed a novel optical fiber-based robust sensor that allows measurement of the residue polymer buildup while not affecting the plasma process.

  13. Effects of retardation in relativistic equations with confining interaction

    NASA Technical Reports Server (NTRS)

    Maung, Khin Maung; Kahana, David E.; Norbury, John W.

    1992-01-01

    A method has been developed for solving two body relativistic bound state equations in momentum space with a confining interaction. A total of six different three dimensional reductions of the Bethe-Salpeter equations are studied with particular emphasis placed on the competing roles of relativistic kinematics and retardation. The results indicate that these two effects counteract each other and this sheds some light on why nonrelativistic models of meson spectroscopy have been quite successful.

  14. Microscopic approach for the n - d effective interaction

    SciTech Connect

    Tomio, L. ); Frederico, T. ); Delfino, A. )

    1990-03-01

    A three-boson model is applied to the nucleon-deuteron ({ital n}-{ital d}) system to construct an effective energy-dependent two-body potential in configuration space. The three-nucleon observables at low energy are well reproduced with just one free parameter (related with the range of the nucleon-nucleon interaction). We show that the present results give support to a previous phenomenological {ital n}-{ital d} potential.

  15. 40 CFR 180.432 - Lactofen; tolerances for residues.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Lactofen; tolerances for residues. (a) General. Tolerances are established for residues of the herbicide... for residues of the herbicide lactofen, including its metabolites and degradates, in or on...

  16. 40 CFR 180.432 - Lactofen; tolerances for residues.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Lactofen; tolerances for residues. (a) General. Tolerances are established for residues of the herbicide... for residues of the herbicide lactofen, including its metabolites and degradates, in or on...

  17. 40 CFR 180.432 - Lactofen; tolerances for residues.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Lactofen; tolerances for residues. (a) General. Tolerances are established for residues of the herbicide... for residues of the herbicide lactofen, including its metabolites and degradates, in or on...

  18. 40 CFR 180.432 - Lactofen; tolerances for residues.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Lactofen; tolerances for residues. (a) General. Tolerances are established for residues of the herbicide... for residues of the herbicide lactofen, including its metabolites and degradates, in or on...

  19. RESIDUAL STRESSES IN 3013 CONTAINERS

    SciTech Connect

    Mickalonis, J.; Dunn, K.

    2009-11-10

    The DOE Complex is packaging plutonium-bearing materials for storage and eventual disposition or disposal. The materials are handled according to the DOE-STD-3013 which outlines general requirements for stabilization, packaging and long-term storage. The storage vessels for the plutonium-bearing materials are termed 3013 containers. Stress corrosion cracking has been identified as a potential container degradation mode and this work determined that the residual stresses in the containers are sufficient to support such cracking. Sections of the 3013 outer, inner, and convenience containers, in both the as-fabricated condition and the closure welded condition, were evaluated per ASTM standard G-36. The standard requires exposure to a boiling magnesium chloride solution, which is an aggressive testing solution. Tests in a less aggressive 40% calcium chloride solution were also conducted. These tests were used to reveal the relative stress corrosion cracking susceptibility of the as fabricated 3013 containers. Significant cracking was observed in all containers in areas near welds and transitions in the container diameter. Stress corrosion cracks developed in both the lid and the body of gas tungsten arc welded and laser closure welded containers. The development of stress corrosion cracks in the as-fabricated and in the closure welded container samples demonstrates that the residual stresses in the 3013 containers are sufficient to support stress corrosion cracking if the environmental conditions inside the containers do not preclude the cracking process.

  20. Residual number processing in dyscalculia.

    PubMed

    Cappelletti, Marinella; Price, Cathy J

    2014-01-01

    Developmental dyscalculia - a congenital learning disability in understanding numerical concepts - is typically associated with parietal lobe abnormality. However, people with dyscalculia often retain some residual numerical abilities, reported in studies that otherwise focused on abnormalities in the dyscalculic brain. Here we took a different perspective by focusing on brain regions that support residual number processing in dyscalculia. All participants accurately performed semantic and categorical colour-decision tasks with numerical and non-numerical stimuli, with adults with dyscalculia performing slower than controls in the number semantic tasks only. Structural imaging showed less grey-matter volume in the right parietal cortex in people with dyscalculia relative to controls. Functional MRI showed that accurate number semantic judgements were maintained by parietal and inferior frontal activations that were common to adults with dyscalculia and controls, with higher activation for participants with dyscalculia than controls in the right superior frontal cortex and the left inferior frontal sulcus. Enhanced activation in these frontal areas was driven by people with dyscalculia who made faster rather than slower numerical decisions; however, activation could not be accounted for by response times per se, because it was greater for fast relative to slow dyscalculics but not greater for fast controls relative to slow dyscalculics. In conclusion, our results reveal two frontal brain regions that support efficient number processing in dyscalculia. PMID:24266008

  1. Optimization of machining and vibration parameters for residual stresses minimization in ultrasonic assisted turning of 4340 hardened steel.

    PubMed

    Sharma, Varun; Pandey, Pulak M

    2016-08-01

    The residual stresses generated in the machined work piece have detrimental effect on fatigue life, corrosion resistance and tribological properties. However, the effect of cutting and vibration parameters on residual stresses in Ultrasonic Assisted Turning (UAT) has not been dealt with. The present paper highlights the effect of feed rate, depth of cut, cutting velocity and percentage intensity of ultrasonic power on residual stress generation. XRD analysis has been carried out to measure the residual stress while turning 4340 hardened steel using UAT. The experiments were performed based on response surface methodology to develop statistical model for residual stress. The outcome of ANOVA revealed that percentage intensity and feed rate significantly affect the residual stress generation. The significant interactions between process parameters have also been presented tin order to understand the thermo-mechanical mechanism responsible for residual stress generation. PMID:27179142

  2. Protein-Protein Docking with Dynamic Residue Protonation States

    PubMed Central

    Kilambi, Krishna Praneeth; Reddy, Kavan; Gray, Jeffrey J.

    2014-01-01

    Protein-protein interactions depend on a host of environmental factors. Local pH conditions influence the interactions through the protonation states of the ionizable residues that can change upon binding. In this work, we present a pH-sensitive docking approach, pHDock, that can sample side-chain protonation states of five ionizable residues (Asp, Glu, His, Tyr, Lys) on-the-fly during the docking simulation. pHDock produces successful local docking funnels in approximately half (79/161) the protein complexes, including 19 cases where standard RosettaDock fails. pHDock also performs better than the two control cases comprising docking at pH 7.0 or using fixed, predetermined protonation states. On average, the top-ranked pHDock structures have lower interface RMSDs and recover more native interface residue-residue contacts and hydrogen bonds compared to RosettaDock. Addition of backbone flexibility using a computationally-generated conformational ensemble further improves native contact and hydrogen bond recovery in the top-ranked structures. Although pHDock is designed to improve docking, it also successfully predicts a large pH-dependent binding affinity change in the Fc–FcRn complex, suggesting that it can be exploited to improve affinity predictions. The approaches in the study contribute to the goal of structural simulations of whole-cell protein-protein interactions including all the environmental factors, and they can be further expanded for pH-sensitive protein design. PMID:25501663

  3. Discrete structural features among interface residue-level classes

    PubMed Central

    2015-01-01

    Background Protein-protein interaction (PPI) is essential for molecular functions in biological cells. Investigation on protein interfaces of known complexes is an important step towards deciphering the driving forces of PPIs. Each PPI complex is specific, sensitive and selective to binding. Therefore, we have estimated the relative difference in percentage of polar residues between surface and the interface for each complex in a non-redundant heterodimer dataset of 278 complexes to understand the predominant forces driving binding. Results Our analysis showed ~60% of protein complexes with surface polarity greater than interface polarity (designated as class A). However, a considerable number of complexes (~40%) have interface polarity greater than surface polarity, (designated as class B), with a significantly different p-value of 1.66E-45 from class A. Comprehensive analyses of protein complexes show that interface features such as interface area, interface polarity abundance, solvation free energy gain upon interface formation, binding energy and the percentage of interface charged residue abundance distinguish among class A and class B complexes, while electrostatic visualization maps also help differentiate interface classes among complexes. Conclusions Class A complexes are classical with abundant non-polar interactions at the interface; however class B complexes have abundant polar interactions at the interface, similar to protein surface characteristics. Five physicochemical interface features analyzed from the protein heterodimer dataset are discriminatory among the interface residue-level classes. These novel observations find application in developing residue-level models for protein-protein binding prediction, protein-protein docking studies and interface inhibitor design as drugs. PMID:26679043

  4. Effective Interactions from No Core Shell Model

    SciTech Connect

    Dikmen, E.; Lisetskiy, A. F.; Barrett, B. R.; Navratil, P.; Vary, J. P.

    2008-11-11

    We construct the many-body effective Hamiltonian for pf-shell by carrying out 2({Dirac_h}/2{pi}){omega}. NCSM calculations at the 2-body cluster level. We demonstrate how the effective Hamiltonian derived from realistic nucleon-nucleon (NN) potentials for the 2({Dirac_h}/2{pi}){omega} NCSM space should be modified to properly account for the many-body correlations produced by truncating to the major pf-shell. We obtain two-body effective interactions for the pf-shell by using direct projection and use them to reproduce the results of large scale NCSM for other light Ca isotopes.

  5. Positive selection moments identify potential functional residues in human olfactory receptors

    NASA Technical Reports Server (NTRS)

    Singer, M. S.; Weisinger-Lewin, Y.; Lancet, D.; Shepherd, G. M.

    1996-01-01

    Correlated mutation analysis and molecular models of olfactory receptors have provided evidence that residues in the transmembrane domains form a binding pocket for odor ligands. As an independent test of these results, we have calculated positive selection moments for the alpha-helical sixth transmembrane domain (TM6) of human olfactory receptors. The moments can be used to identify residues that have been preferentially affected by positive selection and are thus likely to interact with odor ligands. The results suggest that residue 622, which is commonly a serine or threonine, could form critical H-bonds. In some receptors a dual-serine subsite, formed by residues 622 and 625, could bind hydroxyl determinants on odor ligands. The potential importance of these residues is further supported by site-directed mutagenesis in the beta-adrenergic receptor. The findings should be of practical value for future physiological studies, binding assays, and site-directed mutagenesis.

  6. Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis

    NASA Technical Reports Server (NTRS)

    Singer, M. S.; Oliveira, L.; Vriend, G.; Shepherd, G. M.

    1995-01-01

    A family of G-protein-coupled receptors is believed to mediate the recognition of odor molecules. In order to identify potential ligand-binding residues, we have applied correlated mutation analysis to receptor sequences from the rat. This method identifies pairs of sequence positions where residues remain conserved or mutate in tandem, thereby suggesting structural or functional importance. The analysis supported molecular modeling studies in suggesting several residues in positions that were consistent with ligand-binding function. Two of these positions, dominated by histidine residues, may play important roles in ligand binding and could confer broad specificity to mammalian odor receptors. The presence of positive (overdominant) selection at some of the identified positions provides additional evidence for roles in ligand binding. Higher-order groups of correlated residues were also observed. Each group may interact with an individual ligand determinant, and combinations of these groups may provide a multi-dimensional mechanism for receptor diversity.

  7. Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation

    NASA Astrophysics Data System (ADS)

    Pandey, R. B.; Farmer, B. L.

    2009-01-01

    Energy, mobility, and structural profiles of residues in a specific sequence of human immunodeficiency virus (HIV)-1 protease chain and its global conformation and dynamics are studied by a coarse-grained computer simulation model on a cubic lattice. HIV-1 protease is described by a chain of 99 residues (nodes) in a specific sequence (1DIFA) with N- and C-terminals on the lattice, where empty lattice sites represent an effective solvent medium. Internal structures of the residues are ignored but their specificities are captured via an interaction (ɛij) matrix (residue-residue, residue-solvent) of the coefficient (fɛij) of the Lennard-Jones potential. Simulations are performed for a range of interaction strength (f ) with the solvent-residue interaction describing the quality of the solvent. Snapshots of the protein show considerable changes in the conformation of the protein on varying the interaction. From the mobility and energy profiles of the residues, it is possible to identify the active (and not so active) segments of the protein and consequently their role in proteolysis. Contrary to interaction thermodynamics, the hydrophobic residues possess higher configurational energy and lower mobility while the electrostatic and polar residues are more mobile despite their lower interaction energy. Segments of hydrophobic core residues, crucial for the structural evolution of the protein are identified—some of which are consistent with recent molecular dynamics simulation in context to possible clinical observations. Global energy and radius of gyration of the protein exhibit nonmonotonic dependence on the interaction strength (f) with opposite trends, e.g., rapid transition into globular structure with higher energy. Variations of the rms displacement of the protein and that of a tracer residue, Gly49, with the time steps show how they slow down on increasing the interaction strength.

  8. Residual mode filters and adaptive control in large space structures

    NASA Technical Reports Server (NTRS)

    Davidson, Roger A.; Balas, Mark J.

    1989-01-01

    One of the most difficult problems in controlling large systems and structures is compensating for the destructive interaction which can occur between the reduced-order model (ROM) of the plant, which is used by the controller, and the unmodeled dynamics of the plant, often called the residual modes. The problem is more significant in the case of large space structures because their naturally light damping and high performance requirements lead to more frequent, destructive residual mode interaction (RMI). Using the design/compensation technique of residual mode filters (RMF's), effective compensation of RMI can be accomplished in a straightforward manner when using linear controllers. The use of RMF's has been shown to be effective for a variety of large structures, including a space-based laser and infinite dimensional systems. However, the dynamics of space structures is often uncertain and may even change over time due to on-orbit erosion from space debris and corrosive chemicals in the upper atmosphere. In this case, adaptive control can be extremely beneficial in meeting the performance requirements of the structure. Adaptive control for large structures is also based on ROM's and so destructive RMI may occur. Unfortunately, adaptive control is inherently nonlinear, and therefore the known results of RMF's cannot be applied. The purpose is to present the results of new research showing the effects of RMI when using adaptive control and the work which will hopefully lead to RMF compensation of this problem.

  9. Microscopic theory of the residual surface resistivity of Rashba electrons

    NASA Astrophysics Data System (ADS)

    Bouaziz, Juba; Lounis, Samir; Blügel, Stefan; Ishida, Hiroshi

    2016-07-01

    A microscopic expression of the residual electrical resistivity tensor is derived in linear response theory for Rashba electrons scattering at a magnetic impurity with cylindrical or noncylindrical potential. The behavior of the longitudinal and transversal residual resistivity is obtained analytically and computed for an Fe impurity at the Au(111) surface. We studied the evolution of the resistivity tensor elements as a function of the Rashba spin-orbit strength and the magnetization direction of the impurity. We found that the absolute values of longitudinal resistivity reduce with increasing spin-orbit strength of the substrate and that the scattering of the conduction electrons at magnetic impurities with magnetic moments pointing in directions not perpendicular to the surface plane produce a planar Hall effect and an anisotropic magnetoresistance even if the impurity carries no spin-orbit interaction. Functional forms are provided describing the anisotropy of the planar Hall effect and the anisotropic magnetoresistance with respect to the direction of the impurity moment. In the limit of no spin-orbit interaction and a nonmagnetic impurity of cylindrical symmetry, the expression of the residual resistivity of a two-dimensional electron gas has the same simplicity and form as for the three-dimensional electron gas [J. Friedel, J. Nuovo. Cim. 7, 287 (1958), 10.1007/BF02751483] and can also be expressed in terms of scattering phase shifts.

  10. Conformational basis of the effect of cleavage of neurophysin residues 1-8 on neurophysin function

    SciTech Connect

    Breslow, E.; Peyton, D.; Sardana, V.

    1986-05-01

    Tryptic cleavage of neurophysin residues 1-8 leads to a marked reduction in the affinity of neurophysin for peptide hormone analogs, an effect attributable to loss of residues 7 and 8. The authors have studied the basis of this effect by proton NMR spectroscopy. In contrast to results elsewhere, the NMR data indicate that the des 1-8 protein quantitatively retains the ability of the native protein to self-associate. However, the effect of self-association on the behavior of Tyr-49 is markedly and specifically altered in the des 1-8 protein. Studies of the binding of perdeuterated peptides to the native and des 1-8 proteins demonstrate that, in the bound state, peptide residue 1 is proximal to the Tyr-49 ring and peptide residue 3 adjacent to the 1-8 sequence. Binding is shown to perturb residue 9. The results interpreted by a model placing Tyr-49 in simultaneous proximity to residues 7 and 8, to the subunit interface and to bound peptide, loss of stabilizing interactions with residues 7 and 8 altering the interactions of Tyr-49 with the subunit interface and the free energy difference between bound and unbound states. The results additionally suggest that bound peptide is proximal to the subunit interface, possibly accounting for the stronger binding of peptide by the neurophysin dimer than by the monomer.

  11. Computer modeling of the neurotoxin binding site of acetylcholine receptor spanning residues 185 through 196

    NASA Technical Reports Server (NTRS)

    Garduno-Juarez, R.; Shibata, M.; Zielinski, T. J.; Rein, R.

    1987-01-01

    A model of the complex between the acetylcholine receptor and the snake neurotoxin, cobratoxin, was built by molecular model building and energy optimization techniques. The experimentally identified functionally important residues of cobratoxin and the dodecapeptide corresponding to the residues 185-196 of acetylcholine receptor alpha subunit were used to build the model. Both cis and trans conformers of cyclic L-cystine portion of the dodecapeptide were examined. Binding residues independently identified on cobratoxin are shown to interact with the dodecapeptide AChR model.

  12. Quantum Phase Coherence in Mesoscopic Transport Devices with Two-Particle Interaction.

    PubMed

    Wang, Zhimei; Guo, Xiaofang; Xue, Haibin; Xue, Naitao; Liang, J-Q

    2015-01-01

    In this paper we demonstrate a new type of quantum phase coherence (QPC), which is generated by the two-body interaction. This conclusion is based on quantum master equation analysis for the full counting statistics of electron transport through two parallel quantum-dots with antiparallel magnetic fluxes in order to eliminate the Aharonov-Bohm interference of either single-particle or non-interacting two-particle wave functions. The interacting two-particle QPC is realized by the flux-dependent oscillation of the zero-frequency cumulants including the shot noise and skewness with a characteristic period. The accurately quantized peaks of cumulant spectrum may have technical applications to probe the two-body Coulomb interaction. PMID:26255858

  13. Quantum Phase Coherence in Mesoscopic Transport Devices with Two-Particle Interaction

    NASA Astrophysics Data System (ADS)

    Wang, Zhimei; Guo, Xiaofang; Xue, Haibin; Xue, Naitao; Liang, J.-Q.

    2015-08-01

    In this paper we demonstrate a new type of quantum phase coherence (QPC), which is generated by the two-body interaction. This conclusion is based on quantum master equation analysis for the full counting statistics of electron transport through two parallel quantum-dots with antiparallel magnetic fluxes in order to eliminate the Aharonov-Bohm interference of either single-particle or non-interacting two-particle wave functions. The interacting two-particle QPC is realized by the flux-dependent oscillation of the zero-frequency cumulants including the shot noise and skewness with a characteristic period. The accurately quantized peaks of cumulant spectrum may have technical applications to probe the two-body Coulomb interaction.

  14. Quantum Phase Coherence in Mesoscopic Transport Devices with Two-Particle Interaction

    PubMed Central

    Wang, Zhimei; Guo, Xiaofang; Xue, Haibin; Xue, Naitao; Liang, J.-Q.

    2015-01-01

    In this paper we demonstrate a new type of quantum phase coherence (QPC), which is generated by the two-body interaction. This conclusion is based on quantum master equation analysis for the full counting statistics of electron transport through two parallel quantum-dots with antiparallel magnetic fluxes in order to eliminate the Aharonov-Bohm interference of either single-particle or non-interacting two-particle wave functions. The interacting two-particle QPC is realized by the flux-dependent oscillation of the zero-frequency cumulants including the shot noise and skewness with a characteristic period. The accurately quantized peaks of cumulant spectrum may have technical applications to probe the two-body Coulomb interaction. PMID:26255858

  15. Regular versus chaotic dynamics in closed systems of interacting Fermi particles

    SciTech Connect

    Izrailev, F.M.; Castaneda-Mendoza, A.

    2005-07-08

    We discuss dynamical properties of strongly interacting Fermi-particles. Main attention is paid to the evolution of wave packets in the many-particle basis of non-interacting particles. Specifically, we analyze the time dependence of the return probability and the Shannon entropy of packets. We start with the model of two-body random interaction which allows us to obtain analytical expression for the time dependence of the above quantities. Analytical results are compared with numerical data obtained in direct simulation of the wave packet dynamics. To understand to what extent these results are generic, we have considered the spin model of a quantum computation with a non-random (dynamical) interaction between spins. We have found that the linear increase of the Shannon entropy observed in the two-body random model, occurs, under some conditions, in the dynamical model. Finally, we have analyzed the role of weak external perturbation taken in the form of static disorder.

  16. Residual stress patterns in steel welds

    SciTech Connect

    Spooner, S.; Hubbard, C.R.; Wang, X.L.; David, S.A.; Holden, T.M.; Root, J.H.; Swainson, I.

    1994-12-31

    Neutron strain scanning of residual stress is a valuable nondestructive tool for evaluation of residual stress in welds. The penetrating characteristic of neutrons permits mapping of strain patterns with a spatial resolution approaching 1mm at depths of 20mm in steels. While the overall patterns of the residual stress tensor in a weld are understood, the detailed patterns depend on welding process parameters and the effects of solid state transformation. The residual strain profiles in two multi-pass austenitic welds and a ferritic steel weld are presented. The stress-free lattice parameters within the fusion zone and the adjacent heat affected zone in the two austenitic welds show that the interpretation of residual stress from strains are affected by welding parameters. An interpretation of the residual strain pattern in the ferritic steel plate can be made using the strain measurements of a Gleeble test bar which has undergone the solid state austenite decomposition.

  17. Carbohydrate–Aromatic Interactions in Proteins

    PubMed Central

    2015-01-01

    Protein–carbohydrate interactions play pivotal roles in health and disease. However, defining and manipulating these interactions has been hindered by an incomplete understanding of the underlying fundamental forces. To elucidate common and discriminating features in carbohydrate recognition, we have analyzed quantitatively X-ray crystal structures of proteins with noncovalently bound carbohydrates. Within the carbohydrate-binding pockets, aliphatic hydrophobic residues are disfavored, whereas aromatic side chains are enriched. The greatest preference is for tryptophan with an increased prevalence of 9-fold. Variations in the spatial orientation of amino acids around different monosaccharides indicate specific carbohydrate C–H bonds interact preferentially with aromatic residues. These preferences are consistent with the electronic properties of both the carbohydrate C–H bonds and the aromatic residues. Those carbohydrates that present patches of electropositive saccharide C–H bonds engage more often in CH−π interactions involving electron-rich aromatic partners. These electronic effects are also manifested when carbohydrate–aromatic interactions are monitored in solution: NMR analysis indicates that indole favorably binds to electron-poor C–H bonds of model carbohydrates, and a clear linear free energy relationships with substituted indoles supports the importance of complementary electronic effects in driving protein–carbohydrate interactions. Together, our data indicate that electrostatic and electronic complementarity between carbohydrates and aromatic residues play key roles in driving protein–carbohydrate complexation. Moreover, these weak noncovalent interactions influence which saccharide residues bind to proteins, and how they are positioned within carbohydrate-binding sites. PMID:26561965

  18. Intramolecular interactions in pancreatic ribonucleases.

    PubMed

    Kolbanovskaya EYu; Sathyanarayana, B K; Wlodawer, A; Karpeisky MYa

    1992-08-01

    A detailed analysis of the composition and properties of hydrophobic nuclei and microclusters in pancreatic ribonuclease A (RNase A) has been carried out. Distance calculations for all noncovalently bonded atoms revealed that the average number of nonpolar contacts between a side chain of an amino acid and its neighbors is substantially larger if it involves hydrophobic residues rather than nonhydrophobic ones. However, the difference decreased when the number of contacts per nonpolar group and/or atom were calculated. Three main nuclei and five microclusters were identified, and their quantitative parameters were calculated. These nuclei include hydrophobic residues with a substantial number of nonpolar contacts with the environment (Phe 8, Phe 120, Phe 46, Tyr 25, Tyr 97, Ile 107, Leu 35, Ile 81, Val 54, Val 108, Met 29, Met 30). Hydrophobic nuclei of RNase A differ in shape and in composition, in the number of intranuclear contacts and of associated residues, as well as in their internal mobility. All eight cysteine residues are involved in nonpolar interactions with amino acid residues of hydrophobic nuclei. Active site amino acid residues of RNase A form a noncovalent contact network comprised of themselves, as well as of many conserved residues from hydrophobic nuclei. Sequence alignment with some other members of the RNase A family of proteins shows remarkable similarity in positions and in conservation of the main nonpolar residues, comprising cores of two (out of three) hydrophobic nuclei. A correlation was shown to exist between the average density of contacts for side-chain atoms and the number of amino acids to be found in the appropriate positions in the sequences of related mammalian ribonucleases. However, there are certain amino acid positions in the third, smaller nucleus, which are highly variable within the family. Taking into account that this nucleus is composed of residues belonging to different elements of the secondary structure, it is

  19. Optical systolic array processor using residue arithmetic

    NASA Technical Reports Server (NTRS)

    Jackson, J.; Casasent, D.

    1983-01-01

    The use of residue arithmetic to increase the accuracy and reduce the dynamic range requirements of optical matrix-vector processors is evaluated. It is determined that matrix-vector operations and iterative algorithms can be performed totally in residue notation. A new parallel residue quantizer circuit is developed which significantly improves the performance of the systolic array feedback processor. Results are presented of a computer simulation of this system used to solve a set of three simultaneous equations.

  20. Quantitative residue-level structure-evolution relationships in the yeast membrane proteome.

    PubMed

    Franzosa, Eric A; Xue, Ran; Xia, Yu

    2013-01-01

    Membrane proteins exist in distinctly different environments than do soluble proteins, resulting in differences between their respective biophysical and evolutionary properties. In comparison with soluble proteins, relatively little is known about how the unique biophysical properties of membrane proteins affect their evolutionary properties at the residue level. In particular, transmembrane (TM) regions of membrane proteins tend to be more conserved than regions outside of the membrane (extramembrane [EM] regions), but the mechanisms underlying this phenomenon are not well understood. Here, we combine homology-based high-resolution three-dimensional protein models with rigorous evolutionary rate calculations to quantitatively assess residue-level structure-evolution relationships in the yeast membrane proteome. We find that residue evolutionary rate increases linearly with decreasing residue burial, regardless of the hydrophobic or hydrophilic nature of the solvent environment. This finding supports a direct relationship between a residue's selective constraint and the extent of its packing interactions with neighboring residues, independent of hydrophobic effects. Most importantly, for a fixed degree of burial, residues from TM regions tend to evolve more slowly than residues from EM regions. We attribute this difference to the increased importance of packing constraints and the decreased importance of hydrophobic effects in TM regions. This additional selective constraint on TM residues plays a dominant role in explaining why TM regions evolve more slowly than EM regions. In addition to revealing the universality of the linear relationship between residue burial and selective constraint across solvent environments, our work highlights the distinct residue-level evolutionary consequences imposed by the unique biophysical properties of the membrane environment. PMID:23512408

  1. Quantification of Drive-Response Relationships Between Residues During Protein Folding

    PubMed Central

    Qi, Yifei; Im, Wonpil

    2013-01-01

    Mutual correlation and cooperativity are commonly used to describe residue-residue interactions in protein folding/function. However, these metrics do not provide any information on the causality relationships between residues. Such drive-response relationships are poorly studied in protein folding/function and difficult to measure experimentally due to technical limitations. In this study, using the information theory transfer entropy (TE) that provides a direct measurement of causality between two times series, we have quantified the drive-response relationships between residues in the folding/unfolding processes of four small proteins generated by molecular dynamics simulations. Instead of using a time-averaged single TE value, the time-dependent TE is measured with the Q-scores based on residue-residue contacts and with the statistical significance analysis along the folding/unfolding processes. The TE analysis is able to identify the driving and responding residues that are different from the highly correlated residues revealed by the mutual information analysis. In general, the driving residues have more regular secondary structures, are more buried, and show greater effects on the protein stability as well as folding and unfolding rates. In addition, the dominant driving and responding residues from the TE analysis on the whole trajectory agree with those on a single folding event, demonstrating that the drive-response relationships are preserved in the non-equilibrium process. Our study provides detailed insights into the protein folding process and has potential applications in protein engineering and interpretation of time-dependent residue-based experimental observables for protein function. PMID:24223527

  2. Identification of kinetically hot residues in proteins.

    PubMed Central

    Demirel, M. C.; Atilgan, A. R.; Jernigan, R. L.; Erman, B.; Bahar, I.

    1998-01-01

    A number of recent studies called attention to the presence of kinetically important residues underlying the formation and stabilization of folding nuclei in proteins, and to the possible existence of a correlation between conserved residues and those participating in the folding nuclei. Here, we use the Gaussian network model (GNM), which recently proved useful in describing the dynamic characteristics of proteins for identifying the kinetically hot residues in folded structures. These are the residues involved in the highest frequency fluctuations near the native state coordinates. Their high frequency is a manifestation of the steepness of the energy landscape near their native state positions. The theory is applied to a series of proteins whose kinetically important residues have been extensively explored: chymotrypsin inhibitor 2, cytochrome c, and related C2 proteins. Most of the residues previously pointed out to underlie the folding process of these proteins, and to be critically important for the stabilization of the tertiary fold, are correctly identified, indicating a correlation between the kinetic hot spots and the early forming structural elements in proteins. Additionally, a strong correlation between kinetically hot residues and loci of conserved residues is observed. Finally, residues that may be important for the stability of the tertiary structure of CheY are proposed. PMID:9865946

  3. Particulate residue separators for harvesting devices

    DOEpatents

    Hoskinson, Reed L.; Kenney, Kevin L.; Wright, Christopher T.; Hess, John R.

    2010-06-29

    A particulate residue separator and a method for separating a particulate residue stream may include a plenum borne by a harvesting device, and have a first, intake end and a second, exhaust end; first and second particulate residue air streams which are formed by the harvesting device and which travel, at least in part, along the plenum and in a direction of the second, exhaust end; and a baffle assembly which is located in partially occluding relation relative to the plenum, and which substantially separates the first and second particulate residue air streams.

  4. Methods of separating particulate residue streams

    DOEpatents

    Hoskinson, Reed L.; Kenney, Kevin L.; Wright, Christopher T.; Hess, J. Richard

    2011-04-05

    A particulate residue separator and a method for separating a particulate residue stream may include an air plenum borne by a harvesting device, and have a first, intake end and a second, exhaust end; first and second particulate residue air streams that are formed by the harvesting device and that travel, at least in part, along the air plenum and in a direction of the second, exhaust end; and a baffle assembly that is located in partially occluding relation relative to the air plenum and that substantially separates the first and second particulate residue air streams.

  5. Mapping wave breaking and residual foam using infrared remote sensing

    NASA Astrophysics Data System (ADS)

    Carini, R. J.; Jessup, A. T.; Chickadel, C.

    2012-12-01

    Quantifying wave breaking in the surfzone is important for the advancement of models that seek to accurately predict energy dissipation, near-shore circulation, wave-current interactions, and air-sea gas transfer. Electro-optical remote sensing has been used to try to identify breaking waves. However, the residual foam, left over after the wave has broken, is indistinguishable from active foam in the visible band, which makes identification of active breaking difficult. Here, we explore infrared remote sensing of breaking waves at near-grazing incidence angles to differentiate between active and residual foam in the surfzone. Measurements were made at two field sites: Duck, NC, in September 2010 (Surf Zone Optics) and New River Inlet, NC, in May 2012 (RIVET). At both sites, multiple IR cameras were mounted to a tower onshore, viewing the surfzone at near-grazing incidence angles. For near-grazing incidence angles, small changes in viewing angle, such as those produced by the slope of a wave face, cause large modulations of the infrared signal. Therefore, the passage of waves can be seen in IR imagery. Wave breaking, however, is identified by the resulting foam. Foam has a higher emissivity than undisturbed water and thus appears warmer in an IR image. Residual foam cools quickly [Marmorino and Smith, 2005], thereby making its signal distinct from that of foam produced during active wave breaking. We will use these properties to develop a technique to produce spatial and temporal maps of active breaking and residual foam. These products can then be used to validate current models of surfzone bubbles and foam coverage. From the maps, we can also estimate energy dissipation due to wave breaking in the surfzone and compare this to estimates made with in situ data.; Infrared image of the surfzone at Duck, NC. Examples of actively breaking foam and cool residual foam are labeled.

  6. Induction of Soil Suppressiveness Against Rhizoctonia solani by Incorporation of Dried Plant Residues into Soil.

    PubMed

    Kasuya, Masahiro; Olivier, Andriantsoa R; Ota, Yoko; Tojo, Motoaki; Honjo, Hitoshi; Fukui, Ryo

    2006-12-01

    ABSTRACT Suppressive effects of soil amendment with residues of 12 cultivars of Brassica rapa on damping-off of sugar beet were evaluated in soils infested with Rhizoctonia solani. Residues of clover and peanut were tested as noncruciferous controls. The incidence of damping-off was significantly and consistently suppressed in the soils amended with residues of clover, peanut, and B. rapa subsp. rapifera 'Saori', but only the volatile substance produced from water-imbibed residue of cv. Saori exhibited a distinct inhibitory effect on mycelial growth of R. solani. Nonetheless, disease suppression in such residue-amended soils was diminished or nullified when antibacterial antibiotics were applied to the soils, suggesting that proliferation of antagonistic bacteria resident to the soils were responsible for disease suppression. When the seed (pericarps) colonized by R. solani in the infested soil without residues were replanted into the soils amended with such residues, damping-off was suppressed in all cases. In contrast, when seed that had been colonized by microorganisms in the soils containing the residues were replanted into the infested soil, damping-off was not suppressed. The evidence indicates that the laimosphere, but not the spermosphere, is the site for the antagonistic microbial interaction, which is the chief principle of soil suppressiveness against Rhizoctonia damping-off. PMID:18943670

  7. Rotons in Interacting Ultracold Bose Gases

    SciTech Connect

    Cormack, Samuel C.; Schumayer, Daniel; Hutchinson, David A. W.

    2011-09-30

    In three dimensions, noninteracting bosons undergo Bose-Einstein condensation at a critical temperature, T{sub c}, which is slightly shifted by {Delta}T{sub c}, if the particles interact. We calculate the excitation spectrum of interacting Bose systems, {sup 4}He and {sup 87}Rb, and show that a roton minimum emerges in the spectrum above a threshold value of the gas parameter. We provide a general theoretical argument for why the roton minimum and the maximal upward critical temperature shift are related. We also suggest two experimental avenues to observe rotons in condensates. These results, based upon a path-integral Monte Carlo approach, provide a microscopic explanation of the shift in the critical temperature and also show that a roton minimum does emerge in the excitation spectrum of particles with a structureless, short-range, two-body interaction.

  8. Correlations of excited states for sd bosons in the presence of random interactions

    SciTech Connect

    Lei, Y.; Zhao, Y. M.; Yoshida, N.; Arima, A.

    2011-04-15

    In this work we study the yrast states of sd-boson systems in the presence of random interactions. It is found that the yrast states with spin-zero ground states among the random ensemble exhibit strong correlations, characterized by anharmonic vibration, s-boson or d-boson condensation, as well as vibrational and rotational motions. We study these correlations explicitly based on their wave functions and the features of two-body interactions in the random ensemble.

  9. Partitioning Residue-derived and Residue-induced Emissions of N2O Using 15N-labelled Crop Residues

    NASA Astrophysics Data System (ADS)

    Farrell, R. E.; Carverhill, J.; Lemke, R.; Knight, J. D.

    2014-12-01

    Estimates of N2O emissions in Canada indicate that 17% of all agriculture-based emissions are associated with the decomposition of crop residues. However, research specific to the western Canadian prairies (including Saskatchewan) has shown that the N2O emission factor for N sources in this region typically ranges between 0.2 and 0.6%, which is well below the current IPCC default emission factor of 1.0%. Thus, it stands to reason that emissions from crop residues should also be lower than those calculated using the current IPCC emission factor. Current data indicates that residue decomposition, N mineralization and N2O production are affected by a number of factors such as C:N ratio and chemical composition of the residue, soil type, and soil water content; thus, a bench-scale incubation study was conducted to examine the effects of soil type and water content on N2O emissions associated with the decomposition of different crop residues. The study was carried out using soils from the Black, Dark Brown, Brown, and Gray soil zones and was conducted at both 50% and 70% water-filled pore space (WFPS); the soils were amended with 15N-labeled residues of wheat, pea, canola, and flax, or with an equivalent amount of 15N-labeled urea; 15N2O production was monitored using a Picarro G5101-i isotopic N2O analyzer. Crop residue additions to the soils resulted in both direct and indirect emissions of N2O, with residue derived emissions (RDE; measured as 15N2O) generally exceeding residue-induced emissions (RIE) at 50% WFPS—with RDEs ranging from 42% to 88% (mean = 58%) of the total N2O. Conversely, at 70% WFPS, RDEs were generally lower than RIEs—ranging from 21% to 83% (mean = 48%). Whereas both water content and soil type had an impact on N2O production, there was a clear and consistent trend in the emission factors for the residues; i.e., emissions were always greatest for the canola residue and lowest for the wheat residue and urea fertilizer; and intermediate for pea

  10. Functional Residues on the Surface of the N-terminal domain of Yeast Pms1

    PubMed Central

    Arana, Mercedes E.; Holmes, Shannon F.; Fortune, John M.; Moon, Andrea F.; Pedersen, Lars C.; Kunkel, Thomas A.

    2010-01-01

    Saccharomyces cerevisiae MutLα is a heterodimer of Mlh1 and Pms1 that participates in DNA mismatch repair (MMR). Both proteins have weakly conserved C-terminal regions (CTD), with the CTD of Pms1 harboring an essential endonuclease activity. These proteins also have conserved N-terminal domains (NTD) that bind and hydrolyze ATP and bind to DNA. To better understand Pms1 functions and potential interactions with DNA and/or other proteins, we solved the 2.5Å crystal structure of yeast Pms1 (yPms1) NTD. The structure is similar to thehomologous NTDs of E. coli MutL and human PMS2, including the site involved in ATP binding and hydrolysis. The structure reveals a number of conserved, positively charged surface residues that do not interact with other residues in the NTD and are therefore candidates for interactions with DNA, with the CTD and/or with other proteins. When these were replaced with glutamate, several replacements resulted in yeast strains with elevated mutation rates. Two replacements also resulted in NTDs with decreased DNA binding affinity in vitro, suggesting that these residues contribute to DNA binding that is important for mismatch repair. Elevated mutation rates also resulted from surface residue replacements that did not affect DNA binding, suggesting that these conserved residues serve other functions, possibly involving interactions with other MMR proteins. PMID:20138591

  11. Assessment of secondary crop residues. Final report

    SciTech Connect

    Ashare, E.; Leuschner, A.P.; West, C.E.; Langton, B.

    1981-03-01

    This report is the first of three reports assessing the feasibility of converting secondary agricultural residues to energy in the form of either methane gas or ethyl alcohol. Secondary agricultural residues are defined in this study as those residues resulting from biomass processing to produce primary products; e.g., whey from cheese processing, vegetable processing wastes, residues from paper pulping, etc. This report summarizes the first two phases of this study, data compilation, and evaluation. Subsequent reports will analyze the technical and economic feasibility of converting these residues to energy and the implementability of this technology. The industries for which data has been compiled in this report include vegetable, fruit, seafood, meat, poultry, and dairy processing and the pulp, paper, and paperboard industry. The data collected include raw product input, final processed product output, residue types, and quantity, residue concentration, biodegradability, seasonality of production, and geographic distribution of processing facilities. In general, these industries produce a relatively solid residue ranging in total solids concentration from 10 to 50% and a dilute liquid residue with an organic content (measured as COD or BOD) ranging from a few hundred to a few thousand mg/l. Due to the significant quantities of residues generated in each of the industries, it appears that the potential exists for generating a substantial quantity of energy. For a particular industry this quantity of energy can range from only one percent upwards to nearly thirty-five percent of the total processing energy required. The total processing energy required for the industries included in this study is approximately 2.5 quads per year. The potential energy which can be generated from these industrial residues will be 0.05 to 0.10 quads per year or approximately 2 to 4 percent of the total demand.

  12. A Benchmark Study on Casting Residual Stress

    SciTech Connect

    Johnson, Eric M.; Watkins, Thomas R; Schmidlin, Joshua E; Dutler, S. A.

    2012-01-01

    Stringent regulatory requirements, such as Tier IV norms, have pushed the cast iron for automotive applications to its limit. The castings need to be designed with closer tolerances by incorporating hitherto unknowns, such as residual stresses arising due to thermal gradients, phase and microstructural changes during solidification phenomenon. Residual stresses were earlier neglected in the casting designs by incorporating large factors of safety. Experimental measurement of residual stress in a casting through neutron or X-ray diffraction, sectioning or hole drilling, magnetic, electric or photoelastic measurements is very difficult and time consuming exercise. A detailed multi-physics model, incorporating thermo-mechanical and phase transformation phenomenon, provides an attractive alternative to assess the residual stresses generated during casting. However, before relying on the simulation methodology, it is important to rigorously validate the prediction capability by comparing it to experimental measurements. In the present work, a benchmark study was undertaken for casting residual stress measurements through neutron diffraction, which was subsequently used to validate the accuracy of simulation prediction. The stress lattice specimen geometry was designed such that subsequent castings would generate adequate residual stresses during solidification and cooling, without any cracks. The residual stresses in the cast specimen were measured using neutron diffraction. Considering the difficulty in accessing the neutron diffraction facility, these measurements can be considered as benchmark for casting simulation validations. Simulations were performed using the identical specimen geometry and casting conditions for predictions of residual stresses. The simulation predictions were found to agree well with the experimentally measured residual stresses. The experimentally validated model can be subsequently used to predict residual stresses in different cast

  13. Characterization Report on Sand, Slag, and Crucible Residues and on Fluoride Residues

    SciTech Connect

    Murray, A.M.

    1999-02-10

    This paper reports on the chemical characterization of the sand, slag, and crucible (SS and C) residues and the fluoride residues that may be shipped from the Rocky Flats Environmental Technology Site (RFETS) to Savannah River Site (SRS).

  14. 46 CFR 153.1608 - Calculation of total NLS residue and clingage NLS residue.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... MATERIALS Test and Calculation Procedures for Determining Stripping Quantity, Clingage NLS Residue, and... NLS residue for each tank is calculated by adding the stripping quantity and the clingage NLS...

  15. 46 CFR 153.1608 - Calculation of total NLS residue and clingage NLS residue.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... MATERIALS Test and Calculation Procedures for Determining Stripping Quantity, Clingage NLS Residue, and... NLS residue for each tank is calculated by adding the stripping quantity and the clingage NLS...

  16. 46 CFR 153.1608 - Calculation of total NLS residue and clingage NLS residue.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... MATERIALS Test and Calculation Procedures for Determining Stripping Quantity, Clingage NLS Residue, and... NLS residue for each tank is calculated by adding the stripping quantity and the clingage NLS...

  17. 46 CFR 153.1608 - Calculation of total NLS residue and clingage NLS residue.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... MATERIALS Test and Calculation Procedures for Determining Stripping Quantity, Clingage NLS Residue, and... NLS residue for each tank is calculated by adding the stripping quantity and the clingage NLS...

  18. Gunshot residue, ten years later.

    PubMed

    Wilber, C G; Lantz, R K; Sulik, P L

    1991-09-01

    Gunshot residues may be central to a competent reconstruction of a shooting incident. When a young boy was shot in the neck by a playmate using a .22-caliber single-action revolver, permanent paralysis from mid-thorax downward ensued. Ten years later the victim sued the importer, the vendor, the German manufacturer, and the shooter's family. Investigative reports indicated "horseplay" and questionable emergency medical team care. Depositions were contradictory. The entry wound, removed at surgery, was fixed and processed for slides. The histopathologist referred to "black pigment granules" in the wound track. The 10-year-old slides and block were retrieved. The coverslip was removed from a representative slide that was examined under the scanning, x-ray dispersive microscope. The black granules contained amounts of lead, barium, and antimony far beyond any normal range. The firing range had to have been no greater than 6-12 in (15.24-30.48 cm). The case was promptly settled out of court. PMID:1750390

  19. Thermal Insulation from Hardwood Residues

    NASA Astrophysics Data System (ADS)

    Sable, I.; Grinfelds, U.; Vikele, L.; Rozenberga, L.; Zeps, M.; Luguza, S.

    2015-11-01

    Adequate heat is one of the prerequisites for human wellbeing; therefore, building insulation is required in places where the outside temperature is not suitable for living. The climate change, with its rising temperatures and longer dry periods, promotes enlargement of the regions with conditions more convenient for hardwood species than for softwood species. Birch (Betula pendula) is the most common hardwood species in Latvia. The aim of this work was to obtain birch fibres from wood residues of plywood production and to form low-density thermal insulation boards. Board formation and production was done in the presence of water; natural binder, fire retardant and fungicide were added in different concentrations. Board properties such as density, transportability or resistance to particulate loss, thermal conductivity and reaction to fire were investigated. This study included thermal insulation boards with the density of 102-120 kg/m3; a strong correlation between density and the binder amount was found. Transportability also improved with the addition of a binder, and 0.1-0.5% of the binder was the most appropriate amount for this purpose. The measured thermal conductivity was in the range of 0.040-0.043 W/(m·K). Fire resistance increased with adding the fire retardant. We concluded that birch fibres are applicable for thermal insulation board production, and it is possible to diversify board properties, changing the amount of different additives.

  20. An Integrated Model for Assessment of Sustainable Agricultural Residue Removal Limits for Bioenergy Systems

    SciTech Connect

    D. Muth; K. M. Bryden

    2003-12-01

    Agricultural residues have been identified as a significant potential resource for bioenergy production, but serious questions remain about the sustainability of harvesting residues. Agricultural residues play an important role in limiting soil erosion from wind and water and in maintaining soil organic carbon. Because of this, multiple factors must be considered when assessing sustainable residue harvest limits. Validated and accepted modeling tools for assessing these impacts include the Revised Universal Soil Loss Equation Version 2 (RUSLE2), the Wind Erosion Prediction System (WEPS), and the Soil Conditioning Index. Currently, these models do not work together as a single integrated model. Rather, use of these models requires manual interaction and data transfer. As a result, it is currently not feasible to use these computational tools to perform detailed sustainable agricultural residue availability assessments across large spatial domains or to consider a broad range of land management practices. This paper presents an integrated modeling strategy that couples existing datasets with the RUSLE2 water erosion, WEPS wind erosion, and Soil Conditioning Index soil carbon modeling tools to create a single integrated residue removal modeling system. This enables the exploration of the detailed sustainable residue harvest scenarios needed to establish sustainable residue availability. Using this computational tool, an assessment study of residue availability for the state of Iowa was performed. This study included all soil types in the state of Iowa, four representative crop rotation schemes, variable crop yields, three tillage management methods, and five residue removal methods. The key conclusions of this study are that under current management practices and crop yields nearly 26.5 million Mg of agricultural residue are sustainably accessible in the state of Iowa, and that through the adoption of no till practices residue removal could sustainably approach 40