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Sample records for lennard jones interaction site

  1. Collision kernels in the eikonal approximation for Lennard-Jones interaction potential

    International Nuclear Information System (INIS)

    Zielinska, S.

    1985-03-01

    The velocity changing collisions are conveniently described by collisional kernels. These kernels depend on an interaction potential and there is a necessity for evaluating them for realistic interatomic potentials. Using the collision kernels, we are able to investigate the redistribution of atomic population's caused by the laser light and velocity changing collisions. In this paper we present the method of evaluating the collision kernels in the eikonal approximation. We discuss the influence of the potential parameters Rsub(o)sup(i), epsilonsub(o)sup(i) on kernel width for a given atomic state. It turns out that unlike the collision kernel for the hard sphere model of scattering the Lennard-Jones kernel is not so sensitive to changes of Rsub(o)sup(i) as the previous one. Contrary to the general tendency of approximating collisional kernels by the Gaussian curve, kernels for the Lennard-Jones potential do not exhibit such a behaviour. (author)

  2. Single-site Lennard-Jones models via polynomial chaos surrogates of Monte Carlo molecular simulation

    KAUST Repository

    Kadoura, Ahmad Salim

    2016-06-01

    In this work, two Polynomial Chaos (PC) surrogates were generated to reproduce Monte Carlo (MC) molecular simulation results of the canonical (single-phase) and the NVT-Gibbs (two-phase) ensembles for a system of normalized structureless Lennard-Jones (LJ) particles. The main advantage of such surrogates, once generated, is the capability of accurately computing the needed thermodynamic quantities in a few seconds, thus efficiently replacing the computationally expensive MC molecular simulations. Benefiting from the tremendous computational time reduction, the PC surrogates were used to conduct large-scale optimization in order to propose single-site LJ models for several simple molecules. Experimental data, a set of supercritical isotherms, and part of the two-phase envelope, of several pure components were used for tuning the LJ parameters (ε, σ). Based on the conducted optimization, excellent fit was obtained for different noble gases (Ar, Kr, and Xe) and other small molecules (CH4, N2, and CO). On the other hand, due to the simplicity of the LJ model used, dramatic deviations between simulation and experimental data were observed, especially in the two-phase region, for more complex molecules such as CO2 and C2 H6.

  3. Selection and Validation of Charge and Lennard-Jones Parameters for QM/MM Simulations of Hydrocarbon Interactions with Zeolites.

    Science.gov (United States)

    Zimmerman, Paul M; Head-Gordon, Martin; Bell, Alexis T

    2011-06-14

    Quantum mechanics/molecular mechanics (QM/MM) models are an appealing method for performing zeolite simulations. In QM/MM, a small cluster chosen to encompass the active center is described by QM, while the rest of the zeolite is described by MM. In the present study, we demonstrate that the charges and Lennard-Jones parameters on Si and O must be chosen properly for QM/MM calculations of adsorption energies and activation energies to agree closely with full QM calculations. The selection of parameters for Si and O is based on using the ωB97X-D functional for DFT calculations of the QM region, which is effective in capturing the effects of van der Waals interactions. A comparison of the heats of adsorption for a variety of adsorbates and activation energies for the cracking of propane and butane reveals that energies derived from QM/MM calculation carried out with appropriately selected MM parameters agree to within an rms error of ∼1.5 kcal/mol with QM calculations. To avoid reparametrization for new substrates, Lennard-Jones zeolite parameters are chosen to be compatible with existing CHARMM parameters. Transferability of these parameters is demonstrated by tests utilizing the B3LYP density functional and simulations of MFI and FAU zeolites. Moreover, the computational time for QM/MM calculations is considerably lower than that for QM calculations, and the ratio of computational times decreases rapidly with increasing size of the cluster used to represent the zeolite.

  4. Chemical Potential of a Lennard Jones Fluid

    Directory of Open Access Journals (Sweden)

    Celebonovic, V.

    2010-12-01

    Full Text Available The aim of this paper is to present results of analytical calculation of chemical potential of a Lennard Jones (LJ fluid performed in two ways: by using the thermodynamical formalism and the formalism of statistical mechanics. The integration range is divided into two regions. In the small distance region, which is $rleqsigma$ in the usual notation, the integration range had to be cut off in order to avoid the occurence of divergences. In the large distance region, the calculation is technically simpler. The calculation reported here will be useful in all kinds of studies concerning phase equilibrium in a LJ fluid. Interesting kinds of such systems are the giant planets and the icy satellites in various planetary systems, but also the (so far hypothetical quark stars.

  5. Chemical potential of a Lennard Jones fluid

    Directory of Open Access Journals (Sweden)

    Čelebonović V.

    2010-01-01

    Full Text Available The aim of this paper is to present results of analytical calculation of chemical potential of a Lennard Jones (LJ fluid performed in two ways: by using the thermodynamical formalism and the formalism of statistical mechanics. The integration range is divided into two regions. In the small distance region, which is r ≤ σ in the usual notation, the integration range had to be cut off in order to avoid the occurrence of divergences. In the large distance region, the calculation is technically simpler. The calculation reported here will be useful in all kinds of studies concerning phase equilibrium in a LJ fluid. Interesting kinds of such systems are the giant planets and the icy satellites in various planetary systems, but also the (so far hypothetical quark stars.

  6. Mapping the magic numbers in binary Lennard-Jones clusters.

    Science.gov (United States)

    Doye, Jonathan P K; Meyer, Lars

    2005-08-05

    Using a global optimization approach that directly searches for the composition of greatest stability, we have been able to find the particularly stable structures for binary Lennard-Jones clusters with up to 100 atoms for a range of Lennard-Jones parameters. In particular, we have shown that just having atoms of different sizes leads to a remarkable stabilization of polytetrahedral structures, including both polyicosahedral clusters and at larger sizes structures with disclination lines.

  7. Melting of 2D monatomic solids: Lennard-Jones system

    International Nuclear Information System (INIS)

    Yi, Y.M.; Guo, Z.C.

    1987-09-01

    The Lennard-Jones interaction has been introduced into the Collins mix lattice of 2D liquids. By means of rigorous calculation of the total potential and the free area, the Gibbs functions for 2D liquid and solid have been derived. The melting line obtained from the phase transition equation agrees quite well with the result of recent computer simulation experiments. The obtained reduced temperature of the triple point T* t =0.438 agrees with the data measured in experiments of some inert gas monolayers adsorbed on graphite as well as in computer simulation experiments. (author). 11 refs, 7 figs, 3 tabs

  8. Non-equilibrium surface tension of the vapour-liquid interface of active Lennard-Jones particles

    NARCIS (Netherlands)

    Paliwal, Siddharth; Prymidis, Vasileios; Filion, Laura; Dijkstra, Marjolein

    2017-01-01

    We study a three-dimensional system of self-propelled Brownian particles interacting via the Lennard-Jones potential. Using Brownian dynamics simulations in an elongated simulation box, we investigate the steady states of vapour-liquid phase coexistence of active Lennard-Jones particles with planar

  9. Cluster fusion algorithm: application to Lennard-Jones clusters

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2008-01-01

    We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing...... paths up to the cluster size of 150 atoms. We demonstrate that in this way all known global minima structures of the Lennard-Jones clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence...... for the clusters of noble gas atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence of the second derivative of the binding energy per atom on cluster size calculated for the chain of the Lennard-Jones clusters based on the icosahedral symmetry...

  10. More on the melting of Lennard-Jones clusters

    International Nuclear Information System (INIS)

    Garzon, I.L.; Avalos-Borja, M.; Blaisten-Barojas, E.

    1989-01-01

    The melting of 13-atom clusters interacting via Lennard-Jones potentials has been revisited using molecular dynamics coupled to steepest descent quenches. A procedure was devised to account for the fraction of times the global and local minima of the potential energy surface are accessed during a long trajectory. This quantity presents a sigmoid shape. A phenomenological model of melting is given in terms of a correlated walk that maps the short time excursions among the global and local minima in configuration space. Comparison between the simulation results and the theoretical model shows that the melting transition is well described in terms of the temperature changes of the fraction of high energy minima accessed during the cluster trajectory. Cooperativity is clear from the S shape of this quantity, i.e., the access to a local minimum favours the access to other local minima. (orig.)

  11. Thermal conductivity of the Lennard-Jones chain fluid model.

    Science.gov (United States)

    Galliero, Guillaume; Boned, Christian

    2009-12-01

    Nonequilibrium molecular dynamics simulations have been performed to estimate, analyze, and correlate the thermal conductivity of a fluid composed of short Lennard-Jones chains (up to 16 segments) over a large range of thermodynamic conditions. It is shown that the dilute gas contribution to the thermal conductivity decreases when the chain length increases for a given temperature. In dense states, simulation results indicate that the residual thermal conductivity of the monomer increases strongly with density, but is weakly dependent on the temperature. Compared to the monomer value, it has been noted that the residual thermal conductivity of the chain was slightly decreasing with its length. Using these results, an empirical relation, including a contribution due to the critical enhancement, is proposed to provide an accurate estimation of the thermal conductivity of the Lennard-Jones chain fluid model (up to 16 segments) over the domain 0.8values of the Lennard-Jones chain fluid model merge on the same "universal" curve when plotted as a function of the excess entropy. Furthermore, it is shown that the reduced configurational thermal conductivity of the Lennard-Jones chain fluid model is approximately proportional to the reduced excess entropy for all fluid states and all chain lengths.

  12. Cluster fusion algorithm: application to Lennard-Jones clusters

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2006-01-01

    We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing ...

  13. Hopping in a supercooled binary Lennard-Jones liquid

    DEFF Research Database (Denmark)

    Schrøder, Thomas; Dyre, Jeppe

    1998-01-01

    A binary Lennard–Jones liquid has been investigated by molecular dynamics at equilibrium supercooled conditions. At the lowest temperature investigated, hopping is present in the system as indicated by a secondary peak in 4r2Gs(r,t), where Gs(r,t) is the van Hove self correlation function...

  14. Origin of line tension for a Lennard-Jones nanodroplet

    NARCIS (Netherlands)

    Weijs, Joost; Weijs, Joost H.; Marchand, Antonin; Andreotti, Bruno; Lohse, Detlef; Snoeijer, Jacobus Hendrikus

    2011-01-01

    The existence and origin of line tension has remained controversial in literature. To address this issue, we compute the shape of Lennard-Jones nanodrops using molecular dynamics and compare them to density functional theory in the approximation of the sharp kink interface. We show that the

  15. Free energy of the Lennard-Jones solid

    NARCIS (Netherlands)

    van der Hoef, Martin Anton

    2000-01-01

    We have determined a simple expression for the absolute Helmholtz free energy of the fcc Lennard-Jones solid from molecular dynamics simulations. The pressure and energy data from these simulations have been fitted to a simple functional form (18 parameters) for densities ranging from around

  16. Gas-solid coexistence of the Lennard-Jones system

    NARCIS (Netherlands)

    van der Hoef, Martin Anton

    2002-01-01

    Recently, the absolute free energies of the Lennard-Jones system at solid–liquid and solid–gas coexistence were computed from Monte Carlo simulations [J. Chem. Phys. 116, 7145 (2002)]. In this note, we show that the values along the sublimation line are in good agreement with the results from an

  17. Solitons in a One-Dimensional Lennard-Jones Lattice

    OpenAIRE

    Yuji, ISHIMORI; Department of Applied Mathematics and Physics Kyoto University

    1982-01-01

    Nonlinear waves in a one-dimensional lattice with (2n, n) Lennard-Jones potential are studied in small-amplitude and long-wavelength approximations. Equations derived are classified into three types according to the value of the force-range parameter n. For n=2 and ≧4, we get the Benjamin-Ono equation and the Korteweg-de Vries equation, respectively.

  18. Hopping in a supercooled binary Lennard-Jones liquid

    DEFF Research Database (Denmark)

    Schrøder, Thomas; Dyre, Jeppe

    1998-01-01

    A binary Lennard–Jones liquid has been investigated by molecular dynamics at equilibrium supercooled conditions. At the lowest temperature investigated, hopping is present in the system as indicated by a secondary peak in 4r2Gs(r,t), where Gs(r,t) is the van Hove self correlation function......", as often argued, and that the system has a single-peaked distribution of hopping-distances centered around the characteristic intermolecular distance....

  19. Phase separation of a Lennard-Jones fluid interacting with a long, condensed polymer chain: implications for the nuclear body formation near chromosomes.

    Science.gov (United States)

    Oh, Inrok; Choi, Saehyun; Jung, YounJoon; Kim, Jun Soo

    2015-08-28

    Phase separation in a biological cell nucleus occurs in a heterogeneous environment filled with a high density of chromatins and thus it is inevitably influenced by interactions with chromatins. As a model system of nuclear body formation in a cell nucleus filled with chromatins, we simulate the phase separation of a low-density Lennard-Jones (LJ) fluid interacting with a long, condensed polymer chain. The influence of the density variation of LJ particles above and below the phase boundary and the role of attractive interactions between LJ particles and polymer segments are investigated at a fixed value of strong self-interaction between LJ particles. For a density of LJ particles above the phase boundary, phase separation occurs and a dense domain of LJ particles forms irrespective of interactions with the condensed polymer chain whereas its localization relative to the polymer chain is determined by the LJ-polymer attraction strength. Especially, in the case of moderately weak attractions, the domain forms separately from the polymer chain and subsequently associates with the polymer chain. When the density is below the phase boundary, however, the formation of a dense domain is possible only when the LJ-polymer attraction is strong enough, for which the domain grows in direct contact with the interacting polymer chain. In this work, different growth behaviors of LJ particles result from the differences in the density of LJ particles and in the LJ-polymer interaction, and this work suggests that the distinct formation of activity-dependent and activity-independent nuclear bodies (NBs) in a cell nucleus may originate from the differences in the concentrations of body-specific NB components and in their interaction with chromatins.

  20. Origin of line tension for a Lennard-Jones nanodroplet

    Science.gov (United States)

    Weijs, Joost H.; Marchand, Antonin; Andreotti, Bruno; Lohse, Detlef; Snoeijer, Jacco H.

    2011-02-01

    The existence and origin of line tension has remained controversial in literature. To address this issue, we compute the shape of Lennard-Jones nanodrops using molecular dynamics and compare them to density functional theory in the approximation of the sharp kink interface. We show that the deviation from Young's law is very small and would correspond to a typical line tension length scale (defined as line tension divided by surface tension) similar to the molecular size and decreasing with Young's angle. We propose an alternative interpretation based on the geometry of the interface at the molecular scale.

  1. Scaling of the dynamics of flexible Lennard-Jones chains

    DEFF Research Database (Denmark)

    Veldhorst, Arno; Dyre, J. C.; Schrøder, Thomas

    2014-01-01

    S/T , where ρ is density, T is temperature, and γ S is a material specific scaling exponent) is an approximation to a more general scaling predicted by the isomorph theory. Furthermore, the isomorph theory provides an explanation for Rosenfeld scaling (relaxation times and transport coefficients being...... functions of excess entropy) which has been observed in simulations of both molecular and polymeric systems. Doing molecular dynamics simulations of flexible Lennard-Jones chains (LJC) with rigid bonds, we here provide the first detailed test of the isomorph theory applied to flexible chain molecules. We...... confirm the existence of isomorphs, which are curves in the phase diagram along which the dynamics is invariant in the appropriate reduced units. This holds not only for the relaxation times but also for the full time dependence of the dynamics, including chain specific dynamics such as the end...

  2. Glass transitions in one-, two-, three-, and four-dimensional binary Lennard-Jones systems

    Energy Technology Data Exchange (ETDEWEB)

    Bruening, Ralf; St-Onge, Denis A; Patterson, Steve [Physics Department, Mount Allison University, Sackville, NB, E4L 1E6 (Canada); Kob, Walter [Laboratoire des Colloides, Verres et Nanomateriaux, UMR5587, Universite Montpellier II and CNRS, 34095 Montpellier Cedex (France)], E-mail: rbruening@mta.ca

    2009-01-21

    We investigate the calorimetric liquid-glass transition by performing simulations of a binary Lennard-Jones mixture in one through four dimensions. Starting at a high temperature, the systems are cooled to T = 0 and heated back to the ergodic liquid state at constant rates. Glass transitions are observed in two, three and four dimensions as a hysteresis between the cooling and heating curves. This hysteresis appears in the energy and pressure diagrams, and the scanning rate dependence of the area and height of the hysteresis can be described using power laws. The one-dimensional system does not experience a glass transition but its specific heat curve resembles the shape of the D{>=}2 results in the supercooled liquid regime above the glass transition. As D increases, the radial distribution functions reflect reduced geometric constraints. Nearest neighbor distances become smaller with increasing D due to interactions between nearest and next-nearest neighbors. Simulation data for the glasses are compared with crystal and melting data obtained with a Lennard-Jones system with only one type of particle and we find that with increasing D crystallization becomes increasingly more difficult.

  3. Non-equilibrium surface tension of the vapour-liquid interface of active Lennard-Jones particles

    Science.gov (United States)

    Paliwal, Siddharth; Prymidis, Vasileios; Filion, Laura; Dijkstra, Marjolein

    2017-08-01

    We study a three-dimensional system of self-propelled Brownian particles interacting via the Lennard-Jones potential. Using Brownian dynamics simulations in an elongated simulation box, we investigate the steady states of vapour-liquid phase coexistence of active Lennard-Jones particles with planar interfaces. We measure the normal and tangential components of the pressure tensor along the direction perpendicular to the interface and verify mechanical equilibrium of the two coexisting phases. In addition, we determine the non-equilibrium interfacial tension by integrating the difference of the normal and tangential components of the pressure tensor and show that the surface tension as a function of strength of particle attractions is well fitted by simple power laws. Finally, we measure the interfacial stiffness using capillary wave theory and the equipartition theorem and find a simple linear relation between surface tension and interfacial stiffness with a proportionality constant characterized by an effective temperature.

  4. An equation of state for two-center Lennard-Jones fluids

    Science.gov (United States)

    Mecke, M.; Müller, A.; Winkelmann, J.; Fischer, J.

    1997-05-01

    A new equation of state (EOS) is proposed for the Helmholzt energy F of two-center Lennard-Jones fluids. The EOS is written in the form of a generalized van der Waals equation, F=F H + F A , where F H accounts for the hard-body interaction and F A for the attractive dispersion forces. The equation is constructed on the basis of previously published data sets and results from new extensive computer simulation studies. It correlates pressures and internal energies over a wide fluid range for two-center model fluids with elongations up to 0.67 in reduced units with a high accuracy and shows an excellent description of the vapor-liquid coexistence properties. Comparisons of results from the new EOS with other data sets and recently published VLE from the NpT plus test particle method show very good agreement.

  5. Ab initio study of the atomic motion in liquid metal surfaces: comparison with Lennard-Jones systems

    International Nuclear Information System (INIS)

    Gonzalez, Luis E; Gonzalez, David J

    2006-01-01

    It is established that liquid metals exhibit surface layering at the liquid-vapour interface, while dielectric simple systems, like those interacting through Lennard-Jones potentials, show a monotonic decay from the liquid density to that of the vapour. First principles molecular dynamics simulations of the free liquid surface of several liquid metals (Li, Na, K, Rb, Cs, Mg, Ba, Al, Tl and Si), and the Na 3 K 7 alloy near their triple points have been performed in order to study the atomic motion at the interface, mainly at the outer layer. Comparison with the results of classical molecular dynamics simulations of a Lennard-Jones system shows interesting differences and similarities. The probability distribution function of the time of residence in a layer shows a peak at very short times and a long-lasting tail. The mean residence time in a layer increases when approaching the interfacial region, slightly in the Lennard-Jones system but strongly in the metallic systems. The motion within the layers, parallel to the interface, can be described as diffusion enhanced (strongly in the case of the outermost layer) with respect to the bulk, for both types of systems, despite its reduced dimensionality in metals

  6. Effect of Energy Polydispersity on the Nature of Lennard-Jones Liquids

    OpenAIRE

    Ingebrigtsen, Trond S.; Tanaka, Hajime

    2016-01-01

    In the companion paper [T. S. Ingebrigtsen and H. Tanaka, J. Phys. Chem. B 119, 11052 (2015)] the effect of size polydispersity on the nature of Lennard-Jones (LJ) liquids, which represent most molecular liquids without hydrogen bonds, was studied. More specifically, it was shown that even highly size polydisperse LJ liquids are Roskilde-simple (RS) liquids. RS liquids are liquids with strong correlation between constant volume equilibrium fluctuations of virial and potential energy and are s...

  7. Fluctuations and thermodynamic response functions in a Lennard-Jones solid

    International Nuclear Information System (INIS)

    Li, M.; Johnson, W.L.

    1992-01-01

    Thermodynamic response functions of a nearest-neighbor Lennard-Jones solid--heat capacity, thermal-expansion coefficient, compressibility, and elastic constants--are calculated directly from fluctuations using molecular-dynamics simulations. The algorithm used is the earlier Parrinello-Rahman molecular dynamics modified to take into account symmetry and rotation invariance of the system under investigation. The convergence is very fast and results are in good agreement with existing Monte Carlo and molecular-dynamics results

  8. Melting in Two-Dimensional Lennard-Jones Systems: Observation of a Metastable Hexatic Phase

    International Nuclear Information System (INIS)

    Chen, K.; Kaplan, T.; Mostoller, M.

    1995-01-01

    Large scale molecular dynamics simulations of two-dimensional melting have been carried out using a recently revised Parrinello-Rahman scheme on massively parallel supercomputers. A metastable state is observed between the solid and liquid phases in Lennard-Jones systems of 36 864 and 102 400 atoms. This intermediate state shows the characteristics of the hexatic phase predicted by the theory of Kosterlitz, Thouless, Halperin, Nelson, and Young

  9. Analytical tools for solitons and periodic waves corresponding to phonons on Lennard-Jones lattices in helical proteins

    DEFF Research Database (Denmark)

    D'ovidio, Francesco; Bohr, Henrik; Lindgård, Per-Anker

    2005-01-01

    We study the propagation of solitons along the hydrogen bonds of an alpha helix. Modeling the hydrogen and peptide bonds with Lennard-Jones potentials, we show that the solitons can appear spontaneously and have long lifetimes. Remarkably, even if no explicit solution is known for the Lennard-Jon...

  10. Metastability, spectrum, and eigencurrents of the Lennard-Jones-38 network

    International Nuclear Information System (INIS)

    Cameron, Maria K.

    2014-01-01

    We develop computational tools for spectral analysis of stochastic networks representing energy landscapes of atomic and molecular clusters. Physical meaning and some properties of eigenvalues, left and right eigenvectors, and eigencurrents are discussed. We propose an approach to compute a collection of eigenpairs and corresponding eigencurrents describing the most important relaxation processes taking place in the system on its way to the equilibrium. It is suitable for large and complex stochastic networks where pairwise transition rates, given by the Arrhenius law, vary by orders of magnitude. The proposed methodology is applied to the network representing the Lennard-Jones-38 cluster created by Wales's group. Its energy landscape has a double funnel structure with a deep and narrow face-centered cubic funnel and a shallower and wider icosahedral funnel. However, the complete spectrum of the generator matrix of the Lennard-Jones-38 network has no appreciable spectral gap separating the eigenvalue corresponding to the escape from the icosahedral funnel. We provide a detailed description of the escape process from the icosahedral funnel using the eigencurrent and demonstrate a superexponential growth of the corresponding eigenvalue. The proposed spectral approach is compared to the methodology of the Transition Path Theory. Finally, we discuss whether the Lennard-Jones-38 cluster is metastable from the points of view of a mathematician and a chemical physicist, and make a connection with experimental works

  11. Spray flow-network flow transition of binary Lennard-Jones particle system

    KAUST Repository

    Inaoka, Hajime

    2010-07-01

    We simulate gas-liquid flows caused by rapid depressurization using a molecular dynamics model. The model consists of two types of Lennard-Jones particles, which we call liquid particles and gas particles. These two types of particles are distinguished by their mass and strength of interaction: a liquid particle has heavier mass and stronger interaction than a gas particle. By simulations with various initial number densities of these particles, we found that there is a transition from a spray flow to a network flow with an increase of the number density of the liquid particles. At the transition point, the size of the liquid droplets follows a power-law distribution, while it follows an exponential distribution when the number density of the liquid particles is lower than the critical value. The comparison between the transition of the model and that of models of percolation is discussed. The change of the average droplet size with the initial number density of the gas particles is also presented. © 2010 Elsevier B.V. All rights reserved.

  12. Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water

    Science.gov (United States)

    Reif, Maria M.; Hünenberger, Philippe H.

    2011-04-01

    The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [M. A. Kastenholz and P. H. Hünenberger, J. Chem. Phys. 124, 224501 (2006), 10.1529/biophysj.106.083667; M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144103 (2010)], the application of appropriate correction terms permits to obtain methodology-independent results. The corrected values are then exclusively characteristic of the underlying molecular model including in particular the ion-solvent van der Waals interaction parameters, determining the effective ion size and the magnitude of its dispersion interactions. In the present study, the comparison of calculated (corrected) hydration free energies with experimental data (along with the consideration of ionic polarizabilities) is used to calibrate new sets of ion-solvent van der Waals (Lennard-Jones) interaction parameters for the alkali (Li+, Na+, K+, Rb+, Cs+) and halide (F-, Cl-, Br-, I-) ions along with either the SPC or the SPC/E water models. The experimental dataset is defined by conventional single-ion hydration free energies [Tissandier et al., J. Phys. Chem. A 102, 7787 (1998), 10.1021/jp982638r; Fawcett, J. Phys. Chem. B 103, 11181] along with three plausible choices for the (experimentally elusive) value of the absolute (intrinsic) hydration free energy of the proton, namely, Δ G_hyd^{ominus }[H+] = -1100, -1075 or -1050 kJ mol-1, resulting in three sets L, M, and H for the SPC water model and three sets LE, ME, and HE for the SPC/E water model (alternative sets can easily be interpolated to intermediate Δ G_hyd^{ominus }[H+] values). The residual sensitivity of the calculated (corrected) hydration free energies on the volume-pressure boundary conditions and on the effective ionic radius entering into the calculation of the correction terms is

  13. Thermodynamic equivalence between the Lennard-Jones and hard-core attractive Yukawa systems

    International Nuclear Information System (INIS)

    Kadiri, Y.; Albaki, R.; Bretonnet, J.L.

    2008-01-01

    The investigation of the thermodynamic properties of the Lennard-Jones (LJ) fluid is made by means of a system of particles interacting with a potential of hard-core plus attractive Yukawa tail (HCY). Due to the similarity between the LJ potential and the HCY potential in its overall form, it is worthwhile seeking to approximate the LJ potential in much the same way that the hard-sphere reference potential has been so used. The study consists in describing the thermodynamics of the LJ fluid in terms of the equivalent HCY system, whose the properties are known accurately, by means of mapping the thermodynamic quantities for the HCY potential parameters. The method is feasible owing to a convenient analytical expression of the Helmholtz free energy from the mean-spherical approximation expanded in power of the inverse temperature. Two different procedures are used to determine the parameters of the HCY potential as a function of the thermodynamic states: one is based on the simultaneous fits of pressure and internal energy of the LJ system and the other uses the concept of collision frequency. The reasonable homogeneity of the results in both procedures of mapping makes that the HCY potential is a very good reference system, whose the proposed theoretical expressions can be used confidently to predict the thermodynamic properties of more realistic potentials

  14. Modified Benedict-Webb-Rubin Equation of State for the Modified Lennard-Jones Fluid

    Science.gov (United States)

    Asano, Yuta; Fuchizaki, Kazuhiro

    2014-03-01

    We have proposed a modified Lennard-Jones (mLJ) potential to deal with problems, such as the accurate determination of the melting condition, in which an attractive interaction plays an essential role, but its range need not necessarily extend to infinity. An accurate phase diagram, including the triple and the critical points of the system characterized by the mLJ potential, has been investigated using mainly thermodynamic integration. To predict the thermodynamic behavior of the system, it is further desired to construct the equation of state (EOS) as accurately as possible. The modified Benedict-Webb-Rubin EOS was employed to this end. The 33 parameters involved in the equation were carefully determined in order for the EOS to be compatible with the temperature dependences of the virial coefficients as well as with an extremely large set of thermodynamic data obtained from our own molecular dynamics simulation performed over a wide fluid region. The resultant EOS was found to be not only sufficiently accurate at temperatures up to twenty times as high as the critical-point temperature but also effective in practical use.

  15. Formation of global energy minimim structures in the growth process of Lennard-Jones clusters

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Koshelev, Andrey; Shutovich, Andrey

    2003-01-01

    that in this way all known global minimum structures of the Lennard-Jones (LJ) clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic numbers sequence for the clusters of noble gases atoms and compare...... for the clusters of noble gases atoms. Our method serves an efficient alternative to the global optimization techniques based on the Monte-Carlo simulations and it can be applied for the solution of a broad variety of problems in which atomic cluster structure is important....

  16. Evidence of hexatic phase formation in two-dimensional Lennard-Jones binary arrays

    International Nuclear Information System (INIS)

    Li, M.; Johnson, W.L.; Goddard, W.A. III

    1996-01-01

    We report evidence of the hexatic phase formation in Lennard-Jones binary substitutional random arrays from isothermal-isobaric molecular-dynamics simulations. The hexatic phase is analogous to those predicted in Kosterlitz-Thouless theory of melting that is characterized by short-range translational order and quasi-long-range orientational order. At the crystal to hexatic phase transition, dislocation pairs are observed to unbind into isolated dislocations. Further disordering of the hexatic phase, however, does not lead to dissociation of dislocations into disclinations. Instead, the dislocations become clustered and form dislocation networks which results in formation of amorphous phases. copyright 1996 The American Physical Society

  17. Replica exchange molecular simulation of Lennard-Jones particles in a two-dimensional confined system

    Science.gov (United States)

    Doi, Hideo; Yasuoka, Kenji

    2017-05-01

    Confined systems exhibit interesting properties that are applied to the fields of lubrication, adhesion and nanotechnology. The replica exchange molecular simulation method was applied to calculate the phase equilibrium points of Lennard-Jones particles in a two-dimensional confined system. The liquid-solid phase equilibrium points and the solid structure with a dependency of the slit width were determined and the order parameter of the solid structure was analyzed. Such confined systems are shown to be favorable for manipulation of the phase equilibrium points.

  18. Numerical simulation of pool boiling of a Lennard-Jones liquid

    KAUST Repository

    Inaoka, Hajime

    2013-09-01

    We performed a numerical simulation of pool boiling by a molecular dynamics model. In the simulation, a liquid composed of Lennard-Jones particles in a uniform gravitational field is heated by a heat source at the bottom of the system. The model successfully reproduces the change in regimes of boiling from nucleate boiling to film boiling with the increase of the heat source temperature. We present the pool boiling curve by the model, whose general behavior is consistent with those observed in experiments of pool boiling. © 2013 Elsevier B.V. All rights reserved.

  19. Nonlinear transport processes and fluid dynamics: Cylindrical Couette flow of Lennard-Jones fluids

    International Nuclear Information System (INIS)

    Khayat, R.E.; Eu, B.C.

    1988-01-01

    In this paper we report on calculations of flow profiles for cylindrical Couette flow of a Lennard-Jones fluid. The flow is subjected to a temperature gradient and thermoviscous effects are taken into consideration. We apply the generalized fluid dynamic equations which are provided by the modified moment method for the Boltzmann equation reported previously. The results of calculations are in good agreement with the Monte Carlo direct simulation method by K. Nanbu [Phys. Fluids 27, 2632 (1984)] for most of Knudsen numbers for which the simulation data are available

  20. Self-diffusion coefficients of the metastable Lennard-Jones vapor

    Energy Technology Data Exchange (ETDEWEB)

    Nie Chu; Zhou Youhua [School of Physics and Information Engineering, Jianghan University, Wuhan 430056 (China); Marlow, W H; Hassan, Y A [Department of Nuclear Engineering, Texas A and M University, College Station, TX 77843 (United States)], E-mail: yhzhou@jhun.edu.cn

    2008-10-15

    Self-diffusion coefficients of a metastable Lennard-Jones vapor were obtained using the memory function formalism and the frequency moments of the velocity autocorrelation function at reduced temperatures from 0.75 to 1.0. The radial density distribution functions used to evaluate the second, fourth and sixth frequency moments of the velocity autocorrelation function were obtained from the restricted canonical ensemble Monte Carlo simulation (Corti and Debenedetti 1994 Chem. Eng. Sci. 49 2717). The self-diffusion coefficients at reduced temperature 0.75 do not vary monotonically as the density increases, and for the other three temperatures the self-diffusion coefficients vary normally.

  1. Stability limits for the supercooled liquid and superheated crystal of Lennard-Jones particles.

    Science.gov (United States)

    Loscar, Ernesto S; Martin, Daniel A; Grigera, Tomás S

    2017-07-21

    We have studied the limits of stability in the first order liquid-solid phase transition in a Lennard-Jones system by means of the short-time relaxation method and using the bond-orientational order parameter Q 6 . These limits are compared with the melting line. We have paid special attention to the supercooled liquid, comparing our results with the point where the free energy cost of forming a nucleating droplet goes to zero. We also indirectly estimate the dimension associated to the critical nucleus at the spinodal, expected to be fractal according to mean field theories of nucleation.

  2. A comparison of molecular dynamics and diffuse interface model predictions of Lennard-Jones fluid evaporation

    Energy Technology Data Exchange (ETDEWEB)

    Barbante, Paolo [Dipartimento di Matematica, Politecnico di Milano - Piazza Leonardo da Vinci 32 - 20133 Milano (Italy); Frezzotti, Aldo; Gibelli, Livio [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano - Via La Masa 34 - 20156 Milano (Italy)

    2014-12-09

    The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviations of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.

  3. Phase Diagram of Kob-Andersen-Type Binary Lennard-Jones Mixtures

    Science.gov (United States)

    Pedersen, Ulf R.; Schrøder, Thomas B.; Dyre, Jeppe C.

    2018-04-01

    The binary Kob-Andersen (KA) Lennard-Jones mixture is the standard model for computational studies of viscous liquids and the glass transition. For very long simulations, the viscous KA system crystallizes, however, by phase separating into a pure A particle phase forming a fcc crystal. We present the thermodynamic phase diagram for KA-type mixtures consisting of up to 50% small (B ) particles showing, in particular, that the melting temperature of the standard KA system at liquid density 1.2 is 1.028(3) in A particle Lennard-Jones units. At large B particle concentrations, the system crystallizes into the CsCl crystal structure. The eutectic corresponding to the fcc and CsCl structures is cutoff in a narrow interval of B particle concentrations around 26% at which the bipyramidal orthorhombic PuBr3 structure is the thermodynamically stable phase. The melting temperature's variation with B particle concentration at two constant pressures, as well as at the constant density 1.2, is estimated from simulations at pressure 10.19 using isomorph theory. Our data demonstrate approximate identity between the melting temperature and the onset temperature below which viscous dynamics appears. Finally, the nature of the solid-liquid interface is briefly discussed.

  4. Localized fluidity modes and the topology of the constant-potential-energy hypersurfaces of Lennard-Jones matter

    DEFF Research Database (Denmark)

    Cotterill, Rodney M J; Madsen, J.

    1986-01-01

    Sections of configuration space for Lennard-Jones matter were obtained by probing all the normal-mode energy profiles, following diagonalization of the dynamical matrix for a 240-particle system. For the crystal and sufficiently cold glass, these are single welled, whereas increasing numbers...... of double wells occur as the glass is warmed toward the fluid. This indicates that there might be a fundamental difference between the topologies of the constant-potential-energy hypersurfaces of crystalline and noncrystalline Lennard-Jones matter....

  5. Numerical computations of the Lennard-Jones resonances and ''relative displacements'' of the scattered atomic beams from the system He/LiF(001)

    International Nuclear Information System (INIS)

    Garcia, N.

    1976-01-01

    This paper considers the effect of the attractive part of the interaction potential on the scattering of He atoms from a LiF(001) surface. We calculate, in particular, the Lennard-Jones resonances on the intensities and the phases of the scattered amplitudes, using a square well in the front of a hard corrugated surface model. We show that the amplitudes for incident energies smaller than the depth of the well are dominated by the resonances

  6. Influence of DC electric field on the Lennard-Jones potential and phonon vibrations of carbon nanotube on catalyst

    International Nuclear Information System (INIS)

    Saeidi, Mohammadreza; Vaezzadeh, Majid; Badakhshan, Farzaneh

    2011-01-01

    Influence of DC electric field on carbon nanotube (CNT) growth in chemical vapor deposition is studied. Investigation of electric field effect in van der Waals interaction shows that increase in DC electric field raises the magnitude of attractive term of the Lennard-Jones potential. By using a theoretical model based on phonon vibrations of CNT on catalyst, it is shown that there is an optimum field for growth. Also it is observed that CNT under optimum electric field is longer than CNT in the absence of field. Finally, the relation between optimum DC electric field and type of catalyst is investigated and for some intervals of electric field, the best catalyst is introduced, which is very useful for experimental researches. -- Research highlights: → Influence of DC electric field on CNT growth in CVD. → Effect of electric field on van der Waals interaction between CNT and its catalyst. → Applying DC electric field increases attractive term of Lennard-Jonespotential. → There is an optimum DC field for CNT growth. → For catalyst with stronger van der Waals interaction, optimum field is smaller.

  7. Liquid-liquid interfacial properties of a symmetrical Lennard-Jones binary mixture

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Ruiz, F. J.; Blas, F. J., E-mail: felipe@uhu.es [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Física Aplicada, Universidad de Huelva, 21007 Huelva (Spain); Moreno-Ventas Bravo, A. I. [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Geología, Universidad de Huelva, 21007 Huelva (Spain)

    2015-09-14

    We determine the interfacial properties of a symmetrical binary mixture of equal-sized spherical Lennard-Jones molecules, σ{sub 11} = σ{sub 22}, with the same dispersive energy between like species, ϵ{sub 11} = ϵ{sub 22}, but different dispersive energies between unlike species low enough to induce phase separation. We use the extensions of the improved version of the inhomogeneous long-range corrections of Janecek [J. Phys. Chem. B 110, 6264 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] and Martínez-Ruiz et al. [J. Chem. Phys. 141, 184701 (2014)], to deal with the interaction energy and microscopic components of the pressure tensor. We perform Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of the symmetrical mixture with different cut-off distances r{sub c} and in combination with the inhomogeneous long-range corrections. The pressure tensor is obtained using the mechanical (virial) and thermodynamic route. The liquid-liquid interfacial tension is also evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the test-area methodology. This allows to check the validity of the recent extensions presented to deal with the contributions due to long-range corrections for intermolecular energy and pressure tensor in the case of binary mixtures that exhibit liquid-liquid immiscibility. In addition to the pressure tensor and the surface tension, we also obtain density profiles and coexistence densities and compositions as functions of pressure, at a given temperature. According to our results, the main effect of increasing the cut-off distance r{sub c} is to sharpen the liquid-liquid interface and to increase the width of the biphasic coexistence region. Particularly interesting is the presence of a relative minimum in the total density profiles of the symmetrical mixture. This minimum is related

  8. Phase diagram and universality of the Lennard-Jones gas-liquid system

    KAUST Repository

    Watanabe, Hiroshi

    2012-01-01

    The gas-liquid phase transition of the three-dimensional Lennard-Jones particles system is studied by molecular dynamics simulations. The gas and liquid densities in the coexisting state are determined with high accuracy. The critical point is determined by the block density analysis of the Binder parameter with the aid of the law of rectilinear diameter. From the critical behavior of the gas-liquid coexisting density, the critical exponent of the order parameter is estimated to be β = 0.3285(7). Surface tension is estimated from interface broadening behavior due to capillary waves. From the critical behavior of the surface tension, the critical exponent of the correlation length is estimated to be ν = 0.63(4). The obtained values of β and ν are consistent with those of the Ising universality class. © 2012 American Institute of Physics.

  9. Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential.

    Science.gov (United States)

    Geada, Isidro Lorenzo; Ramezani-Dakhel, Hadi; Jamil, Tariq; Sulpizi, Marialore; Heinz, Hendrik

    2018-02-19

    Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard-Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals.

  10. Viscoelastic crack propagation and closing with Lennard-Jones surface forces

    International Nuclear Information System (INIS)

    Greenwood, J A

    2007-01-01

    An analysis of the opening and closing of a crack in a viscoelastic solid has been made assuming a Lennard-Jones law of force acting between the crack faces. The results are compared with those of an earlier analysis in which a simple Dugdale model of the surface forces was assumed. The approximate 'reciprocal rule' between the apparent surface energies for opening and closing cracks is confirmed. At low speeds a linear relation between the apparent surface energy and the crack speed is found. The lengths of the process zone for opening and closing cracks are found to be very similar and so presumably are not responsible for the very different values of the apparent surface energy

  11. Viscoelastic crack propagation and closing with Lennard-Jones surface forces

    Energy Technology Data Exchange (ETDEWEB)

    Greenwood, J A [Department of Engineering, Trumpington Street, Cambridge, CB2 1PZ (United Kingdom)

    2007-03-21

    An analysis of the opening and closing of a crack in a viscoelastic solid has been made assuming a Lennard-Jones law of force acting between the crack faces. The results are compared with those of an earlier analysis in which a simple Dugdale model of the surface forces was assumed. The approximate 'reciprocal rule' between the apparent surface energies for opening and closing cracks is confirmed. At low speeds a linear relation between the apparent surface energy and the crack speed is found. The lengths of the process zone for opening and closing cracks are found to be very similar and so presumably are not responsible for the very different values of the apparent surface energy.

  12. Dynamics of vacancies in two-dimensional Lennard-Jones crystals

    Science.gov (United States)

    Yao, Zhenwei; Olvera de La Cruz, Monica

    2015-03-01

    Vacancies represent an important class of crystallographic defects, and their behaviors can be strongly coupled with relevant material properties. We report the rich dynamics of vacancies in two-dimensional Lennard-Jones crystals in several thermodynamic states. Specifically, we numerically observe significantly faster diffusion of the 2-point vacancy with two missing particles in comparison with other types of vacancies; it opens the possibility of doping 2-point vacancies into atomic materials to enhance atomic migration. In addition, the resulting dislocations in the healing of a long vacancy suggest the intimate connection between vacancies and topological defects that may provide an extra dimension in the engineering of defects in extensive crystalline materials for desired properties. We thank the financial support from the U.S. Department of Commerce, National Institute of Standards and Technology, the Office of the Director of Defense Research and Engineering (DDR&E) and the Air Force Office of Scientific Research.

  13. Viscous Growth in Spinodal Decomposition of the Two-component Lennard-Jones Model in Two Dimensions

    DEFF Research Database (Denmark)

    Laradji, M.; Toxvaerd, S.; Mouritsen, Ole G.

    1997-01-01

    The dynamics of phase separation of a two-component Lennard-Jones model in three dimensions is investigated by means of large scale molecular dynamics simulation. A systematic study over a wide range of quench temperatures within the coexistence region shows that the binary system reaches...

  14. Lennard-Jones parameters for small diameter carbon nanotubes and water for molecular mechanics simulations from van der Waals density functional calculations.

    Science.gov (United States)

    Kaukonen, M; Gulans, A; Havu, P; Kauppinen, E

    2012-03-05

    Lennard-Jones (LJ) parameters are derived for classical nonpolarizable force fields for carbon nanotubes (CNTs) and for CNT-water interaction from van der Waals (vdW) enhanced density functional calculations. The new LJ parameters for carbon-carbon interactions are of the same order as those previously used in the literature but differ significantly for CNT-water interactions. This may partially originate from the fact that in addition to pure vdW interactions the polarization and other quantum mechanics effects are embedded into the LJ-potential. Copyright © 2012 Wiley Periodicals, Inc.

  15. Enhancement of the droplet nucleation in a dense supersaturated Lennard-Jones vapor

    Energy Technology Data Exchange (ETDEWEB)

    Zhukhovitskii, D. I., E-mail: dmr@ihed.ras.ru [Joint Institute of High Temperatures, Russian Academy of Sciences, Izhorskaya 13, Bd. 2, 125412 Moscow (Russian Federation)

    2016-05-14

    The vapor–liquid nucleation in a dense Lennard-Jones system is studied analytically and numerically. A solution of the nucleation kinetic equations, which includes the elementary processes of condensation/evaporation involving the lightest clusters, is obtained, and the nucleation rate is calculated. Based on the equation of state for the cluster vapor, the pre-exponential factor is obtained. The latter diverges as a spinodal is reached, which results in the nucleation enhancement. The work of critical cluster formation is calculated using the previously developed two-parameter model (TPM) of small clusters. A simple expression for the nucleation rate is deduced and it is shown that the work of cluster formation is reduced for a dense vapor. This results in the nucleation enhancement as well. To verify the TPM, a simulation is performed that mimics a steady-state nucleation experiments in the thermal diffusion cloud chamber. The nucleating vapor with and without a carrier gas is simulated using two different thermostats for the monomers and clusters. The TPM proves to match the simulation results of this work and of other studies.

  16. Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems

    KAUST Repository

    Watanabe, H.

    2011-08-01

    Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also explained. A simple spatialdecomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute for Fusion Science (NIFS) and an SGI Altix ICE 8400EX system consisting of Intel Xeon processors which are 2.93 GHz at the Institute for Solid State Physics (ISSP), the University of Tokyo. The parallelization efficiency of the largest run, consisting of 4.1 billion particles with 8192 MPI processes, is about 73% relative to that of the smallest run with 128 MPI processes at NIFS, and it is about 66% relative to that of the smallest run with 4 MPI processes at ISSP. The factors causing the parallel overhead are investigated. It is found that fluctuations of the execution time of each process degrade the parallel efficiency. These fluctuations may be due to the interference of the operating system, which is known as OS Jitter.

  17. Comprehensive representation of the Lennard-Jones equation of state based on molecular dynamics simulation data

    Science.gov (United States)

    Pieprzyk, S.; Brańka, A. C.; Maćkowiak, Sz.; Heyes, D. M.

    2018-03-01

    The equation of state (EoS) of the Lennard-Jones fluid is calculated using a new set of molecular dynamics data which extends to higher temperature than in previous studies. The modified Benedict-Webb-Rubin (MBWR) equation, which goes up to ca. T ˜ 6, is reparametrized with new simulation data. A new analytic form for the EoS, which breaks the fluid range into two regions with different analytic forms and goes up to ca. T ≃ 35, is also proposed. The accuracy of the new formulas is at least as good as the MBWR fit and goes to much higher temperature allowing it to now encompass the Amagat line. The fitted formula extends into the high temperature range where the system can be well represented by inverse power potential scaling, which means that our specification of the equation of state covers the entire (ρ, T) plane. Accurate analytic fit formulas for the Boyle, Amagat, and inversion curves are presented. Parametrizations of the extrema loci of the isochoric, CV, and isobaric, CP, heat capacities are given. As found by others, a line maxima of CP terminates in the critical point region, and a line of minima of CP terminates on the freezing line. The line of maxima of CV terminates close to or at the critical point, and a line of minima of CV terminates to the right of the critical point. No evidence for a divergence in CV in the critical region is found.

  18. Effect of gold nanoparticles on structure and dynamics of binary Lennard-Jones liquid: Wave-vector space analysis

    Science.gov (United States)

    Separdar, L.; Davatolhagh, S.

    2016-12-01

    Molecular dynamics simulations at constant (N , V , T) are used to study the mutual effects of gold nanoparticles on the structure and dynamics of Kob-Andersen binary Lennard-Jones (BLJ) liquid within the framework of mode coupling theory of dynamic glass transition in the reciprocal space. The results show the 'softening' effect of the gold nanoparticles on the liquid dynamics in terms of (i) reducing the mode coupling crossover temperature Tc with respect to that of the bulk BLJ (i.e. BLJ without nanoparticles), (ii) decreasing the time interval of β-relaxation, and (iii) decreasing the exponent γ characterizing the power-law behavior of the α-relaxation time. This softening effect is explained in terms of the van der Waals attraction between the gold atoms comprising the nanoparticle and the BLJ host atoms, such that adsorption of host atoms onto the nanoparticle surface creates more space or free-volume for the other atoms to diffuse. By the same token interactions of purely excluded-volume-type are expected to result in the opposite effect. It is also noted that, much unlike BLJ host particles, the dynamics of gold nanoparticles is much less dependent on the wave-vector and that it exhibits a nearly exponential behavior in the α-relaxation regime.

  19. Equation of state and Helmholtz free energy for the atomic system of the repulsive Lennard-Jones particles.

    Science.gov (United States)

    Mirzaeinia, Ali; Feyzi, Farzaneh; Hashemianzadeh, Seyed Majid

    2017-12-07

    Simple and accurate expressions are presented for the equation of state (EOS) and absolute Helmholtz free energy of a system composed of simple atomic particles interacting through the repulsive Lennard-Jones potential model in the fluid and solid phases. The introduced EOS has 17 and 22 coefficients for fluid and solid phases, respectively, which are regressed to the Monte Carlo (MC) simulation data over the reduced temperature range of 0.6≤T * ≤6.0 and the packing fraction range of 0.1 ≤ η ≤ 0.72. The average absolute relative percent deviation in fitting the EOS parameters to the MC data is 0.06 and 0.14 for the fluid and solid phases, respectively. The thermodynamic integration method is used to calculate the free energy using the MC simulation results. The Helmholtz free energy of the ideal gas is employed as the reference state for the fluid phase. For the solid phase, the values of the free energy at the reduced density equivalent to the close-packed of a hard sphere are used as the reference state. To check the validity of the predicted values of the Helmholtz free energy, the Widom particle insertion method and the Einstein crystal technique of Frenkel and Ladd are employed. The results obtained from the MC simulation approaches are well agreed to the EOS results, which show that the proposed model can reliably be utilized in the framework of thermodynamic theories.

  20. Drying and wetting transitions of a Lennard-Jones fluid: Simulations and density functional theory

    Science.gov (United States)

    Evans, Robert; Stewart, Maria C.; Wilding, Nigel B.

    2017-07-01

    We report a theoretical and simulation study of the drying and wetting phase transitions of a truncated Lennard-Jones fluid at a flat structureless wall. Binding potential calculations predict that the nature of these transitions depends on whether the wall-fluid attraction has a long ranged (LR) power law decay or is instead truncated, rendering it short ranged (SR). Using grand canonical Monte Carlo simulation and classical density functional theory, we examine both cases in detail. We find that for the LR case wetting is first order, while drying is continuous (critical) and occurs exactly at zero attractive wall strength, i.e., in the limit of a hard wall. In the SR case, drying is also critical but the order of the wetting transition depends on the truncation range of the wall-fluid potential. We characterize the approach to critical drying and wetting in terms of the density and local compressibility profiles and via the finite-size scaling properties of the probability distribution of the overall density. For the LR case, where the drying point is known exactly, this analysis allows us to estimate the exponent ν∥, which controls the parallel correlation length, i.e., the extent of vapor bubbles at the wall. Surprisingly, the value we obtain is over twice that predicted by mean field and renormalization group calculations, despite the fact that our three dimensional system is at the upper critical dimension where mean field theory for critical exponents is expected to hold. Possible reasons for this discrepancy are discussed in the light of fresh insights into the nature of near critical finite-size effects.

  1. Chemical potential and solid-solid equilibrium of near-spherical Lennard-Jones dumbbell crystal

    International Nuclear Information System (INIS)

    Lee, Sangwon; Kim, Minkyu; Chang, Jaeeon

    2016-01-01

    We studied the orientational order-disorder transition of crystals made up of near-spherical Lennard-Jones dumbbells, of which reduced bond lengths are 0.225, 0.250 and 0.275. Various techniques of Monte Carlo (MC) simulations are used to calculate the chemical potentials of ordered and disordered crystals, and thereby to predict order disorder phase transition. First, we performed NPT MC simulations to determine crystal structure, equilibrium positions and orientations of the molecules. We then calculated the free energies of the crystals using the expanded ensemble MC simulations combined with the Einstein-molecule method and the thermodynamic integration method. The solid-solid phase equilibrium is determined from the free energy profiles of the individual phases by equating the chemical potential. The predictions of phase transition obtained from the conventional NPT MC simulation and the free energy simulation were in excellent agreement with each other, which confirms the validity of the present method of calculating the chemical potential of crystal. In addition, the Gibbs-Duhem integration was performed to obtain a complete coexistence curve between the two crystal phases. Orientational probability distributions of molecular axes were analyzed to find the characteristic behavior of rotational motion of molecule in the crystal. At sufficiently low temperature, flipping rotation of molecule in the ordered crystal is suppressed. In contrast, the flipping rotation occurs at higher temperature close to the transition while orientationally ordered structure is still maintained. In the free energy calculation, such a unique rotational behavior requires to use a suitable form of external rotational potential with proper symmetry number. The present study demonstrates how one can judiciously choose a correct simulation scheme for the calculation of chemical potentials of molecular crystals.

  2. Drying and wetting transitions of a Lennard-Jones fluid: Simulations and density functional theory.

    Science.gov (United States)

    Evans, Robert; Stewart, Maria C; Wilding, Nigel B

    2017-07-28

    We report a theoretical and simulation study of the drying and wetting phase transitions of a truncated Lennard-Jones fluid at a flat structureless wall. Binding potential calculations predict that the nature of these transitions depends on whether the wall-fluid attraction has a long ranged (LR) power law decay or is instead truncated, rendering it short ranged (SR). Using grand canonical Monte Carlo simulation and classical density functional theory, we examine both cases in detail. We find that for the LR case wetting is first order, while drying is continuous (critical) and occurs exactly at zero attractive wall strength, i.e., in the limit of a hard wall. In the SR case, drying is also critical but the order of the wetting transition depends on the truncation range of the wall-fluid potential. We characterize the approach to critical drying and wetting in terms of the density and local compressibility profiles and via the finite-size scaling properties of the probability distribution of the overall density. For the LR case, where the drying point is known exactly, this analysis allows us to estimate the exponent ν ∥ , which controls the parallel correlation length, i.e., the extent of vapor bubbles at the wall. Surprisingly, the value we obtain is over twice that predicted by mean field and renormalization group calculations, despite the fact that our three dimensional system is at the upper critical dimension where mean field theory for critical exponents is expected to hold. Possible reasons for this discrepancy are discussed in the light of fresh insights into the nature of near critical finite-size effects.

  3. Size-effects on the surface tension near the critical point: Monte Carlo simulations of the Lennard-Jones fluid

    Science.gov (United States)

    Goujon, Florent; Ghoufi, Aziz; Malfreyt, Patrice

    2018-02-01

    We report Monte Carlo (MC) simulations of the Lennard-Jones (LJ) fluid at the liquid-vapor interface in the critical region. A slab-based tail method is associated with the MC simulations to approach as close as possible the critical point (T∗ = 0.98 TC∗) . We investigate then the impact of system-sizes on the surface tension and coexisting densities by considering very large box dimensions for which the surface tension is independent of system-sizes at low temperatures.

  4. The self-referential method for linear rigid bodies: application to hard and Lennard-Jones dumbbells.

    Science.gov (United States)

    Sweatman, Martin B; Atamas, Alexander; Leyssale, Jean-Marc

    2009-01-14

    The self-referential (SR) method incorporating thermodynamic integration (TI) [Sweatman et al., J. Chem. Phys. 128, 064102 (2008)] is extended to treat systems of rigid linear bodies. The method is then applied to obtain the canonical ensemble Helmholtz free energy of the alpha-N(2) and plastic face centered cubic phases of systems of hard and Lennard-Jones dumbbells using Monte Carlo simulations. Generally good agreement with reference literature data is obtained, which indicates that the SR-TI method is potentially very general and robust.

  5. Density-scaling exponents and virial potential-energy correlation coefficients for the (2n, n) Lennard-Jones system

    DEFF Research Database (Denmark)

    Friisberg, Ida Marie; Costigliola, Lorenzo; Dyre, Jeppe C.

    2017-01-01

    This paper investigates the relation between the density-scaling exponent γ and the virial potentialenergy coefficient R at several thermodynamic state points in three dimensions for the generalized (2n, n) Lennard-Jones (LJ) system for n = 4, 9, 12, 18, as well as for the standard n = 6 LJ system...... in two, three, and four dimensions. The state points studied include many low-density states at which the virial potentialenergy correlations are not strong. For these state points we find the roughly linear relation γ ∼= 3n R/d in d dimensions. This result is discussed in light of the approximate...... → 1, a limit that is approached at high densities and/or high temperatures at which the repulsive r−2n term dominates the physics....

  6. Premelting, solid-fluid equilibria, and thermodynamic properties in the high density region based on the Lennard-Jones potential

    Science.gov (United States)

    Köster, Andreas; Mausbach, Peter; Vrabec, Jadran

    2017-10-01

    The Lennard-Jones potential is used to study the high density fluid and face centered cubic solid state region, including solid-fluid equilibria. Numerous thermodynamic properties are considered, elucidating the behavior of matter in this poorly studied region. The present molecular simulation results are extensively compared to the latest and most accurate equation of state models for fluid and solid phases. It is shown that current models do not cover the thermodynamics of the system adequately near the solid-fluid phase transition. Furthermore, thermodynamic stability is analyzed, indicating that published solid-fluid coexistence data may not be correct at high temperatures. Particular attention is paid to the premelting zone, a range of states close to the melting line, which is characterized by strong variations of several thermodynamic properties. Because the underlying microscopic mechanisms are not yet fully understood, it is hoped that these data may contribute to the development of a theoretical framework for describing premelting effects.

  7. Fusion process of Lennard-Jones clusters: global minima and magic numbers formation

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2004-01-01

    measured for the clusters of noble gas atoms. Our method serves as an efficient alternative to the global optimization techniques based on the Monte-Carlo simulations and it can be applied for the solutions of a broad variety of problems in which atomic cluster structure is important.......We present a new theoretical framework for modeling the fusion process of Lennard–Jones (LJ) clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing paths up to the cluster size of 150 atoms....... We demonstrate that in this way all known global minima structures of the (LJ)-clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence for the clusters of noble gas atoms and compare...

  8. Icosahedron-fcc transition size by molecular dynamics simulation of Lennard-Jones clusters at a finite temperature.

    Science.gov (United States)

    Ikeshoji, T; Torchet, G; de Feraudy, M F; Koga, K

    2001-03-01

    We studied finite-temperature ensembles of solid clusters produced by cooling liquid droplets either by evaporation or by a thermostat through a molecular dynamics calculation using the Lennard-Jones potential. The ensembles consist of either single or binary component clusters with 25% of the atoms 8% smaller in diameter than the other 75%. These clusters (380 clusters in total) exhibit various structures in the size range of n=160-2200, where n is the number of atoms in a cluster. For increasing size, the clusters show a gradual transition from icosahedral to a variety of structures: decahedral, face centered cubic, a small amount of hexagonal, and some icosahedral structures. They are asymmetrical or faulted. Electron diffraction patterns calculated with average structure factors of clusters after grouping them into several size regions are very similar to those experimentally observed. The size transition is around n=450 for single component clusters whatever the cooling process, evaporation or thermostat. This size is smaller than the experimental transition size estimated for argon clusters formed in a supersonic expansion. The transition size for binary component clusters is around n=600 for evaporative cooling, and larger for thermostatic cooling. The larger transition size found for the binary component clusters is consistent with the large icosahedral Au-Fe and Au-Cu alloy clusters observed experimentally.

  9. Scaling relation and regime map of explosive gas–liquid flow of binary Lennard-Jones particle system

    KAUST Repository

    Inaoka, Hajime

    2012-02-01

    We study explosive gasliquid flows caused by rapid depressurization using a molecular dynamics model of Lennard-Jones particle systems. A unique feature of our model is that it consists of two types of particles: liquid particles, which tend to form liquid droplets, and gas particles, which remain supercritical gaseous states under the depressurization realized by simulations. The system has a pipe-like structure similar to the model of a shock tube. We observed physical quantities and flow regimes in systems with various combinations of initial particle number densities and initial temperatures. It is observed that a physical quantity Q, such as pressure, at position z measured along a pipe-like system at time t follows a scaling relation Q(z,t)=Q(zt) with a scaling function Q(ζ). A similar scaling relation holds for time evolution of flow regimes in a system. These scaling relations lead to a regime map of explosive flows in parameter spaces of local physical quantities. The validity of the scaling relations of physical quantities means that physics of equilibrium systems, such as an equation of state, is applicable to explosive flows in our simulations, though the explosive flows involve highly nonequilibrium processes. In other words, if the breaking of the scaling relations is observed, it means that the explosive flows cannot be fully described by physics of equilibrium systems. We show the possibility of breaking of the scaling relations and discuss its implications in the last section. © 2011 Elsevier B.V. All rights reserved.

  10. Vapour-liquid equilibria of two-centre Lennard-Jones fluids from the NpT plus test particle method

    Science.gov (United States)

    Kriebel, Christian; Müller, Andreas; Winkelmann, Jochen; Fischer, Johann

    Vapour-liquid phase equilibria (VLE) are determined from the NpT plus test particle method for two-centre Lennard-Jones fluids of elongations L* = 0·22, 0·3292, 0·505, and 0·67. The resulting vapour pressures as well as the saturated vapour and liquid densities are correlated by simple equations. The thermodynamic consistency of the VLE data is confirmed on the basis of the Clausius-Clapeyron equation. Comparison is made with results from previous simulations, and from perturbation theory.

  11. Monte Carlo simulation of some thermophysical properties of two-centre Lennard-Jones fluids along the vapour-liquid equilibrium curve

    Science.gov (United States)

    Kronome, Gergely; Liszi, Janos; Szalai, Istvan

    The vapour pressures, saturated liquid and vapour densities, enthalpies of vaporization, isobaric, and saturation heat capacities are calculated for ethane and ethylene along their vapour-liquid equilibrium (VLE) curves from Monte Carlo simulations using the extended NpT plus test particle (XNpT + TP) method (Boda, D., Liszi, J., and Szalai, I., 1995, Chem. Phys. Lett. , 235, 140). The substances are modelled by two-centre Lennard-Jones molecules of elongations L * = 0.67 for ethane and L * = 0.74 for ethylene. Simulation results are compared with correlated experimental data. In the case of ethylene new values are required for the model parameters to obtain a good agreement with experimental data along the VLE curve. Our results show that the XNpT + TP method is appropriate for the simulation of caloric properties of molecular fluids along the VLE curve.

  12. Effect of dispersive long-range corrections to the pressure tensor: The vapour-liquid interfacial properties of the Lennard-Jones system revisited

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Ruiz, F. J.; Blas, F. J., E-mail: felipe@uhu.es [Departamento de Física Aplicada, Universidad de Huelva, 21071 Huelva (Spain); Centro de Investigación de Física Teórica y Matemática, Universidad de Huelva, 21071 Huelva (Spain); Mendiboure, B. [Laboratoire des Fluides Complexes et leurs Réservoirs, UMR5150, Université de Pau et des Pays de l’Adour, B. P. 1155, Pau Cedex 64014 (France); Moreno-Ventas Bravo, A. I. [Centro de Investigación de Física Teórica y Matemática, Universidad de Huelva, 21071 Huelva (Spain); Departamento de Geología, Facultad de Ciencias Experimentales, Universidad de Huelva, 21071 Huelva (Spain)

    2014-11-14

    We propose an extension of the improved version of the inhomogeneous long-range corrections of Janeček [J. Phys. Chem. B 110, 6264–6269 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] to account for the intermolecular potential energy of spherical, rigid, and flexible molecular systems, to deal with the contributions to the microscopic components of the pressure tensor due to the dispersive long-range corrections. We have performed Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of spherical Lennard-Jones molecules with different cutoff distances, r{sub c} = 2.5, 3, 4, and 5σ. In addition, we have also considered cutoff distances r{sub c} = 2.5 and 3σ in combination with the inhomogeneous long-range corrections proposed in this work. The normal and tangential microscopic components of the pressure tensor are obtained using the mechanical or virial route in combination with the recipe of Irving and Kirkwood, while the macroscopic components are calculated using the Volume Perturbation thermodynamic route proposed by de Miguel and Jackson [J. Chem. Phys. 125, 164109 (2006)]. The vapour-liquid interfacial tension is evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the Test-Area methodology. In addition to the pressure tensor and the surface tension, we also obtain density profiles, coexistence densities, vapour pressure, critical temperature and density, and interfacial thickness as functions of temperature, paying particular attention to the effect of the cutoff distance and the long-range corrections on these properties. According to our results, the main effect of increasing the cutoff distance (at fixed temperature) is to sharpen the vapour-liquid interface, to decrease the vapour pressure, and to increase the width of the biphasic coexistence region. As a result, the interfacial

  13. Effect of surface tension on the behavior of adhesive contact based on Lennard-Jones potential law

    Science.gov (United States)

    Zhu, Xinyao; Xu, Wei

    2018-02-01

    The present study explores the effect of surface tension on adhesive contact behavior where the adhesion is interpreted by long-range intermolecular forces. The adhesive contact is analyzed using the equivalent system of a rigid sphere and an elastic half space covered by a membrane with surface tension. The long-range intermolecular forces are modeled with the Lennard‒Jones (L‒J) potential law. The current adhesive contact issue can be represented by a nonlinear integral equation, which can be solved by Newton‒Raphson method. In contrast to previous studies which consider intermolecular forces as short-range, the present study reveals more details of the features of adhesive contact with surface tension, in terms of jump instabilities, pull-off forces, pressure distribution within the contact area, etc. The transition of the pull-off force is not only consistent with previous studies, but also presents some new interesting characteristics in the current situation.

  14. Explicit expressions of self-diffusion coefficient, shear viscosity, and the Stokes-Einstein relation for binary mixtures of Lennard-Jones liquids

    International Nuclear Information System (INIS)

    Ohtori, Norikazu; Ishii, Yoshiki

    2015-01-01

    Explicit expressions of the self-diffusion coefficient, D i , and shear viscosity, η sv , are presented for Lennard-Jones (LJ) binary mixtures in the liquid states along the saturated vapor line. The variables necessary for the expressions were derived from dimensional analysis of the properties: atomic mass, number density, packing fraction, temperature, and the size and energy parameters used in the LJ potential. The unknown dependence of the properties on each variable was determined by molecular dynamics (MD) calculations for an equimolar mixture of Ar and Kr at the temperature of 140 K and density of 1676 kg m −3 . The scaling equations obtained by multiplying all the single-variable dependences can well express D i and η sv evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for D i can also explain the dual atomic-mass dependence, i.e., the average-mass and the individual-mass dependence; the latter accounts for the “isotope effect” on D i . The Stokes-Einstein (SE) relation obtained from these equations is fully consistent with the SE relation for pure LJ liquids and that for infinitely dilute solutions. The main differences from the original SE relation are the presence of dependence on the individual mass and on the individual energy parameter. In addition, the packing-fraction dependence turned out to bridge another gap between the present and original SE relations as well as unifying the SE relation between pure liquids and infinitely dilute solutions

  15. A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution.

    Science.gov (United States)

    Sumi, Tomonari; Maruyama, Yutaka; Mitsutake, Ayori; Koga, Kenichiro

    2016-06-14

    In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids.

  16. Explicit expressions of self-diffusion coefficient, shear viscosity, and the Stokes-Einstein relation for binary mixtures of Lennard-Jones liquids

    Energy Technology Data Exchange (ETDEWEB)

    Ohtori, Norikazu, E-mail: ohtori@chem.sc.niigata-u.ac.jp [Department of Chemistry, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181 (Japan); Ishii, Yoshiki [Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181 (Japan)

    2015-10-28

    Explicit expressions of the self-diffusion coefficient, D{sub i}, and shear viscosity, η{sub sv}, are presented for Lennard-Jones (LJ) binary mixtures in the liquid states along the saturated vapor line. The variables necessary for the expressions were derived from dimensional analysis of the properties: atomic mass, number density, packing fraction, temperature, and the size and energy parameters used in the LJ potential. The unknown dependence of the properties on each variable was determined by molecular dynamics (MD) calculations for an equimolar mixture of Ar and Kr at the temperature of 140 K and density of 1676 kg m{sup −3}. The scaling equations obtained by multiplying all the single-variable dependences can well express D{sub i} and η{sub sv} evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for D{sub i} can also explain the dual atomic-mass dependence, i.e., the average-mass and the individual-mass dependence; the latter accounts for the “isotope effect” on D{sub i}. The Stokes-Einstein (SE) relation obtained from these equations is fully consistent with the SE relation for pure LJ liquids and that for infinitely dilute solutions. The main differences from the original SE relation are the presence of dependence on the individual mass and on the individual energy parameter. In addition, the packing-fraction dependence turned out to bridge another gap between the present and original SE relations as well as unifying the SE relation between pure liquids and infinitely dilute solutions.

  17. Lennard-Jones fluids in a nanochannel

    NARCIS (Netherlands)

    Hartkamp, Remco; Luding, Stefan; Nuernberg Messe GmbH,

    2010-01-01

    During the past few decades molecular dynamics has been a widely applied tool to simulate fluid confined in micro/nano geometries. What makes interfacial fluids fundamentally different from the bulk fluid is the fact that their density varies considerably over microscopic distances. A class of such

  18. Daniel Jones

    DEFF Research Database (Denmark)

    underrated, impact on the American structuralist school. This eight volume collection makes available the first editions of Jones' standard books, i.e. The Pronunciation of English (1909), An English Pronouncing Dictionary (1917) and An Outline of English Phonetics (1918). In addition, Jones' crucial......Daniel Jones (1881-1967) played a significant role in the emergence of phonetics as a fully developed academic discipline in the first half of the twentieth century. His views on the subject not only provided the foundations for the British tradition but also had a considerable, and often...... pioneering works, now out of print for many decades, are made easily accessible to scholars once again. Numerous articles encompassing a variety of phonetic/phonological topics, for example, phonemic analysis, juncture, models of pronunciation, and historiography, are also included (converted where necessary...

  19. Equilibrium fluctuations of the Lennard-Jones cluster surface

    Science.gov (United States)

    Zhukhovitskii, D. I.

    2008-11-01

    Spectra of the cluster surface equilibrium fluctuations are treated by decomposition into the bulk and net capillary ones. The bulk fluctuations without capillary ones are simulated by the surface of a cluster truncated by a sphere. The bulk fluctuation spectrum is shown to be generated primarily by the discontinuity in the spatial distribution of cluster internal particles. The net capillary fluctuation slice spectrum is obtained in molecular dynamics simulation by subtraction of the bulk fluctuation spectrum from the total one. This net spectrum is in the best agreement with a theoretical estimation if we assume the intrinsic surface tension to be independent of the wave number. The wave number cutoff is brought in balance with the intrinsic surface tension and excess surface area induced by the capillary fluctuations. It is shown that the ratio of the ordinary surface tension to the intrinsic one can be considered as a universal constant independent of the temperature and cluster size.

  20. Intermolecular interactions and the thermodynamic properties of supercritical fluids.

    Science.gov (United States)

    Yigzawe, Tesfaye M; Sadus, Richard J

    2013-05-21

    The role of different contributions to intermolecular interactions on the thermodynamic properties of supercritical fluids is investigated. Molecular dynamics simulation results are reported for the energy, pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound of fluids interacting via both the Lennard-Jones and Weeks-Chandler-Andersen potentials. These properties were obtained for a wide range of temperatures, pressures, and densities. For each thermodynamic property, an excess value is determined to distinguish between attraction and repulsion. It is found that the contributions of intermolecular interactions have varying effects depending on the thermodynamic property. The maxima exhibited by the isochoric and isobaric heat capacities, isothermal compressibilities, and thermal expansion coefficient are attributed to interactions in the Lennard-Jones well. Repulsion is required to obtain physically realistic speeds of sound and both repulsion and attraction are necessary to observe a Joule-Thomson inversion curve. Significantly, both maxima and minima are observed for the isobaric and isochoric heat capacities of the supercritical Lennard-Jones fluid. It is postulated that the loci of these maxima and minima converge to a common point via the same power law relationship as the phase coexistence curve with an exponent of β = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids.

  1. Impact of wall potential on the fluid-wall interaction in a cylindrical capillary and a generalized Kelvin equation

    International Nuclear Information System (INIS)

    Jakubov, T.S.; Mainwaring, D.E.

    2006-01-01

    In the present work a generalized Kelvin equation for a fluid confined in thick-walled cylindrical capillary is developed. This has been accomplished by including the potential energy function for interaction between a solid wall of a capillary and a confined fluid into the Kelvin equation. Using the Lennard-Jones 12-6 potential, an explicit form of the potential energy functions as expressed by hypergeometrical functions have been derived-firstly, for the interaction between a solid wall and a test atom placed at an arbitrary point in a long open-end capillary, and thereafter for the body-body interaction between the solid wall and a confined Lennard-Jones fluid. Further, this generalized Kelvin equation has been applied to detailed description hysteresis phenomena in such capillaries. All numerical calculations have been carried out for the model argon-graphite system at 90 K

  2. Koltunud Indiana Jones / Kutt Kommel

    Index Scriptorium Estoniae

    Kommel, Kutt

    2008-01-01

    Steven Spielbergi neljas Indiana Jones'i film Harrison Fordiga nimiosas "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull") : Ameerika Ühendriigid 2008

  3. The impact range for smooth wall–liquid interactions in nanoconfined liquids

    DEFF Research Database (Denmark)

    Ingebrigtsen, Trond; Dyre, J. C.

    2014-01-01

    decade. Inspired by these observations, we present results from molecular dynamics computer simulations of four nanoconfined liquids (the single-component Lennard-Jones liquid, the Kob–Andersen binary Lennard-Jones mixture, an asymmetric dumbbell model, and the Dzugutov liquid) demonstrating also...

  4. Molecular Force Field Development for Aqueous Electrolytes: 1. Incorporating Appropriate Experimental Data and the Inadequacy of Simple Electrolyte Force Fields Based on Lennard-Jones and Point Charge Interactions with Lorentz-Berthelot Rules

    Czech Academy of Sciences Publication Activity Database

    Moučka, F.; Nezbeda, Ivo; Smith, W. R.

    2013-01-01

    Roč. 9, č. 11 (2013), s. 5076-5085 ISSN 1549-9618 Grant - others:GA MŠMT(CZ) LH12019; NSERCC(CA) OGP1041; UJEP(CZ) GAP208/12/0105 Institutional support: RVO:67985858 Keywords : sodium-chloride * ionic hydration * free-energy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.310, year: 2013

  5. Formerly Utilized MED/AEC Sites Remedial Action Program. Project management plan for the decontamination of Jones Laboratory, Ryerson Physical Laboratory, and Eckhart Hall, the University of Chicago, Chicago, Illinois

    International Nuclear Information System (INIS)

    Flynn, K.F.; Smith, W.H.; Wynveen, R.A.

    1984-01-01

    The Department of Energy (DOE) has in place a plan for the decontamination and decommissioning of contaminated sites that had been formerly utilized by the Manhattan Engineering District (MED) and/or the Atomic Energy Commission. This plan is referred to as the Formerly Utilized Sites Remedial Action Program (FUSRAP). Among these sites are Jones Laboratory, Ryerson Physical Laboratory and Eckhart Hall of The University of Chicago at Chicago, Illinois. This document represents the Project Management Plan for the decontamination of these facilities. 13 references, 3 figures, 1 table

  6. Formerly Utilized MED/AEC Sites Remedial Action Program. Project management plan for the decontamination of Jones Laboratory, Ryerson Physical Laboratory, and Eckhart Hall, the University of Chicago, Chicago, Illinois

    Energy Technology Data Exchange (ETDEWEB)

    Flynn, K.F.; Smith, W.H.; Wynveen, R.A.

    1984-01-01

    The Department of Energy (DOE) has in place a plan for the decontamination and decommissioning of contaminated sites that had been formerly utilized by the Manhattan Engineering District (MED) and/or the Atomic Energy Commission. This plan is referred to as the Formerly Utilized Sites Remedial Action Program (FUSRAP). Among these sites are Jones Laboratory, Ryerson Physical Laboratory and Eckhart Hall of The University of Chicago at Chicago, Illinois. This document represents the Project Management Plan for the decontamination of these facilities. 13 references, 3 figures, 1 table.

  7. B Stanly Jones Retnam

    Indian Academy of Sciences (India)

    Volume 33 Issue 5 October 2010 pp 525-528. Effect of nanoparticles on tensile, impact and fatigue properties of fibre reinforced plastics · R Nagalingam S ... Volume 37 Issue 5 August 2014 pp 1059-1064. Effects of fibre orientation on mechanical properties of hybrid bamboo/glass fibre polymer composites · B Stanly Jones ...

  8. Formerly utilized MED/AEC sites Remedial Action Program. Report of the decontamination of Jones Chemical Laboratory, Ryerson Physical Laboratory, and Eckhart Hall, the University of Chicago, Chicago, Illinois

    Energy Technology Data Exchange (ETDEWEB)

    Wynuveen, R.A.; Smith, W.H.; Sholeen, C.M.; Flynn, K.F.

    1984-08-01

    The US Department of Energy (DOE) has implemented a program to decontaminate radioactively contaminated sites that were formerly utilized by the Manhattan Engineer District (MED) and/or the Atomic Energy Commission (AEC) for activities that included handling of radioactive material. This program is referred to as the ''Formerly Utilized Sites Remedial Action Program'' (FUSRAP). Among these sites are Jones Chemical Laboratory, Ryerson Physical Laboratory, Kent Chemical Laboratory, and Eckhart Hall of The University of Chicago, Chicago, Illinois. Since 1977, the University of Chicago decontaminated Kent Chemical Laboratory as part of a facilities renovation program. All areas of Eckhart Hall, Ryerson Physical Laboratory, and Jones Chemical Laboratory that had been identified as contaminated in excess of current guidelines in the 1976-1977 surveys were decontaminated to levels where no contamination could be detected relative to natural backgrounds. All areas that required defacing to achieve this goal were restored to their original condition. The radiological evaluation of the sewer system, based primarily on the radiochemical analyses of sludge and water samples, indicated that the entire sewer system is potentially contaminated. While this evaluation was defined as part of this project, the decontamination of the sewer system was not included in the purview of this effort. The documentation included in this report substantiates the judgment that all contaminated areas identified in the earlier reports in the three structures included in the decontamination effort (Eckhart Hall, Ryerson Physical Laboratory, and Jones Chemical Laboratory) were cleaned to levels commensurate with release for unrestricted use.

  9. Note: Nonpolar solute partial molar volume response to attractive interactions with water.

    Science.gov (United States)

    Williams, Steven M; Ashbaugh, Henry S

    2014-01-07

    The impact of attractive interactions on the partial molar volumes of methane-like solutes in water is characterized using molecular simulations. Attractions account for a significant 20% volume drop between a repulsive Weeks-Chandler-Andersen and full Lennard-Jones description of methane interactions. The response of the volume to interaction perturbations is characterized by linear fits to our simulations and a rigorous statistical thermodynamic expression for the derivative of the volume to increasing attractions. While a weak non-linear response is observed, an average effective slope accurately captures the volume decrease. This response, however, is anticipated to become more non-linear with increasing solute size.

  10. Evaluation of HIV drug interaction web sites.

    Science.gov (United States)

    Sheehan, Nancy L; Kelly, Deborah V; Tseng, Alice L; van Heeswijk, Rolf P G; Béïque, Lizanne C; Hughes, Christine A

    2003-11-01

    Clinicians frequently consult HIV drug interaction Web sites of unknown quality. To systematically review and identify HIV drug interaction Web sites of high quality and usefulness for healthcare professionals. Relevant Web sites were identified through a structured search on commonly used search engines. An assessment tool containing 4 domains (content, reliability, access restrictions, ease of navigation) was developed. English and French Web sites were selected for review if they included HIV drug interaction information directed to healthcare professionals. Web sites were excluded if antiretroviral interaction data were not available or were out of date. Commercial online databases and sites that required payment were not included. Seventeen HIV pharmacists from across Canada participated in the review. The Web sites were ranked with total mean scores. Mean scores for each domain were then analyzed. Interrater agreement and ANOVA using the rater as a covariate were determined. Nine Web sites met the criteria for review. Web sites from Toronto General Hospital (Canada), HIVinSite (beta version) (US), and the University of Liverpool (UK) ranked highest for total mean scores and for content. Other Web sites were found to be reliable, accessible, and easy to navigate; however, they did not consistently include unpublished data or data on herbal preparations, recreational drugs, or multiple interactions. Three HIV interaction Web sites of high quality were identified that can be valuable tools for HIV and non-HIV health-care professionals. Regular reviews are necessary in order to keep pace with the growing body of HIV interaction data and the constant evolution of Web sites.

  11. Thermodynamic properties of confined square-well fluids with multiple associating sites

    Science.gov (United States)

    Trejos, Víctor M.; Quintana-H, Jacqueline

    2018-02-01

    In this work, a molecular simulation study of confined hard-spheres particles with square-well (SW) attractive interactions with two and four associating SW sites based on the first-order perturbation form of Wertheim's theory is presented. An extended version of the Gibbs ensemble technique for inhomogeneous fluids [A. Z. Panagiotopoulos, Mol. Phys. 62, 701 (1987)] is used to predict the adsorption density profiles for associating fluids confined between opposite parallel walls. The fluid is confined in four kinds of walls: hard-wall, SW wall, Lennard-Jones (LJ) 12-6 wall potential, and LJ 10-4 wall potential. We analyze the behavior of the confined system for several supercritical temperatures as a function of variation of molecular parameters: potential range λ, bulk densities ρb*, pore width H, cutoff range interaction rc*, and range of the potential and depth of the particle-wall (λw, ɛw*). Additionally, we include predictions for liquid-vapor coexistence of bulk associative particles and how their critical properties are modified by the presence of associative sites in the molecule. The molecular simulation data presented in this work are of prime importance to the development of theoretical approaches for inhomogeneous fluids as classical density functional theory. The simulation results presented here are resourceful for predicting adsorption isotherms of real associating fluids such as water.

  12. Tagging, Encoding, and Jones Optimality

    DEFF Research Database (Denmark)

    Danvy, Olivier; López, Pablo Ernesto Martínes

    2003-01-01

    A partial evaluator is said to be Jones-optimal if the result of specializing a self-interpreter with respect to a source program is textually identical to the source program, modulo renaming. Jones optimality has already been obtained if the self-interpreter is untyped. If the selfinterpreter is...

  13. Indiana Jones ja kristallpealuu kuningriik / Jaanus Noormets

    Index Scriptorium Estoniae

    Noormets, Jaanus

    2008-01-01

    Steven Spielbergi neljas Indiana Jones'i film Harrison Fordiga nimiosas "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull") : Ameerika Ühendriigid 2008

  14. Thermal motion in proteins: Large effects on the time-averaged interaction energies

    Energy Technology Data Exchange (ETDEWEB)

    Goethe, Martin, E-mail: martingoethe@ub.edu; Rubi, J. Miguel [Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona (Spain); Fita, Ignacio [Institut de Biologia Molecular de Barcelona, Baldiri Reixac 10, 08028 Barcelona (Spain)

    2016-03-15

    As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.

  15. Stabiilne Ashley Jones / Svea Suvi

    Index Scriptorium Estoniae

    Suvi, Svea

    2006-01-01

    Ameerika teleseriaali "Vaprad ja ilusad" ("The Bold and the Beautiful") osatäitja Ashley Jones (Bridget Forrester). Sama artikkel pealkirjaga "Uus Bridget" : Nädal, 30. jan. 2006, nr. 4, lk. 12 : ill

  16. Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials.

    Science.gov (United States)

    Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D

    2017-08-14

    Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.

  17. Optimization of linear and branched alkane interactions with water to simulate hydrophobic hydration

    Science.gov (United States)

    Ashbaugh, Henry S.; Liu, Lixin; Surampudi, Lalitanand N.

    2011-08-01

    Previous studies of simple gas hydration have demonstrated that the accuracy of molecular simulations at capturing the thermodynamic signatures of hydrophobic hydration is linked both to the fidelity of the water model at replicating the experimental liquid density at ambient pressure and an accounting of polarization interactions between the solute and water. We extend those studies to examine alkane hydration using the transferable potentials for phase equilibria united-atom model for linear and branched alkanes, developed to reproduce alkane phase behavior, and the TIP4P/2005 model for water, which provides one of the best descriptions of liquid water for the available fixed-point charge models. Alkane site/water oxygen Lennard-Jones cross interactions were optimized to reproduce the experimental alkane hydration free energies over a range of temperatures. The optimized model reproduces the hydration free energies of the fitted alkanes with a root mean square difference between simulation and experiment of 0.06 kcal/mol over a wide temperature range, compared to 0.44 kcal/mol for the parent model. The optimized model accurately reproduces the temperature dependence of hydrophobic hydration, as characterized by the hydration enthalpies, entropies, and heat capacities, as well as the pressure response, as characterized by partial molar volumes.

  18. Long-range interaction of anisotropic systems

    KAUST Repository

    Zhang, Junyi

    2015-02-01

    The first-order electrostatic interaction energy between two far-apart anisotropic atoms depends not only on the distance between them but also on their relative orientation, according to Rayleigh-Schrödinger perturbation theory. Using the first-order interaction energy and the continuum model, we study the long-range interaction between a pair of parallel pristine graphene sheets at zero temperature. The asymptotic form of the obtained potential density, &epsi:(D) &prop: ?D ?3 ?O(D?4), is consistent with the random phase approximation and Lifshitz theory. Accordingly, neglectance of the anisotropy, especially the nonzero first-order interaction energy, is the reason why the widely used Lennard-Jones potential approach and dispersion corrections in density functional theory give a wrong asymptotic form ε(D) &prop: ?D?4. © EPLA, 2015.

  19. No More Indiana Jones Warehouses

    Science.gov (United States)

    Pannapacker, William

    2012-01-01

    In "Raiders of the Lost Ark," Indiana Jones--perhaps the last heroic professor to appear in a major Hollywood film--survives a series of adventures involving spiders, snakes, treacherous colleagues, and countless Nazis who are determined to recover the ark of the covenant for their "Fuhrer." Apparently the ark has mystical powers. Ultimately,…

  20. Interface bonding in silicon oxide nanocontacts: interaction potentials and force measurements

    Science.gov (United States)

    Wierez-Kien, M.; Craciun, A. D.; Pinon, A. V.; Le Roux, S.; Gallani, J. L.; Rastei, M. V.

    2018-04-01

    The interface bonding between two silicon-oxide nanoscale surfaces has been studied as a function of atomic nature and size of contacting asperities. The binding forces obtained using various interaction potentials are compared with experimental force curves measured in vacuum with an atomic force microscope. In the limit of small nanocontacts (typically measured with sensitive probes the bonding is found to be influenced by thermal-induced fluctuations. Using interface interactions described by Morse, embedded atom model, or Lennard-Jones potential within reaction rate theory, we investigate three bonding types of covalent and van der Waals nature. The comparison of numerical and experimental results reveals that a Lennard-Jones-like potential originating from van der Waals interactions captures the binding characteristics of dry silicon oxide nanocontacts, and likely of other nanoscale materials adsorbed on silicon oxide surfaces. The analyses reveal the importance of the dispersive surface energy and of the effective contact area which is altered by stretching speeds. The mean unbinding force is found to decrease as the contact spends time in the attractive regime. This contact weakening is featured by a negative aging coefficient which broadens and shifts the thermal-induced force distribution at low stretching speeds.

  1. How Competitive Interactions Affect the Self-Assembly of Confined Janus Dumbbells.

    Science.gov (United States)

    Bordin, José Rafael; Krott, Leandro B

    2017-04-27

    We explore the self-assembled morphologies of Janus nanoparticles under cylindrical confinement. Langevin dynamics simulations are employed to study the behavior of two types of dimers inside cylinders with distinct radius. The first type of nanoparticle was modeled using one monomer that interacts by a standard Lennard-Jones potential and another monomer that is modeled using a purely repulsive two length scale shoulder potential. The second type is composed by a Lennard-Jones monomer and a repulsive monomer which interacts by the purely repulsive Weeks-Chandler-Andersen potential, which have only one length scale. The two length scale potential used in the first type of nanoparticle models a monomer with competitive interaction. Our results show that the aggregated structures are completely distinct for each type of nanoparticle. Also, our simulations indicate that the cylinder radius can be used to control the type of self-assembled cluster. Small clusters, tubular and donut-like micelles with central holes, with potential application to molecule encapsulation were observed regarding the nanoparticle specificities and the cylinder radii. Also, bilayer lamellae structures were obtained depending on the type of nanoparticle and the cylinder size.

  2. GPU-accelerated Gibbs ensemble Monte Carlo simulations of Lennard-Jonesium

    Science.gov (United States)

    Mick, Jason; Hailat, Eyad; Russo, Vincent; Rushaidat, Kamel; Schwiebert, Loren; Potoff, Jeffrey

    2013-12-01

    This work describes an implementation of canonical and Gibbs ensemble Monte Carlo simulations on graphics processing units (GPUs). The pair-wise energy calculations, which consume the majority of the computational effort, are parallelized using the energetic decomposition algorithm. While energetic decomposition is relatively inefficient for traditional CPU-bound codes, the algorithm is ideally suited to the architecture of the GPU. The performance of the CPU and GPU codes are assessed for a variety of CPU and GPU combinations for systems containing between 512 and 131,072 particles. For a system of 131,072 particles, the GPU-enabled canonical and Gibbs ensemble codes were 10.3 and 29.1 times faster (GTX 480 GPU vs. i5-2500K CPU), respectively, than an optimized serial CPU-bound code. Due to overhead from memory transfers from system RAM to the GPU, the CPU code was slightly faster than the GPU code for simulations containing less than 600 particles. The critical temperature Tc∗=1.312(2) and density ρc∗=0.316(3) were determined for the tail corrected Lennard-Jones potential from simulations of 10,000 particle systems, and found to be in exact agreement with prior mixed field finite-size scaling calculations [J.J. Potoff, A.Z. Panagiotopoulos, J. Chem. Phys. 109 (1998) 10914].

  3. A detailed investigation on the global minimum structures of mixed rare-gas clusters: geometry, energetics, and site occupancy.

    Science.gov (United States)

    Marques, Jorge M C; Pereira, Francisco B

    2013-03-05

    We performed a global minimum search of mixed rare-gas clusters by applying an evolutionary algorithm (EA), which was recently proposed for binary atomic systems (Marques and Pereira, Chem. Phys. Lett. 2010, 485, 211). Before being applied to the potentials used in this work, the EA was further tested against results previously reported for the Ar(N)Xe(38-N) clusters and several new putative global minima were discovered. We employed either simple Lennard-Jones (LJ) potentials or more realistic functions to describe pair interactions in Ar(N)Kr(38-N), Ar(N)Xe(38-N), and Kr(N)Xe(38-N) clusters. The long-range tail of the pair-potentials shows some influence on the energetic features and shape of the structure of clusters. In turn, core-shell type structures are mostly observed for global minima of the binary rare-gas clusters, for both accurate and LJ potentials. However, the long-range tail of the potential may have influence on the type of atoms that segregate on the surface or form the core of the cluster. While relevant differences for the preferential site occupancy occur between the two potentials for Ar(N)Kr(38-N) (for N > 21), the type of atoms that segregate on the surface for Ar(N)Xe(38-N) and Kr(N)Xe(38-N) clusters is unaffected by the accuracy of the long-range part of the interaction in almost all cases. Moreover, the global minimum search for model-potentials in binary systems reveals that the surface-site occupancy is mainly determined by the combination of two parameters: the size ratio of the two types of particles forming the cluster and the minimum-energy ratio corresponding to the pair-interactions between unlike atoms. Copyright © 2012 Wiley Periodicals, Inc.

  4. Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains.

    Science.gov (United States)

    Makowski, Mariusz; Liwo, Adam; Sobolewski, Emil; Scheraga, Harold A

    2011-05-19

    A new model of side-chain-side-chain interactions for charged side-chains of amino acids, to be used in the UNRES force-field, has been developed, in which a side chain consists of a nonpolar and a charged site. The interaction energy between the nonpolar sites is composed of a Gay-Berne and a cavity term; the interaction energy between the charged sites consists of a Lennard-Jones term, a Coulombic term, a generalized-Born term, and a cavity term, while the interaction energy between the nonpolar and charged sites is composed of a Gay-Berne and a polarization term. We parametrized the energy function for the models of all six pairs of natural like-charged amino-acid side chains, namely propionate-propionate (for the aspartic acid-aspartic acid pair), butyrate-butyrate (for the glutamic acid-glutamic acid pair), propionate-butyrate (for the aspartic acid-glutamic acid pair), pentylamine cation-pentylamine cation (for the lysine-lysine pair), 1-butylguanidine cation-1-butylguanidine cation (for the arginine-arginine pair), and pentylamine cation-1-butylguanidine cation (for the lysine-arginine pair). By using umbrella-sampling molecular dynamics simulations in explicit TIP3P water, we determined the potentials of mean force of the above-mentioned pairs as functions of distance and orientation and fitted analytical expressions to them. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules were well represented by analytical expressions for all systems. The values of the parameters of all the energy components are physically reasonable, which justifies use of such potentials in coarse-grain protein-folding simulations. © 2011 American Chemical Society

  5. STS-98 Crew Interview: Tom Jones

    Science.gov (United States)

    2001-01-01

    The STS-98 Mission Specialist Tom Jones is seen being interviewed. He answers questions about his inspiration to become an astronaut, his career path, and his training. He gives details on the mission's goals and significance, and the payload and hardware it brings to the International Space Station (ISS). Mr. Jones discusses his role in the mission's spacewalks and activities.

  6. Bacterial Biofilms in Jones Tubes.

    Science.gov (United States)

    Ahn, Eric S; Hauck, Matthew J; Kirk Harris, Jonathan; Robertson, Charles E; Dailey, Roger A

    To investigate the presence and microbiology of bacterial biofilms on Jones tubes (JTs) by direct visualization with scanning electron microscopy and polymerase chain reaction (PCR) of representative JTs, and to correlate these findings with inflammation and/or infection related to the JT. In this study, prospective case series were performed. JTs were recovered from consecutive patients presenting to clinic for routine cleaning or recurrent irritation/infection. Four tubes were processed for scanning electron microscopy alone to visualize evidence of biofilms. Two tubes underwent PCR alone for bacterial quantification. One tube was divided in half and sent for scanning electron microscopy and PCR. Symptoms related to the JTs were recorded at the time of recovery. Seven tubes were obtained. Five underwent SEM, and 3 out of 5 showed evidence of biofilms (60%). Two of the 3 biofilms demonstrated cocci and the third revealed rods. Three tubes underwent PCR. The predominant bacteria identified were Pseudomonadales (39%), Pseudomonas (16%), and Staphylococcus (14%). Three of the 7 patients (43%) reported irritation and discharge at presentation. Two symptomatic patients, whose tubes were imaged only, revealed biofilms. The third symptomatic patient's tube underwent PCR only, showing predominantly Staphylococcus (56%) and Haemophilus (36%) species. Two of the 4 asymptomatic patients also showed biofilms. All symptomatic patients improved rapidly after tube exchange and steroid antibiotic drops. Bacterial biofilms were variably present on JTs, and did not always correlate with patients' symptoms. Nevertheless, routine JT cleaning is recommended to treat and possibly prevent inflammation caused by biofilms.

  7. Strategic Analysis and Associated Management Products Supporting the Reengineering of Bayne-Jones Army Community Hospital: Consultative Products and Findings

    National Research Council Canada - National Science Library

    Fulton, Larry

    1998-01-01

    .... ̂Product 2 - "Bayne-Jones Army Community Hospital Web Site," a strategic Internet web site for marketing health and wellness, the TRICARE medical network, the Joint Readiness Training Center Surgeon's...

  8. Interaction potentials and their effect on crystal nucleation and symmetry

    International Nuclear Information System (INIS)

    Hsu, C.S.; Rahman, A.

    1979-01-01

    Molecular dynamics technique has been used to study the effect of the interaction potential on crystal nucleation and the symmetry of the nucleated phase. Four systems, namely rubidium, Lennard-Jones, rubidium-truncated, and Lennard-Jones-truncated, have been studied each at reduced density 0.95. Two types of calculations were performed. Firstly, starting from a liquid state, each system was quenched rapidly to a reduced temperature of approx.0.1. The nucleation process for these systems was monitored by studying the time dependence of temperature and the pair correlation function, and the resulting crystalline structure analyzed using among other properties the Voronoi polyhedra. Only in the case of rubidium was a b.c.c. structure nucleated. In the other three cases we obtained a f.c.c. ordering. Secondly, we have studied the effect of changing the interaction potential in a system which has already achieved an ordered state under the action of some other potential. After establishing a b.c.c. structure in a rubidium system, the change in the symmetry of the system was studied when the pair potential was modified to one of the other three forms. The results from both types of calculations are consistent: the rubidium potential leads to a b.c.c. structure while the other three potentials give an f.c.c. structure. Metastable disordered structures were not obtained in any of the calculations. However, the time elapse between the moment when the system is quick-quenched and the moment when nucleation occurs appears to depend upon the potential of interaction

  9. Biomechanical Comparison of Intramedullary Screw Versus Low-Profile Plate Fixation of a Jones Fracture.

    Science.gov (United States)

    Huh, Jeannie; Glisson, Richard R; Matsumoto, Takumi; Easley, Mark E

    2016-04-01

    Intramedullary screw fixation of fifth metatarsal Jones fractures often produces satisfactory results, however, nonunion and refracture rates are not negligible. The low-profile "hook" plate is an alternative fixation method that has been promoted to offer improved rotational control at the fracture site, but this remains to be proven. The purpose of this study was to document biomechanical performance differences between this type of plate and a contemporary solid, dual-pitch intramedullary screw in a cadaveric Jones fracture model. Simulated Jones fractures were created in 8 matched pairs of fresh-frozen cadaveric fifth metatarsals. One bone from each pair was stabilized using an intramedullary TriMed Jones Screw and the other using a TriMed Jones Fracture Plate (TriMed, Inc, Santa Clarita, CA). Controlled bending and torsional loads were applied. Bending stiffness and fracture site angulation, as well as torsional stiffness, peak torque, and fracture site rotation were quantified and compared. Intramedullary screw fixation demonstrated greater bending stiffness and less fracture site angulation than plate fixation during plantar-to-dorsal and lateral-to-medial bending. Torsional stiffness of screw-fixed metatarsals exceeded that of plate-fixed bones at initial loading; however, as rotation progressed, the plate resisted torque better than the screw. No difference in peak torque was demonstrable between fixation methods, but it was reached earlier in specimens fixed with screws and later in those fixed with plates as rotation progressed. In this cadaveric Jones fracture model, intramedullary screw fixation demonstrated bending stiffness and resistance to early torsional loading that was superior to that offered by plate fixation. Although low-profile "hook" plates offer an alternative for fixation of fifth metatarsal Jones fractures, intramedullary screw fixation may provide better resistance to bending and initiation of fracture site rotation. The influence of

  10. Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models

    DEFF Research Database (Denmark)

    Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob

    2018-01-01

    embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdWTS) scheme aimed......Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable...... at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdWTSexpression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We...

  11. Review of "Cultures merging" by Eric Jones

    OpenAIRE

    Schlicht, Ekkehart

    2016-01-01

    This is an electronic reprint of a review of the book "Cultures Merging: A Historical and Economic Critique of Culture" by Eric L. Jones, Princeton: Princeton University Press that appeared in the Journal of Institutional and Theoretical Economics 2007, vol. 163, issue 3, pages 526-529, URL \\url{http://www.jstor.org/stable/40752660}.

  12. Formerly utilized MED/AEC sites remedial action program. Radiological survey of The George Herbert Jones Chemical Laboratory, The University of Chicago, Chicago, Illinois, June 13-17, 1977

    International Nuclear Information System (INIS)

    Wynveen, R.A.; Smith, W.H.; Mayes, C.B.; Justus, A.L.

    1982-05-01

    A comprehensive radiological survey was conducted at George Herbert Jones Chemical Laboratory at the University of Chicago, Chicago, Illinois. Radiochemistry for the MED/AEC project was performed in this building in the 1940s. The building is now used as laboratories, offices, and classrooms. The survey was undertaken to determine the location and quantities of any radioactive materials remaining from the MED/AEC operations. Forty-three spots of contamination possibly resulting from MED/AEC occupancy in 17 rooms exceeded the allowable limits as given in the ANSI Standard N13.12. Under current use conditions, the potential for radiation exposure to occupants of this building from these sources of contamination is remote. Concentrations of radon daughters in the air of the building, as measured with grab-sampling techniques, were below the limit of 0.01 WL above background as given in the Surgeon General's Guidelines. No long-lived radionuclides were detected in any air sample. Concentrations of radionuclides in soil samples from near the laboratory generally indicated background levels. In order to reduce the potential for radiation exposure, remedial measures such as stabilization of the contamination in place would be applicable as a short-term measure. In order to reduce the risk in the event that building modifications take place in the future, health physics procedures and coverage are recommended. The long-term solution would involve decontamination by removal of the radioactive residues from the 17 rooms or areas where contamination possibly resulting from MED/AEC activities was detected

  13. Atomistic modeling of interfacial interaction between polyvinyl chloride and polypropylene with Boron-Nitride monolayer sheet: A density functional theory study

    Science.gov (United States)

    Hamed Mashhadzadeh, A.; Fereidoon, A.; Ghorbanzadeh Ahangari, M.

    2017-11-01

    In present work, we performed Density Functional Theory calculation (DFT) to prepare polypropylene (PP) and polyvinyl chloride (PVC) nanocomposite. For mentioned purpose, we chose Boron-Nitride graphene (BN-graphene) sheet as nano reinforcement. Next, we calculated adsorbed energy between these two polymeric matrixes with BN-monolayer sheet. Our DFT results demonstrated that interaction energy between PP/BN-graphene and PVC/BN-graphene are equal, approximately, because in mentioned two nanocomposite systems, polymer matrix approached to nano reinforcement from hydrogen atom in optimized structure. Then, the adsorbed energy and equilibrium distance between mentioned polymeric matrixes and BN-graphene sheet in nanocomposite with increasing the number of polymer monomers onto surface of BN-graphene were calculated. Finally, we modeled van der Waals interfacial interaction between polymer matrixes and nano reinforcement with linear classical spring by using lennard-jones parameters.

  14. 75 FR 20802 - Safety Zone; New York Air Show at Jones Beach State Park, Atlantic Ocean off of Jones Beach...

    Science.gov (United States)

    2010-04-21

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; New York Air Show at Jones Beach State Park, Atlantic Ocean off of Jones Beach, Wantagh, NY AGENCY: Coast Guard, DHS. ACTION: Notice of proposed... Air Show at Jones Beach State Park in Wantagh, New York. This proposed safety zone is necessary to...

  15. Environmental Research Translation: Enhancing Interactions with Communities at Contaminated Sites

    Science.gov (United States)

    Ramirez-Andreotta, Monica D.; Brusseau, Mark L.; Artiola, Janick F.; Maier, Raina M.; Gandolfi, A. Jay

    2014-01-01

    The characterization and remediation of contaminated sites are complex endeavors fraught with numerous challenges. One particular challenge that is receiving increased attention is the development and encouragement of full participation by communities and community members affected by a given site in all facets of decision-making. Many disciplines have been grappling with the challenges associated with environmental and risk communication, public participation in environmental data generation, and decision-making and increasing community capacity. The concepts and methods developed by these disciplines are reviewed, with a focus on their relevance to the specific dynamics associated with environmental contamination sites. The contributions of these disciplines are then synthesized and integrated to help develop Environmental Research Translation (ERT), a proposed framework for environmental scientists to promote interaction and communication among involved parties at contaminated sites. This holistic approach is rooted in public participation approaches to science, which includes: a transdisciplinary team, effective collaboration, information transfer, public participation in environmental projects, and a cultural model of risk communication. Although there are challenges associated with the implementation of ERT, it is anticipated that application of this proposed translational science method could promote more robust community participation at contaminated sites. PMID:25173762

  16. Repository site characterization and development - interaction with the public

    International Nuclear Information System (INIS)

    Beale, H.

    1993-01-01

    Radioactive waste management policy in the UK has a chequered past. Endeavours to develop new disposal facilities for radioactive waste have included consideration of green field sites and existing underground openings. Currently Nirex is implementing a programme of geological investigations at Sellafield, in Cumbria, and has brought forwards its plans for development there of an underground rock characterization facility (RCF). This paper reviews the evolution of UK radioactive waste management policy, since the 1970s, outlines the Company's current activities at Sellafield and points to the importance of interactions with the local community. 2 refs

  17. Reduction U(VI) using jones reductor

    International Nuclear Information System (INIS)

    Simbolon, S.

    1996-01-01

    Reduction of dissolved oxide uranium in sulfuric acid use of reductor Jones Zn (Hg) was carried out. The reduced uranium sulfate solution was analyzed its U(IV) by measuring its absorbance on 652 nm and compared to oxidation U(IV) solution with KMnO 4 solution. It was found that the comparison was in a good agreement. However, measuring of absorbance of U(VI) solution on 429 nm result of oxidation U(IV) with KMnO 4 solution was not change. (author)

  18. Interactivity in brand web sites: cognitive, affective, and behavioral responses explained by consumers’ online flow experience

    NARCIS (Netherlands)

    van Noort, G.; Voorveld, H.A.M.; van Reijmersdal, E.A.

    2012-01-01

    Web site interactivity creates numerous opportunities for marketers to persuade online consumers and receives extensive attention in the marketing literature. However, research on cognitive and behavioral responses to web site interactivity is scarce, and more importantly, it does not provide

  19. Plutonium volumetric titration after reduction on a Jones' column

    International Nuclear Information System (INIS)

    Description of a plutonium analysis method, in hydrochloric or sulfuric solution, for plutonium content over 2 mg, by reduction from plutonium IV to plutonium III in a Jones' column. Volumetic titration by ceric sulfate with ferrous orthophenanthroline [fr

  20. The interactive authority of brand web sites: a new tool provides new insights

    NARCIS (Netherlands)

    Voorveld, H.; Neijens, P.; Smit, E.

    2010-01-01

    This study aims to develop a new coding instrument to examine the interactivity of the Web sites of brands. A new instrument contains 47 interactive functions and is directly linked to theory on interactivity. To test the applicability of the instrument, the study investigates the interactivity of

  1. Chuck Jones lahkus, tema kangelased elavad edasi / Neeme Korv

    Index Scriptorium Estoniae

    Korv, Neeme, 1974-

    2002-01-01

    Suri Chuck Jones (1912-2002), kuulus USA animafilmirežissöör, kelle animasari "Tom & Jerry" on praegugi Eestis väga populaarne. Ta on loonud enam kui 300 animafilmi, saanud 3 Oscarit ning 1996. aastal ka elutöö Oscari. Eesti lapsed nägid nõukogude ajal esmakordselt Chuck Jones'i loomingut Raivo Järvi lastesaadetes "Laupäeval koos isaga"

  2. Jones phase microscopy of transparent and anisotropic samples.

    Science.gov (United States)

    Wang, Zhuo; Millet, Larry J; Gillette, Martha U; Popescu, Gabriel

    2008-06-01

    We developed an interferometric microscopy technique, referred to as Jones phase microscopy, capable of extracting the spatially resolved Jones polarization matrix associated with transparent and anisotropic samples. This is a generalization of quantitative phase imaging, which is recovered from one diagonal element of the measured matrix. The principle of the technique is demonstrated with measurements of a liquid crystal spatial light modulator and the potential for live cell imaging with experiments on live neurons in culture.

  3. Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

    Science.gov (United States)

    Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei

    2012-01-01

    Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with

  4. 21 CFR 866.5150 - Bence-Jones proteins immunological test system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Bence-Jones proteins immunological test system....5150 Bence-Jones proteins immunological test system. (a) Identification. A Bence-Jones proteins... the Bence-Jones proteins in urine and plasma. Immunoglobulin molecules normally consist of pairs of...

  5. Social Networking Sites as Communication, Interaction, and Learning Environments: Perceptions and Preferences of Distance Education Students

    Science.gov (United States)

    Bozkurt, Aras; Karadeniz, Abdulkadir; Kocdar, Serpil

    2017-01-01

    The advent of Web 2.0 technologies transformed online networks into interactive spaces in which user-generated content has become the core material. With the possibilities that emerged from Web 2.0, social networking sites became very popular. The capability of social networking sites promises opportunities for communication and interaction,…

  6. NEWS: John Goronwy Jones (1920-1999)

    Science.gov (United States)

    Jennison, Brenda M.

    2000-05-01

    John Goronwy Jones Gron Jones, as he was known to all, was a champion of Physics Education and his death, shortly before his eightieth birthday, robbed physics teachers of a colleague who fought many battles on their behalf. He was not shy of taking issue with anyone in authority who might be putting forward policies which would harm his great love: Physics Education and Physics Teaching. His photograph shows a man with an impish grin, looking friend and foe alike straight in the eye, before delivering the death blow to an argument which was founded on less than common sense. At other times he would listen patiently to the woes of colleagues before offering them fatherly/grandfatherly advice so that whoever was on the receiving end would go away feeling better for the encounter. Gron was born in Swansea and educated at Lewis Boys Grammar School in Glamorgan before entering University College Cardiff first of all as a mathematician before graduating in Physics in 1941. After his war service in the RAF, working on signals and radar development, he returned to do an MSc in X-ray crystallography before completing a PGCE in Bristol. What then passed for teacher training in all institutions left him wary of returning to train teachers himself but after 14 years spent teaching physics in three schools he returned to Cardiff and began a 25 year career in teacher training. He and his two colleagues, Clifford Othen (chemistry) and Douglas Hillier (biology) built up the Cardiff Science Centre as a focus for initial and in-service science teacher training in South Wales. The triumvirate was well known and a power to be reckoned with. They created links between the University Science Departments and the Schools. Gron knew the local schools and their physics teachers intimately. Cardiff became a focus for science education both nationally and internationally. He was a frequent attender at both ICPE (International Commission for Physics Education) and GIREP (International Physics

  7. Networked Mobilities and new sites of mediated interaction

    DEFF Research Database (Denmark)

    Jensen, Ole B.

    2008-01-01

    This paper takes point of departure in an understanding of mobility as an important cultural dimension to contemporary life. The movement of objects, signs, and people constitutes material sites of networked relationships. However, as an increasing number of mobility practices are making up our...

  8. Peptide microarrays to probe for competition for binding sites in a protein interaction network

    NARCIS (Netherlands)

    Sinzinger, M.D.S.; Ruttekolk, I.R.R.; Gloerich, J.; Wessels, H.; Chung, Y.D.; Adjobo-Hermans, M.J.W.; Brock, R.E.

    2013-01-01

    Cellular protein interaction networks are a result of the binding preferences of a particular protein and the entirety of interactors that mutually compete for binding sites. Therefore, the reconstruction of interaction networks by the accumulation of interaction networks for individual proteins

  9. Evaluation of the Jones jig appliance for distal molar movement.

    Science.gov (United States)

    Brickman, C D; Sinha, P K; Nanda, R S

    2000-11-01

    The purpose of this study was to determine the effects of the Jones jig appliance on distal movement of maxillary molars and reciprocal effects on premolars and maxillary incisors. Cephalometric radiographs before and after orthodontic treatment of 72 consecutively treated patients, 46 females and 26 males, were measured to define treatment changes attributed to the Jones jig. Comparative measurements were made on a matched sample of 35 patients (20 females and 15 males) treated with cervical headgear by the same clinician. Both series of patients were treated to correct an Angle Class II molar relationship. The molar correction in the Jones jig patients consisted primarily of molar distal movement. Dental, soft tissue, and skeletal changes were evaluated and compared for significant differences between techniques. The results from the Jones jig sample showed the mean maxillary first molar distal movement was 2.51 mm, with distal tipping of 7.53 degrees. The mean reciprocal mesial movement of the maxillary premolar was 2.0 mm, with mesial tipping of 4.76 degrees. The maxillary first molar extruded 0.14 mm; the maxillary premolar extruded 1.88 mm. The maxillary second molars were also moved distally 2.02 mm and tipped distally 7.89 degrees. The longitudinal assessment (initial to completion of orthodontic treatment) showed significant differences between the Jones jig sample and the cervical headgear sample for lower lip to E-line and SNA. The Jones jig sample showed a mean decrease in lower lip to E-line of 0.25 mm versus 1.20 mm (P jig sample versus 1.20 degrees (P jig sample and cervical headgear sample did not show significant differences of the final position in either linear or angular measurements of the maxillary first molars and corresponding premolar-incisor anchor units. The Jones jig appliance demonstrated treatment results comparable with those of the sample treated with cervical headgear. The Jones jig sample demonstrated effective distal molar

  10. Flight into sanity. Jones's allegation of Ferenczi's mental deterioration reconsidered.

    Science.gov (United States)

    Bonomi, C

    1999-06-01

    In 'The Life and Work of Sigmund Freud', Volume III, Ernest Jones explained Ferenczi's final contributions as the product of a mental deterioration based on a progressive psychosis. Erich Fromm collected various testimonies by witnesses of Ferenczi's last years, all contrasting with Jones's assertions, and challenged Jones's manner of writing history. However, since Fromm was himself a dissident, and his witnesses were pupils, relatives or friends of Ferenczi's, they were discarded as 'partisans'. The present study aims at reconsidering the question of Ferenczi's insanity on the basis of many unpublished documents. The consulted documents do not support Jones's allegation of Ferenczi's insanity. At the same time, they show that Jones's allegation was not a one-man fabrication, but reflected a shared belief, eliciting many questions about the nature of this belief, the lack of scrutiny that characterised its spreading, and its possible function within the psychoanalytic community. It is suggested that Ferenczi's personality and teaching, especially his emphasis on the need to accept the patient's criticism, contrasted with the dominant conception of psychoanalysis, based on the analyst's infallibility.

  11. Interactive web site and app for early magnetic resonance education

    DEFF Research Database (Denmark)

    Hanson, Lars G.

    2016-01-01

    formulations of MR are much closer to classical descriptions than to typical quantum inspired myths frequent in literature. This opens for intuitive educational computer simulation using modern web technologies offering excellent interactive possibilities for experimentation.......Teaching and understanding basic Magnetic Resonance (MR) is a challenge. This is clear from the educational literature that often repeats misinterpretations of quantum mechanics reminiscent of its earliest formulations (see www.drcmr.dk/MR that also links to the developed software). Modern quantum...

  12. Wetting behavior of nonpolar nanotubes in simple dipolar liquids for varying nanotube diameter and solute-solvent interactions.

    Science.gov (United States)

    Rana, Malay Kumar; Chandra, Amalendu

    2015-01-21

    Atomistic simulations of model nonpolar nanotubes in a Stockmayer liquid are carried out for varying nanotube diameter and nanotube-solvent interactions to investigate solvophobic interactions in generic dipolar solvents. We have considered model armchair type single-walled nonpolar nanotubes with increasing radii from (5,5) to (12,12). The interactions between solute and solvent molecules are modeled by the well-known Lennard-Jones and repulsive Weeks-Chandler-Andersen potentials. We have investigated the density profiles and microscopic arrangement of Stockmayer molecules, orientational profiles of their dipole vectors, time dependence of their occupation, and also the translational and rotational motion of solvent molecules in confined environments of the cylindrical nanopores and also in their external peripheral regions. The present results of structural and dynamical properties of Stockmayer molecules inside and near atomistically rough nonpolar surfaces including their wetting and dewetting behavior for varying interactions provide a more generic picture of solvophobic effects experienced by simple dipolar liquids without any specific interactions such as hydrogen bonds.

  13. Fibromodulin Interacts with Collagen Cross-linking Sites and Activates Lysyl Oxidase*

    Science.gov (United States)

    Bihan, Dominique; Bonna, Arkadiusz; Rubin, Kristofer; Farndale, Richard W.

    2016-01-01

    The hallmark of fibrotic disorders is a highly cross-linked and dense collagen matrix, a property driven by the oxidative action of lysyl oxidase. Other fibrosis-associated proteins also contribute to the final collagen matrix properties, one of which is fibromodulin. Its interactions with collagen affect collagen cross-linking, packing, and fibril diameter. We investigated the possibility that a specific relationship exists between fibromodulin and lysyl oxidase, potentially imparting a specific collagen matrix phenotype. We mapped the fibromodulin-collagen interaction sites using the collagen II and III Toolkit peptide libraries. Fibromodulin interacted with the peptides containing the known collagen cross-linking sites and the MMP-1 cleavage site in collagens I and II. Interestingly, the interaction sites are closely aligned within the quarter-staggered collagen fibril, suggesting a multivalent interaction between fibromodulin and several collagen helices. Furthermore, we detected an interaction between fibromodulin and lysyl oxidase (a major collagen cross-linking enzyme) and mapped the interaction site to 12 N-terminal amino acids on fibromodulin. This interaction also increases the activity of lysyl oxidase. Together, the data suggest a fibromodulin-modulated collagen cross-linking mechanism where fibromodulin binds to a specific part of the collagen domain and also forms a complex with lysyl oxidase, targeting the enzyme toward specific cross-linking sites. PMID:26893379

  14. Fibromodulin Interacts with Collagen Cross-linking Sites and Activates Lysyl Oxidase.

    Science.gov (United States)

    Kalamajski, Sebastian; Bihan, Dominique; Bonna, Arkadiusz; Rubin, Kristofer; Farndale, Richard W

    2016-04-08

    The hallmark of fibrotic disorders is a highly cross-linked and dense collagen matrix, a property driven by the oxidative action of lysyl oxidase. Other fibrosis-associated proteins also contribute to the final collagen matrix properties, one of which is fibromodulin. Its interactions with collagen affect collagen cross-linking, packing, and fibril diameter. We investigated the possibility that a specific relationship exists between fibromodulin and lysyl oxidase, potentially imparting a specific collagen matrix phenotype. We mapped the fibromodulin-collagen interaction sites using the collagen II and III Toolkit peptide libraries. Fibromodulin interacted with the peptides containing the known collagen cross-linking sites and the MMP-1 cleavage site in collagens I and II. Interestingly, the interaction sites are closely aligned within the quarter-staggered collagen fibril, suggesting a multivalent interaction between fibromodulin and several collagen helices. Furthermore, we detected an interaction between fibromodulin and lysyl oxidase (a major collagen cross-linking enzyme) and mapped the interaction site to 12 N-terminal amino acids on fibromodulin. This interaction also increases the activity of lysyl oxidase. Together, the data suggest a fibromodulin-modulated collagen cross-linking mechanism where fibromodulin binds to a specific part of the collagen domain and also forms a complex with lysyl oxidase, targeting the enzyme toward specific cross-linking sites. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Regulatory site of inorganic pyrophosphatase. Interaction with substrate analogs

    International Nuclear Information System (INIS)

    Baikov, A.A.; Pavlov, A.R.; Avaeva, S.M.

    1986-01-01

    The effect of four PP 1 analogs with the structure PXP (X = N, C), phosphate, and the complex Cr(H 2 O) 4 PP 1 on the activity of inorganic pyrophosphatase from baker's yeast was studied over a wide range of substrate (Mg-PP 1 ) concentrations (lower limit 0.5 μM). The enzyme activity decreased in the presence of imidodiphosphate, hydroxymethane diphosphonate [PC(OH)P], and P 1 , and a double reciprocal plot of the rate of hydrolysis of Mg-PP 1 versus its concentration became linear. Small amounts of methane diphosphonate (PCP), ethane-1-hydroxy-1,1-diphosphonate (0.1-1μM), and Cr(H 2 O) 4 PP 1 (10 μM) activated the enzyme almost 2-fold by a competitive mechanism. The activation was due to an increase in the affinity of the protein for the activating Mg 2+ ion. Ultrafiltration showed that the pyrophosphatase molecule has 2.1 and 3.1 binding sites for PCP and PC(OHP)P, respectively. These results confirm the hypothesis that the enzyme contains a regulatory site whose occupation by PP 1 , P 1 , and substrate analogs increases the affinity of the protein for the activating metal

  16. Interactive learning tool: site-specific schema crossword puzzles.

    Science.gov (United States)

    Berryhill, Tammy Lynn

    2011-01-01

    Staying abreast of the TNM and Collaborative Staging updates can be overwhelming. Reading voluminous amounts of study material may be the last task on a to-do list for the busy cancer registrar. Crossword puzzles can provide an alternative, interesting learning tool to support continuing education. Researching puzzle clue answers serves as an interactive approach. Puzzles included in this article are considered "informal" as their layout is not symmetrical, but the learning value is not adversely affected. Try them out and see what you know, or don't know. It can be fun!

  17. Guts of surfaces and the colored Jones polynomial

    CERN Document Server

    Futer, David; Purcell, Jessica

    2013-01-01

    This monograph derives direct and concrete relations between colored Jones polynomials and the topology of incompressible spanning surfaces in knot and link complements. Under mild diagrammatic hypotheses, we prove that the growth of the degree of the colored Jones polynomials is a boundary slope of an essential surface in the knot complement. We show that certain coefficients of the polynomial measure how far this surface is from being a fiber for the knot; in particular, the surface is a fiber if and only if a particular coefficient vanishes. We also relate hyperbolic volume to colored Jones polynomials. Our method is to generalize the checkerboard decompositions of alternating knots. Under mild diagrammatic hypotheses, we show that these surfaces are essential, and obtain an ideal polyhedral decomposition of their complement. We use normal surface theory to relate the pieces of the JSJ decomposition of the  complement to the combinatorics of certain surface spines (state graphs). Since state graphs have p...

  18. Method of predicting Splice Sites based on signal interactions

    Directory of Open Access Journals (Sweden)

    Deogun Jitender S

    2006-04-01

    Full Text Available Abstract Background Predicting and proper ranking of canonical splice sites (SSs is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan. Results According to our tests, the Bayesian sensor outperforms the contemporary Maximum Entropy sensor for 5' SS detection. We report a number of putative Exonic (ESE and Intronic (ISE Splicing Enhancers found by MHMMotif tool. T-test statistics on mouse/rat intronic alignments indicates, that detected elements are on average more conserved as compared to other oligos, which supports our assumption of their functional importance. The tool has been shown to outperform the SpliceView, GeneSplicer, NNSplice, Genio and NetUTR tools for the test set of human genes. SpliceScan outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments. Conclusion Designed methods have many attractive properties, compared to existing approaches. Bayesian sensor, MHMMotif program and SpliceScan tools are freely available on our web site. Reviewers This article was reviewed by Manyuan Long, Arcady Mushegian and Mikhail Gelfand.

  19. Imaginando Palmares: a obra de Gayl Jones Imagining Palmares: the work of Gayl Jones

    Directory of Open Access Journals (Sweden)

    Stelamaris Coser

    2005-12-01

    Full Text Available O longo poema narrativo Song for Anninho (1981, da escritora negra Gayl Jones (Estados Unidos, interfere na narrativa da história colonial brasileira ao resgatar a figura feminina na República de Palmares, reescrever a saga de resistência dos palmaristas do ponto de vista imaginário de uma mulher negra do século XVII e, através dela, reinventar o cotidiano, os amores, as disputas e os sonhos das pessoas comuns que integravam o quilombo. O texto reflete sobre a verdade histórica, o aspecto construído de documentos, as seleções e exclusões da linguagem, e a importância do relato oral para o conhecimento de vivências e identidades à margem da história oficial. Nessa versão especial, o relato dramático do sonho, da luta e da destruição do mais famoso quilombo brasileiro usa a imaginação literária para expandir a memória e os arquivos de um dos fatos mais importantes da história das Américas, contribuindo para estimular o diálogo interamericano e iluminar a diáspora africana no Brasil e no continente.The long narrative poem Song for Anninho (1981, written by black U.S. writer Gayl Jones, interferes in the narrative of Brazilian colonial history as it highlights the female presence in the Republic of Palmares, rewrites the tale of resistance from the point of view of a black woman in the 17th Century, and, through her, reinvents the everyday lives, loves, disputes, and dreams of common people in the quilombo. The text reflects about historical truth, the constructed character of documents, selections and exclusions in language, and the importance of oral accounts to give visibility to experiences and identities marginalized by official history. In this special version, the dramatic report of the dreams, struggles, and destruction of the most famous Brazilian quilombo uses literary imagination to expand the memory and the archives of one of the most important facts in the history of the Americas, contributing to stimulate

  20. Elisabeth Bennet y Bridget Jones: del protofeminismo al postfeminismo

    OpenAIRE

    Valero Valero, Dori

    2013-01-01

    XVIII Jornades de Foment de la Investigació de la Facultat de Ciències Humanes i Socials (Any 2013) Las teorías feministas se han introducido en la literatura de ficción facilitando modelos alternativos a las lectoras. Las heroínas llevan a cabo una tarea de «resistencia feminista», y tomaremos los siguientes ejemplos: Elizabeth Bennet, Orgullo y prejuicio (1813) y Bridget Jones, El diario de Bridget Jones (1999). Jane Austen construye protagonistas femeninas que responden a las est...

  1. Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

    Science.gov (United States)

    Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

    Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiency has been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume.

  2. Simplified TiO2 force fields for studies of its interaction with biomolecules

    Science.gov (United States)

    Luan, Binquan; Huynh, Tien; Zhou, Ruhong

    2015-06-01

    Engineered TiO2 nanoparticles have been routinely applied in nanotechnology, as well as in cosmetics and food industries. Despite active experimental studies intended to clarify TiO2's biological effects, including potential toxicity, the relation between experimentally inferred nanotoxicity and industry standards for safely applying nanoparticles remains somewhat ambiguous with justified concerns. Supplemental to experiments, molecular dynamics simulations have proven to be efficacious in investigating the molecular mechanism of a biological process occurring at nanoscale. In this article, to facilitate the nanotoxicity and nanomedicine research related to this important metal oxide, we provide a simplified force field, based on the original Matsui-Akaogi force field but compatible to the Lennard-Jones potentials normally used in modeling biomolecules, for simulating TiO2 nanoparticles interacting with biomolecules. The force field parameters were tested in simulating the bulk structure of TiO2, TiO2 nanoparticle-water interaction, as well as the adsorption of proteins on the TiO2 nanoparticle. We demonstrate that these simulation results are consistent with experimental data/observations. We expect that simulations will help to better understand the interaction between TiO2 and molecules.

  3. Collision of hydrogen molecules interacting with two grapheme sheets

    Directory of Open Access Journals (Sweden)

    Malivuk-Gak Dragana

    2017-01-01

    Full Text Available It have been performed the computational experiments with two hydrogen molecules and two graphene sheets. Hydrogen - hydrogen and hydrogen - carbon interactions are described by Lennard - Jones potential. Equations of motion of the wave packet centre are solved numerically. The initial molecule velocity was determined by temperature and collisions occur in central point between two sheets. The molecules after collision stay near or get far away of graphene sheets. Then one can find what temperatures, graphene sheet sizes and their distances are favourable for hydrogen storage. It is found that quantum corrections of the molecule classical trajectories are not significant here. Those investigations of possibility of hydrogen storage by physisorption are of interest for improvement of the fuel cell systems. The main disadvantages of computational experiments are: (1 it cannot compute with very large number of C atoms, (2 it is assumed that carbon atoms are placed always in their equilibrium positions and (3 the changes of wave packet width are not considered.

  4. Multiple magnetic interactions in A-site-ordered perovskite-structure oxides.

    Science.gov (United States)

    Shimakawa, Yuichi; Mizumaki, Masaichiro

    2014-11-26

    Multiple magnetic interactions in A-site-ordered perovskite-structure oxides AA'3B2B'2O12 with A'-site Cu and B-site Fe ions are highlighted here. Several new compounds with this structure type were obtained by high-pressure synthesis and have been given unusual magnetic properties due to multiple interactions of Cu and Fe ions (A'-A', A'-B, A'-B', B-B, B-B', and B'-B' interactions). The magnetic interaction is discussed here in light of the results of magnetic structure analysis with neutron powder diffraction data and x-ray magnetic circular dichroism spectra obtained in x-ray absorption experiments. The characteristic structural framework with ordered cation arrangements and the variation in the oxidation state of the ions at the A' and B sites are shown to play roles crucial for the diverse and intriguing physical properties of these new compounds.

  5. The Barrett-Lennard Relationship Inventory (BLRI): current and potential uses with family systems.

    Science.gov (United States)

    Ganley, R M

    1989-03-01

    The search for and measurement of important relationship qualities have always been of interest to family therapists. Within a Rogerian perspective, empathy, regard, and congruence are believed to be among the most important indicators of the quality of human relationships. These variables, or conceptually similar ones, are also important in several current models of family functioning. Barrett-Lennard (1,2) developed an instrument, the Barrett-Lennard Relationship Inventory (BLRI), to measure empathy, regard, and congruence. Although the major use of the BLRI has been in psychotherapy outcome research (13), several studies have shown that it is a sensitive indicator of marital satisfaction and of changes occurring in marital-improvement programs. The present study is a factor analysis of the BLRI based on data from 345 women who rated levels of empathy, regard, and congruence in their relationship with their husbands. The results robustly confirm the three-factor structure of the BLRI in what is believed to be the first factor analysis in the context of a family member rating a relationship within the family. The replication of the BLRI's structure in a new relationship context suggests that the dimensions tapped by the BLRI may have some generality and warrant further exploration in a family-systems context. Several advantages of the BLRI over other currently available instruments are discussed, as are potential uses of the BLRI in systems research beyond the marital unit.

  6. Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

    Science.gov (United States)

    Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

    2018-03-13

    Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

  7. The Importance of Synchronous Interaction for Student Satisfaction with Course Web Sites

    Science.gov (United States)

    Cao, Qidong; Griffin, Thomas E.; Bai, Xue

    2009-01-01

    As more affordable synchronous communications are becoming available, the use of synchronous interactions has not been noted in course Web sites as often as asynchronous communications. Previous research indicated that the integration of synchronous tools into course Web sites has made a positive impact on students. While most of the previous…

  8. Birefringence of Cellotape: Jones Representation and Experimental Analysis

    Science.gov (United States)

    Belendez, Augusto; Fernandez, Elena; Frances, Jorge; Neipp, Cristian

    2010-01-01

    In this paper, we analyse a simple experiment to study the effects of polarized light. A simple optical system composed of a polarizer, a retarder (cellotape) and an analyser is used to study the effect on the polarization state of the light which impinges on the setup. The optical system is characterized by means of a Jones matrix, and a simple…

  9. Comparative distalization effects of Jones jig and pendulum appliances.

    Science.gov (United States)

    Patel, Mayara Paim; Janson, Guilherme; Henriques, José Fernando Castanha; de Almeida, Renato Rodrigues; de Freitas, Marcos Roberto; Pinzan, Arnaldo; de Freitas, Karina Maria Salvatore

    2009-03-01

    In this study, we compared the dentoalveolar changes of Class II patients treated with Jones jig and pendulum appliances. The experimental group comprised 40 Class II malocclusion subjects, divided into 2 groups: group 1 consisted of 20 patients (11 boys, 9 girls) at a mean pretreatment age of 13.17 years, treated with the Jones jig appliance for 0.91 years; group 2 comprised 20 patients (8 boys, 12 girls) at a mean pretreatment age of 13.98 years, treated with the pendulum appliance for 1.18 years. Only active treatment time of molar distalization was evaluated in the predistalization and postdistalization lateral cephalograms. Molar, second premolar, and incisor angular and linear variables were obtained. The intergroup treatment changes in these variables were compared with independent t tests. The maxillary second premolars showed greater mesial tipping and extrusion in the Jones jig group, indicating more anchorage loss during molar distalization with this appliance. The amounts and the monthly rates of molar distalization were similar in both groups. The Jones jig group showed greater mesial tipping and extrusion of the maxillary second premolars. The mean amounts and the monthly rates of first molar distalization were similar in both groups.

  10. C. Rick Jones Is IRPA Keynote Lecturer on Stakeholder Engagement

    International Nuclear Information System (INIS)

    Strom, Daniel J.

    2008-01-01

    At the recent IRPA 12 Conference in Buenos Aires, Argentina, C. Rick Jones gave the keynote lecture 'Stakeholder Engagement in Practice - Now Is the Time to Act' This was one of the very best talks at the conference, covering IRPA's draft 'Guiding Principles for Radiation Protection Professionals on Stakeholder Engagement'

  11. A note on Valeriana jatamansi Jones (Caprifoliaceae s.l.)

    NARCIS (Netherlands)

    Mabberley, D.J.; Noltie, H.J.

    2014-01-01

    The tangled arguments around the names of jatamansi drug plants are examined and the correct synonymies and typifications for Nardostachys jatamansi (D.Don) DC. and V. jatamansi Jones (both Caprifoliaceae s.l.) are provided. The conservation status of the former, and the need for further work on the

  12. Public lecture | "Science and society" by Bob Jones | 22 May

    CERN Multimedia

    2014-01-01

    Public lecture: "Science and society: the impact of computing at CERN on society" by Bob Jones 22 May at 7.30 p.m. Globe of Science and Innovation Lecture in English, translated in French. Entrance free. Limited number of seats. Reservation essential: +41 22 767 76 76 or cern.reception@cern.ch

  13. Shelley Jones: Helping Ugandan girls stay in school | IDRC ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    IDRC research awardee Shelley Jones travelled to Uganda to explore the obstacles the country's young women face in their efforts to pursue secondary education. Her research motivated young social entrepreneurs to launch a company that is keeping girls in school and providing them with jobs.

  14. Highlight: Dr David Butler-Jones on fighting pandemics | IDRC ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2016-04-15

    Apr 15, 2016 ... In the context of developing countries, Butler-Jones drew attention to the importance of public healthcare teams of doctors and paramedics, data, and accreditation standards in identifying appropriate interventions. There is a need to explore the public-private nexus, traditional medicines, and public health ...

  15. Highlight: Dr David Butler-Jones on fighting pandemics | CRDI ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    15 avr. 2016 ... Dr David Butler-Jones, professor in the Faculty of Medicine at the University of Manitoba and former Chief Medical Health Officer of Canada, delivered a lecture on lessons learned from the 2009 flu pandemic in Canada. He also commented on India's draft National Health Policy 2015 at the India ...

  16. Return on interactivity? The characteristics and effectiveness of Web sites during the 2010 Dutch local elections

    NARCIS (Netherlands)

    van Noort, G.; Vliegenthart, R.; Kruikemeier, S.

    2016-01-01

    This article examines the use of interactive features (i.e., discussion and participation features) on the Web sites of Dutch political parties during the 2010 local elections campaign and investigates whether a relationship exists between interactivity and election results. A manual content

  17. User-Centric Secure Cross-Site Interaction Framework for Online Social Networking Services

    Science.gov (United States)

    Ko, Moo Nam

    2011-01-01

    Social networking service is one of major technological phenomena on Web 2.0. Hundreds of millions of users are posting message, photos, and videos on their profiles and interacting with other users, but the sharing and interaction are limited within the same social networking site. Although users can share some content on a social networking site…

  18. Prediction of protein-protein interaction sites in sequences and 3D structures by random forests.

    Directory of Open Access Journals (Sweden)

    Mile Sikić

    2009-01-01

    Full Text Available Identifying interaction sites in proteins provides important clues to the function of a protein and is becoming increasingly relevant in topics such as systems biology and drug discovery. Although there are numerous papers on the prediction of interaction sites using information derived from structure, there are only a few case reports on the prediction of interaction residues based solely on protein sequence. Here, a sliding window approach is combined with the Random Forests method to predict protein interaction sites using (i a combination of sequence- and structure-derived parameters and (ii sequence information alone. For sequence-based prediction we achieved a precision of 84% with a 26% recall and an F-measure of 40%. When combined with structural information, the prediction performance increases to a precision of 76% and a recall of 38% with an F-measure of 51%. We also present an attempt to rationalize the sliding window size and demonstrate that a nine-residue window is the most suitable for predictor construction. Finally, we demonstrate the applicability of our prediction methods by modeling the Ras-Raf complex using predicted interaction sites as target binding interfaces. Our results suggest that it is possible to predict protein interaction sites with quite a high accuracy using only sequence information.

  19. Empirical intermolecular potential from depolarized interaction-induced light scattering spectra for tetrafluoromethane

    Science.gov (United States)

    Kader, Mohamed Sayed Abdel

    2002-07-01

    Depolarized interaction-induced light scattering spectra of tetrafluoromethane in the frequency range 2-150 cm-1 at 294.5 K and 0.91 mol/l with the interaction pressure virial coefficient and viscosity have been used for deriving the empirical multiparameter Morse-Morse-Morse-Spline-van der Waals (M3SV), Lennard-Jones, Kihara, and exp-6 intermolecular potentials. The line shape at relatively low frequencies is determined largely by the effect of bound and free transitions. At intermediate frequencies it is sensitive to both the attractive part of the potential and the short-range part of the polarizability anisotropy. The high frequency wings are discussed in terms of the collision-induced rotational Raman effect and estimates for the dipole-quadrupole and dipole-octopole polarizabilities A and E, respectively, are obtained. Absolute zeroth and second moments have been measured and compared with theoretical calculations using these models of the intermolecular potentials. The results show that M3SV is the most accurate potential yet reported for this system.

  20. Indiana Jones on tagasi ja näitab, kuidas käituda / Kristiina Davidjants

    Index Scriptorium Estoniae

    Davidjants, Kristiina, 1974-

    2008-01-01

    22 mail esilinastub Steven Spielbergi järjekordne Indiana Jones'i film, kaasstsenaristiks ja produtsendiks George Lucas ja Harrison Fordiga nimiosas "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull"). Saaga varasemast kolmest filmist

  1. The interpersonal relationship in clinical practice. The Barrett-Lennard Relationship Inventory as an assessment instrument.

    Science.gov (United States)

    Simmons, J; Roberge, L; Kendrick, S B; Richards, B

    1995-03-01

    The biomedical model that has long been central to medical practice is gradually being expanded to a broader biopsychosocial model. Relationship-building skills commensurate with the new paradigm need to be understood by educators and taught to medical practitioners. The person-centered, or humanistic, model of psychologist Carl Rogers provides a theoretical approach for the development of effective biopsychosocial relationships. The Barrett-Lennard Relationship Inventory (BLRI) was developed in 1962 as an assessment instrument for the person-centered model. In this article, the person-centered model and the use of the BLRI as an assessment instrument of this model are discussed. Current and potential uses of the BLRI are explored.

  2. Some interactive factors affecting trench-cover integrity on low-level waste sites

    International Nuclear Information System (INIS)

    Hakonson, T.E.; Lane, L.J.; Steger, J.G.; DePoorter, G.L.

    1982-01-01

    This paper describes important mechanisms by which radionuclide can be transported from low-level waste disposal sites into biological pathways, discuss interactions of abiotic and biotic processes, and recommends environmental characteristics that should be measured to design sites that minimize this transport. Past experience at shallow land burial sites for low-level radioactive wastes suggest that occurrences of waste exposure and radionuclide transport are often related to inadequate trench cover designs. Meeting performance standards at low-level waste sites can only be achieved by recognizing that physical, chemical, and biological processes operating on and in a trench cover profile are highly interactive. Failure to do so can lead to improper design criteria and subsequent remedial action procedures that can adversely affect site stability. Based upon field experiments and computer modeling, recommendations are made on site characteristics that require measurement in order to design systems that reduce surface runoff and erosion, manage soil moisture and biota in the cover profile to maximize evapotranspiration and minimize percolation, and place bounds on the intrusion potential of plants and animals into the waste material. Major unresolved problems include developing probabilistic approaches that include climatic variability, improved knowledge of soil-water-plant-erosion relationships, development of practical vegetation establishment and maintenance procedures, prediction and quantification of site potential and plant succession, and understanding the interaction of processes occurring on and in the cover profile with deeper subsurface processes

  3. Characterization of the protein Z-dependent protease inhibitor interactive-sites of protein Z.

    Science.gov (United States)

    Qureshi, Shabir H; Lu, Qiuya; Manithody, Chandrashekhara; Yang, Likui; Rezaie, Alireza R

    2014-09-01

    Protein Z (PZ) has been reported to promote the inactivation of factor Xa (FXa) by PZ-dependent protease inhibitor (ZPI) by about three orders of magnitude. Previously, we prepared a chimeric PZ in which its C-terminal pseudo-catalytic domain was grafted on FX light-chain (Gla and EGF-like domains) (PZ/FX-LC). Characterization of PZ/FX-LC revealed that the ZPI interactive-site is primarily located within PZ pseudo-catalytic domain. Nevertheless, the cofactor function and apparent Kd of PZ/FX-LC for interaction with ZPI remained impaired ~6-7-fold, suggesting that PZ contains a ZPI interactive-site outside pseudo-catalytic domain. X-ray structural data indicates that Tyr-240 of ZPI interacts with EGF2-domain of PZ. Structural data further suggests that 3 other ZPI surface loops make salt-bridge interactions with PZ pseudo-catalytic domain. To identify ZPI interactive-sites on PZ, we grafted the N-terminal EGF2 subdomain of PZ onto PZ/FX-LC chimera (PZ-EGF2/FX-LC) and also generated two compensatory charge reversal mutants of PZ pseudo-catalytic domain (Glu-244 and Arg-212) and ZPI surface loops (Lys-239 and Asp-293). PZ chimeras were expressed in mammalian cells and ZPI derivatives were expressed in Escherichia coli. The PZ EGF2 subdomain fusion restored the defective cofactor function of PZ/FX-LC. The activities of PZ and ZPI mutants were all impaired if assayed individually, but partially restored if the compensatory charge reversal mutants were used in the assay. PZ EGF2 subdomain constitutes an interactive-site for ZPI. Data with compensatory charge reversal mutants validates structural data that the identified residues are part of interactive-sites. Insight is provided into mechanisms through which specificity of ZPI-PZ-FXa complex formation is determined. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Mutated primer binding sites interacting with different tRNAs allow efficient murine leukemia virus replication

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M; Lovmand, J

    1993-01-01

    Two Akv murine leukemia virus-based retroviral vectors with primer binding sites matching tRNA(Gln-1) and tRNA(Lys-3) were constructed. The transduction efficiency of these mutated vectors was found to be comparable to that of a vector carrying the wild-type primer binding site matching t......RNA(Pro). Polymerase chain reaction amplification and sequence analysis of transduced proviruses confirmed the transfer of vectors with mutated primer binding sites and further showed that tRNA(Gln-2) may act efficiently in conjunction with the tRNA(Gln-1) primer binding site. We conclude that murine leukemia virus...... can replicate by using various tRNA molecules as primers and propose primer binding site-tRNA primer interactions to be of major importance for tRNA primer selection. However, efficient primer selection does not require perfect Watson-Crick base pairing at all 18 positions of the primer binding site....

  5. Off-site interaction effect in the Extended Hubbard Model with the SCRPA method

    International Nuclear Information System (INIS)

    Harir, S; Bennai, M; Boughaleb, Y

    2007-01-01

    The self consistent random phase approximation (SCRPA) and a direct analytical (DA) method are proposed to solve the Extended Hubbard Model (EHM) in one dimension (1D). We have considered an EHM including on-site and off-site interactions for closed chains in 1D with periodic boundary conditions. The comparison of the SCRPA results with the ones obtained by a DA approach shows that the SCRPA treats the problem of these closed chains in a rigorous manner. The analysis of the nearest-neighbour repulsion effect on the dynamics of our closed chains shows that this repulsive interaction between the electrons of the neighbouring atoms induces supplementary conductivity, since, the SCRPA energygap vanishes when these closed chains are governed by a strong repulsive on-site interaction and intermediate nearest-neighbour repulsion

  6. Structure, single-particle and many-particle coefficients of Lennard ...

    Indian Academy of Sciences (India)

    through migrations of atoms from the first shell in the pair distribution function. The dynamics of atomic pairs in the short-time regime in liquid aluminium may be said to be governed by the potential of mean force, which ... The input parameters for the Lennard–Jones model are σ = 2.62 Å and (ϵ/KB) = 4551.28 K. In §2, we ...

  7. Jones matrix treatment for optical Fourier processors with structured polarization.

    Science.gov (United States)

    Moreno, Ignacio; Iemmi, Claudio; Campos, Juan; Yzuel, Maria J

    2011-02-28

    We present a Jones matrix method useful to analyze coherent optical Fourier processors employing structured polarization. The proposed method is a generalization of the standard classical optical Fourier transform processor, but considering vectorial spatial functions with two complex components corresponding to two orthogonal linear polarizations. As a result we derive a Jones matrix that describes the polarization output in terms of two vectorial functions defining respectively the structured polarization input and the generalized polarization impulse response. We apply the method to show and analyze an experiment in which a regular scalar diffraction grating is converted into equivalent polarization diffraction gratings by means of an appropriate polarization filtering. The technique is further demonstrated to generate arbitrary structured polarizations. Excellent experimental results are presented.

  8. Birefringence of cellotape: Jones representation and experimental analysis

    Energy Technology Data Exchange (ETDEWEB)

    Belendez, Augusto; Frances, Jorge; Neipp, Cristian [Departamento de Fisica, Ingenieria de Sistemas y Teoria de la Senal, Universidad de Alicante, Apartado 99, E-03080 Alicante (Spain); Fernandez, Elena [Departamento de Optica, FarmacologIa y Anatomia, Universidad de Alicante, Apartado 99, E-03080 Alicante (Spain)], E-mail: a.belendez@ua.es

    2010-05-15

    In this paper, we analyse a simple experiment to study the effects of polarized light. A simple optical system composed of a polarizer, a retarder (cellotape) and an analyser is used to study the effect on the polarization state of the light which impinges on the setup. The optical system is characterized by means of a Jones matrix, and a simple procedure based on Jones vectors is used to obtain an expression for the intensity after the light passes through the optical system. The light intensity is measured by a photodetector and the expression obtained theoretically is experimentally validated. By fitting the experimental intensity data, the value of the retardation introduced by the retarder can also be obtained.

  9. Tubo de Lester-Jones: indicações e resultados Lester-Jones tube: indications and results

    Directory of Open Access Journals (Sweden)

    Walberto Passos Junior

    2004-12-01

    Full Text Available OBJETIVO: Avaliar as indicações, resultados e complicações advindas do seu uso. MÉTODOS: Avaliaram-se retrospectivamente 25 pacientes submetidos a 27 conjuntivorrinostomias com colocação de tubo de Lester-Jones. Foram estudados os dados do portador, a etiologia da afecção e as complicações que ocorreram no intra e no pós-operatório. Os dados foram avaliados segundo a freqüência de ocorrência. RESULTADOS: O tubo de Lester-Jones foi usado igualmente em ambos os sexos, mais em indivíduos abaixo dos 10 ou acima dos 50 anos de idade. As causas mais freqüentes para utilização foram a idiopática ou a agenesia congênita de pontos e canalículos. Houve melhora dos sintomas em 88% dos pacientes. Complicações ocorreram em 59,25% dos casos, dentre as quais: extrusão (40,74% e a migração (14,8% do tubo. CONCLUSÃO: Apesar das complicações observadas, o índice de cura com a utilização do tubo de Lester-Jones é alto, sendo boa opção para o tratamento das obstruções lacrimais altas.PURPOSE: To evaluate the results and the complications occurring with this procedure. METHODS: The authors retrospectively reviewed charts of 25 patients (27 lacrimal viers with upper lacrimal system obstruction who underwent conjunctivorhinostomy and Lester-Jones tube bypass. The patients were evaluated according to gender, causative factors and the com plications during and after surgery. The data were submitted to statistical analysis. RESULTS: The Lester-Jones bypass tube was used in both sexes and most frequently in patients under 10 or above 50 years. The most common obstructive factor was unknown and congenital agenesis. Eighty-eight per cent of the patients had no epiphora at the end of the treatment. Complications occurred in 59.25% of the patients, most of them related to tube extrusion (40.74% or migration (14.8%. The authors concluded that the Lester-Jones bypass tube is a good option to treat the upper lacrimal obstruction, in spite

  10. Topological phases in the Haldane model with spin–spin on-site interactions

    Science.gov (United States)

    Rubio-García, A.; García-Ripoll, J. J.

    2018-04-01

    Ultracold atom experiments allow the study of topological insulators, such as the non-interacting Haldane model. In this work we study a generalization of the Haldane model with spin–spin on-site interactions that can be implemented on such experiments. We focus on measuring the winding number, a topological invariant, of the ground state, which we compute using a mean-field calculation that effectively captures long-range correlations and a matrix product state computation in a lattice with 64 sites. Our main result is that we show how the topological phases present in the non-interacting model survive until the interactions are comparable to the kinetic energy. We also demonstrate the accuracy of our mean-field approach in efficiently capturing long-range correlations. Based on state-of-the-art ultracold atom experiments, we propose an implementation of our model that can give information about the topological phases.

  11. Early Experience with the StopLoss Jones Tube.

    Science.gov (United States)

    Bagdonaite, Laura; Pearson, Andrew R

    2015-06-01

    Extrusion is the most common reason for failure after Jones tube placement. The StopLoss Jones tube (SLJT) is a new innovation in Jones tubes that incorporates a flexible silicone internal flange to resist extrusion. We present our early experience of using this new tube and associated introducer system. We retrospectively analysed the case notes of a single surgeon consecutive series of patients having SLJT placement from November 2011 to November 2013. 29 SLJTs were placed in 25 eyes of 19 patients. Tube follow-up ranged from 1-25 months (mean 10 months) with a total of 291 tube-months. The indications for SLJT placement were: previous LJT complications (52%), failed canalicular-DCR surgery (31%), primary placement for inoperable canalicular occlusion (14%) and patent non-functioning DCR (3%). Tube length ranged from 10-16 mm. The tube introducer system was simple and effective and there were no intra-operative complications. The tube extrusion rate was 0%. Complications occurred in 5 tubes: 1 was too long, and 4 others (14%) developed conjunctival overgrowth/medial tube migration. Patient satisfaction with the tube was: 86% fully satisfied, 10% was moderately satisfied, 3% not satisfied. The overall final surgical success rate at last follow-up was 92%. In this short follow-up initial study the SLJT is simple to use and has a high rate of success and patient satisfaction. The addition of the internal silicone flange appears to prevent the previously common problem of extrusion.

  12. A Viola-Jones based hybrid face detection framework

    Science.gov (United States)

    Murphy, Thomas M.; Broussard, Randy; Schultz, Robert; Rakvic, Ryan; Ngo, Hau

    2013-12-01

    Improvements in face detection performance would benefit many applications. The OpenCV library implements a standard solution, the Viola-Jones detector, with a statistically boosted rejection cascade of binary classifiers. Empirical evidence has shown that Viola-Jones underdetects in some instances. This research shows that a truncated cascade augmented by a neural network could recover these undetected faces. A hybrid framework is constructed, with a truncated Viola-Jones cascade followed by an artificial neural network, used to refine the face decision. Optimally, a truncation stage that captured all faces and allowed the neural network to remove the false alarms is selected. A feedforward backpropagation network with one hidden layer is trained to discriminate faces based upon the thresholding (detection) values of intermediate stages of the full rejection cascade. A clustering algorithm is used as a precursor to the neural network, to group significant overlappings. Evaluated on the CMU/VASC Image Database, comparison with an unmodified OpenCV approach shows: (1) a 37% increase in detection rates if constrained by the requirement of no increase in false alarms, (2) a 48% increase in detection rates if some additional false alarms are tolerated, and (3) an 82% reduction in false alarms with no reduction in detection rates. These results demonstrate improved face detection and could address the need for such improvement in various applications.

  13. Simple expression for the dependence of the nanodrop contact angle on liquid-solid interactions and temperature

    Science.gov (United States)

    Berim, Gersh O.; Ruckenstein, Eli

    2009-01-01

    The density distributions and contact angles of nanodrops on smooth solid surfaces are calculated on the basis of a nonlocal density functional theory in wide ranges of temperature and parameters of the Lennard-Jones potentials representing the fluid-fluid and fluid-solid interactions. A simple linear dependence of the contact angle on the fluid-solid energy parameter ɛfs was found for various temperatures, hard core fluid-solid parameters σfs, and average fluid density of the system. A simple expression is suggested which represents all the above results in a unified form that relates the contact angle θ to the parameters of the interaction potentials and temperature. The most intriguing feature was that for each considered σfs there is a value ɛfs0 of ɛfs for which the contact angle θ=θ0 can be considered independent of temperature and of σfs. It is shown that ɛfs=ɛfs0 divides the materials for which θ increases from those for which θ decreases with increasing temperature. The results obtained for the dependence of the contact angle on the parameters of the model are in qualitative agreement with known molecular dynamics results.

  14. Analysis of topological relationships and network properties in the interactions of human beings.

    Directory of Open Access Journals (Sweden)

    Ye Yuan

    Full Text Available In the animal world, various kinds of collective motions have been found and proven to be efficient ways of carrying out some activities such as searching for food and avoiding predators. Many scholars research the interactions of collective behaviors of human beings according to the rules of collective behaviors of animals. Based on the Lennard-Jones potential function and a self-organization process, our paper proposes a topological communication model to simulate the collective behaviors of human beings. In the results of simulations, we find various types of collective behavior and fission behavior and discover the threshold for the emergence of collective behavior, which is the range five to seven for the number of topology K. According to the analysis of network properties of the model, the in-degree of individuals is always equal to the number of topology. In the stable state, the out-degrees of individuals distribute around the value of the number of topology K, except that the out-degree of a single individual is approximately double the out-degrees of the other individuals. In addition, under different initial conditions, some features of different kinds of networks emerge from the model. We also find the leader and herd mentality effects in the characteristics of the behaviors of human beings in our model. Thus, this work could be used to discover how to promote the emergence of beneficial group behaviors and prevent the emergence of harmful behaviors.

  15. Identification of functional interaction sites on proteins using bacteriophage-displayed random epitope libraries

    NARCIS (Netherlands)

    van Zonneveld, A. J.; van den Berg, B. M.; van Meijer, M.; Pannekoek, H.

    1995-01-01

    We describe a phage-display-based method to identify epitopes or interaction sites on proteins. DNA encoding the protein of interest is partially degraded with DNase I to generate random fragments of 50-200 bp. These fragments are then cloned into a phagemid vector that has been modified to allow

  16. FLS2-BAK1 extracellular domain interaction sites required for defense signaling activation.

    Directory of Open Access Journals (Sweden)

    Teresa Koller

    Full Text Available Signaling initiation by receptor-like kinases (RLKs at the plasma membrane of plant cells often requires regulatory leucine-rich repeat (LRR RLK proteins such as SERK or BIR proteins. The present work examined how the microbe-associated molecular pattern (MAMP receptor FLS2 builds signaling complexes with BAK1 (SERK3. We first, using in vivo methods that validate separate findings by others, demonstrated that flg22 (flagellin epitope ligand-initiated FLS2-BAK1 extracellular domain interactions can proceed independent of intracellular domain interactions. We then explored a candidate SERK protein interaction site in the extracellular domains (ectodomains; ECDs of the significantly different receptors FLS2, EFR (MAMP receptors, PEPR1 (damage-associated molecular pattern (DAMP receptor, and BRI1 (hormone receptor. Repeat conservation mapping revealed a cluster of conserved solvent-exposed residues near the C-terminus of models of the folded LRR domains. However, site-directed mutagenesis of this conserved site in FLS2 did not impair FLS2-BAK1 ECD interactions, and mutations in the analogous site of EFR caused receptor maturation defects. Hence this conserved LRR C-terminal region apparently has functions other than mediating interactions with BAK1. In vivo tests of the subsequently published FLS2-flg22-BAK1 ECD co-crystal structure were then performed to functionally evaluate some of the unexpected configurations predicted by that crystal structure. In support of the crystal structure data, FLS2-BAK1 ECD interactions were no longer detected in in vivo co-immunoprecipitation experiments after site-directed mutagenesis of the FLS2 BAK1-interaction residues S554, Q530, Q627 or N674. In contrast, in vivo FLS2-mediated signaling persisted and was only minimally reduced, suggesting residual FLS2-BAK1 interaction and the limited sensitivity of co-immunoprecipitation data relative to in vivo assays for signaling outputs. However, Arabidopsis plants

  17. An Overview of Tubulin Inhibitors That Interact with the Colchicine Binding Site

    Science.gov (United States)

    Lu, Yan; Chen, Jianjun; Xiao, Min; Li, Wei

    2013-01-01

    Tubulin dynamics is a promising target for new chemotherapeutic agents. The colchicine binding site is one of the most important pockets for potential tubulin polymerization destabilizers. Colchicine binding site inhibitors (CBSI) exert their biological effects by inhibiting tubulin assembly and suppressing microtubule formation. A large number of molecules interacting with the colchicine binding site have been designed and synthesized with significant structural diversity. CBSIs have been modified as to chemical structure as well as pharmacokinetic properties, and tested in order to find a highly potent, low toxicity agent for treatment of cancers. CBSIs are believed to act by a common mechanism via binding to the colchicine site on tubulin. The present review is a synopsis of compounds that have been reported in the past decade that have provided an increase in our understanding of the actions of CBSIs. PMID:22814904

  18. Quantum mechanics study of the hydroxyethylamines-BACE-1 active site interaction energies

    Science.gov (United States)

    Gueto-Tettay, Carlos; Drosos, Juan Carlos; Vivas-Reyes, Ricardo

    2011-06-01

    The identification of BACE-1, a key enzyme in the production of Amyloid-β (Aβ) peptides, generated by the proteolytic processing of amyloid precursor protein, was a major advance in the field of Alzheimer's disease as this pathology is characterized by the presence of extracellular senile plaques, mainly comprised of Aβ peptides. Hydroxyethylamines have demonstrated a remarkable potential, like candidate drugs, for this disease using BACE-1 as target. Density Functional Theory calculations were employed to estimate interaction energies for the complexes formed between the hydroxyethylamine derivated inhibitors and 24 residues in the BACE-1 active site. The collected data offered not only a general but a particular quantitative description that gives a deep insight of the interactions in the active site, showing at the same time how ligand structural variations affect them. Polar interactions are the major energetic contributors for complex stabilization and those ones with charged aspartate residues are highlighted, as they contribute over 90% of the total attractive interaction energy. Ligand-ARG296 residue interaction reports the most repulsive value and decreasing of the magnitude of this repulsion can be a key feature for the design of novel and more potent BACE-1 inhibitors. Also it was explained why sultam derivated BACE-1 inhibitors are better ones than lactam based. Hydrophobic interactions concentrated at S1 zone and other relevant repulsions and attractions were also evaluated. The comparison of two different theory levels (X3LYP and M062X) allowed to confirm the relevance of the detected interactions as each theory level has its own strength to depict the forces involved, as is the case of M062X which is better describing the hydrophobic interactions. Those facts were also evaluated and confirmed by comparing the quantitative trend, of selected ligand-residue interactions, with MP2 theory level as reference standard method for electrostatic plus

  19. A Biomechanical Comparison of Fifth Metatarsal Jones Fracture Fixation Methods.

    Science.gov (United States)

    Duplantier, Neil L; Mitchell, Ronald J; Zambrano, Steve; Stone, Aaron C; Delgado, Domenica A; Lambert, Bradley S; Moreno, Michael R; Harris, Joshua D; McCulloch, Patrick C; Lintner, David M; Varner, Kevin E

    2018-04-01

    Fifth metatarsal base fractures of the metaphyseal-diaphyseal watershed junction (Jones fracture) are commonly treated with surgical fixation in athletes. Intramedullary screw fixation remains the most utilized construct, although plantar-lateral plating is an alternative. Purpose/Hypothesis: The purpose was to compare the mechanical strength of fracture fixation between an intramedullary screw and plantar-lateral plating. The hypothesis was that plantar-lateral plate fixation would allow for more cycles and higher peak loads before failure, as well as less fracture gapping, than would an intramedullary screw in cadaveric foot specimens with simulated Jones fractures exposed to cantilever bending. Controlled laboratory study. Twelve pairs of male cadaver feet were separated into 2 groups (plate or screw) to conduct contralateral comparative testing of 2 devices with equally numbered right and left feet. For each fifth metatarsal, an osteotomy with a microsagittal saw was created to simulate a Jones fracture. The plate group underwent fixation with a 3.0-mm 4-hole low-profile titanium plate placed plantar-laterally with 3 locking screws and 1 nonlocking screw. The screw group underwent fixation with a 40- or 45-mm × 5.5-mm partially threaded solid titanium intramedullary screw. After fixation, the metatarsals were excised for biomechanical testing. Cyclic cantilever failure testing was conducted with a gradient-cycle method. Sinusoidal loading forces were applied, increasing by 5.0-pound-force increments per 10 cycles, until each specimen experienced mechanical failure of implant or bone. Failure mode, number of cycles to failure, peak failure load, gap width at the last mutual prefailure loading, and video data were recorded. Paired 2-tailed t test (α = 0.05) was used to compare groups ( P Plate fixation resulted in significantly higher mean ± SD values for cycles to failure (63.9 ± 27.0 vs 37.3 ± 36.9, P = .01) and peak failure load (159.2 ± 60.5 N vs 96.5

  20. Partial molar volume of proteins studied by the three-dimensional reference interaction site model theory.

    Science.gov (United States)

    Imai, Takashi; Kovalenko, Andriy; Hirata, Fumio

    2005-04-14

    The three-dimensional reference interaction site model (3D-RISM) theory is applied to the analysis of hydration effects on the partial molar volume of proteins. For the native structure of some proteins, the partial molar volume is decomposed into geometric and hydration contributions using the 3D-RISM theory combined with the geometric volume calculation. The hydration contributions are correlated with the surface properties of the protein. The thermal volume, which is the volume of voids around the protein induced by the thermal fluctuation of water molecules, is directly proportional to the accessible surface area of the protein. The interaction volume, which is the contribution of electrostatic interactions between the protein and water molecules, is apparently governed by the charged atomic groups on the protein surface. The polar atomic groups do not make any contribution to the interaction volume. The volume differences between low- and high-pressure structures of lysozyme are also analyzed by the present method.

  1. Iridoids and sesquiterpenoids from the roots of Valeriana jatamansi Jones.

    Science.gov (United States)

    Dong, Fa-Wu; Liu Yang; Wu, Zhi-Kun; Wei-Gao; Zi, Chen-Ting; Dan Yang; Luo, Huai-Rong; Jun Zhou; Hu, Jiang-Miao

    2015-04-01

    Three new iridoids, jatamanvaltrates R-S (1-2) and jatamanin Q (3), as well as three new sesquiterpenoids, valeriananoids D-E (4, 5) and clovane-2β-isovaleroxy-9α-ol (6), together with nine known compounds were isolated from the roots of Valeriana jatamansi Jones. Compound 2 was the first reported iridoid with fatty acid esters in the Valerianaceae family. The structures of new compounds were established on the basis of extensive spectroscopic analysis. Moreover, all the isolates were evaluated for inhibitory activity on acetylcholinesterase (AChE). Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure.

    Science.gov (United States)

    Li, Tao; Li, Qian-Zhong

    2012-11-07

    RNA-protein interactions play important roles in various biological processes. The precise detection of RNA-protein interaction sites is very important for understanding essential biological processes and annotating the function of the proteins. In this study, based on various features from amino acid sequence and structure, including evolutionary information, solvent accessible surface area and torsion angles (φ, ψ) in the backbone structure of the polypeptide chain, a computational method for predicting RNA-binding sites in proteins is proposed. When the method is applied to predict RNA-binding sites in three datasets: RBP86 containing 86 protein chains, RBP107 containing 107 proteins chains and RBP109 containing 109 proteins chains, better sensitivities and specificities are obtained compared to previously published methods in five-fold cross-validation tests. In order to make further examination for the efficiency of our method, the RBP107 dataset is used as training set, RBP86 and RBP109 datasets are used as the independent test sets. In addition, as examples of our prediction, RNA-binding sites in a few proteins are presented. The annotated results are consistent with the PDB annotation. These results show that our method is useful for annotating RNA binding sites of novel proteins.

  3. The fish and fisheries of Jones Bank and the wider Celtic Sea

    Science.gov (United States)

    Martinez, I.; Ellis, J. R.; Scott, B.; Tidd, A.

    2013-10-01

    information on the ichthyofauna of the Jones Bank. Further site-specific data for bank and off-bank habitats were collected during dedicated surveys on the Jones Bank in 2008 using commercial trawlers and baited camera deployments. Twenty-three species were recorded on the top of the bank, where horse mackerel, haddock and boarfish were the most abundant species; 18 species were found along the slope of the bank (with blue whiting, poor cod, hake and horse mackerel predominant) and 18 species observed off the bank (where catches were dominated by blue whiting, poor cod and hake). The differences between camera and trawls were important with cameras only picking up 28% of the species seen in the trawls. However both camera and trawl results suggest that some species are very habitat specific, with species such as haddock only observed on the top of the bank, whilst Nephrops norvegicus was abundant on the flat areas off the bank but was infrequent on the top of the bank. These results suggest that future surveys of offshore sandbank habitats should stratify sampling more specifically to deal with smaller scale features that may play an important role in providing a greater range of habitats than just their relative size would suggest.

  4. Carbene footprinting accurately maps binding sites in protein-ligand and protein-protein interactions

    Science.gov (United States)

    Manzi, Lucio; Barrow, Andrew S.; Scott, Daniel; Layfield, Robert; Wright, Timothy G.; Moses, John E.; Oldham, Neil J.

    2016-11-01

    Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.

  5. Development of the knowledge-based and empirical combined scoring algorithm (KECSA) to score protein-ligand interactions.

    Science.gov (United States)

    Zheng, Zheng; Merz, Kenneth M

    2013-05-24

    We describe a novel knowledge-based protein-ligand scoring function that employs a new definition for the reference state, allowing us to relate a statistical potential to a Lennard-Jones (LJ) potential. In this way, the LJ potential parameters were generated from protein-ligand complex structural data contained in the Protein Databank (PDB). Forty-nine (49) types of atomic pairwise interactions were derived using this method, which we call the knowledge-based and empirical combined scoring algorithm (KECSA). Two validation benchmarks were introduced to test the performance of KECSA. The first validation benchmark included two test sets that address the training set and enthalpy/entropy of KECSA. The second validation benchmark suite included two large-scale and five small-scale test sets, to compare the reproducibility of KECSA, with respect to two empirical score functions previously developed in our laboratory (LISA and LISA+), as well as to other well-known scoring methods. Validation results illustrate that KECSA shows improved performance in all test sets when compared with other scoring methods, especially in its ability to minimize the root mean square error (RMSE). LISA and LISA+ displayed similar performance using the correlation coefficient and Kendall τ as the metric of quality for some of the small test sets. Further pathways for improvement are discussed for which would allow KECSA to be more sensitive to subtle changes in ligand structure.

  6. The Effects of Day-to-Day Interaction via Social Network Sites on Interpersonal Relationships

    OpenAIRE

    Houghton, David J

    2012-01-01

    The current research identifies the impact of sharing day-to-day information insocial network sites (SNS) on the relationships we hold within and outside of them. Stemming from the literature on self-disclosure, uncertainty reduction, personal relationships, privacy and computer-mediated communication (CMC), a concurrent triangulation research strategy is adopted to identify the patterns of relationship development and interaction in SNS. Using a mixed methods approach, five studies were cond...

  7. Platform for Manipulating Polarization Modes Realized with Jones Vectors in MATHEMATICA

    Directory of Open Access Journals (Sweden)

    Yong-Dae Choi

    2015-06-01

    Full Text Available The fundamental conception in physics of the propagation of the electromagnetic wave polarization in matter is newly understood as the cardinal keyword in free-space quantum communication technology and cosmology in astrophysics. Interactive visualization of the propagation mechanism of polarized electromagnetism in a medium with its helicity has accordingly received attention from scientists exploiting the protocol of quantum key distribution (QKD to guarantee unconditional security in cryptography communication. We have provided a dynamic polarization platform for presenting the polarization modes of a transverse electromagnetic wave, converting the state of polarization through the arrangement of optical elements, using Jones vectors calculations in Methematica. The platform graphically simulates the mechanism of production and propagation of the polarized waves in a medium while satisfying Maxwell's equations.

  8. Motogenic Sites in Human Fibronectin Are Masked by Long Range Interactions

    Science.gov (United States)

    Vakonakis, Ioannis; Staunton, David; Ellis, Ian R.; Sarkies, Peter; Flanagan, Aleksandra; Schor, Ana M.; Schor, Seth L.; Campbell, Iain D.

    2009-01-01

    Fibronectin (FN) is a large extracellular matrix glycoprotein important for development and wound healing in vertebrates. Recent work has focused on the ability of FN fragments and embryonic or tumorigenic splicing variants to stimulate fibroblast migration into collagen gels. This activity has been localized to specific sites and is not exhibited by full-length FN. Here we show that an N-terminal FN fragment, spanning the migration stimulation sites and including the first three type III FN domains, also lacks this activity. A screen for interdomain interactions by solution-state NMR spectroscopy revealed specific contacts between the Fn N terminus and two of the type III domains. A single amino acid substitution, R222A, disrupts the strongest interaction, between domains 4–5FnI and 3FnIII, and restores motogenic activity to the FN N-terminal fragment. Anastellin, which promotes fibril formation, destabilizes 3FnIII and disrupts the observed 4–5FnI-3FnIII interaction. We discuss these findings in the context of the control of cellular activity through exposure of masked sites. PMID:19366708

  9. Interaction of Palmitic Acid with Metoprolol Succinate at the Binding Sites of Bovine Serum Albumin

    Directory of Open Access Journals (Sweden)

    Mashiur Rahman

    2014-12-01

    Full Text Available Purpose: The aim of this study was to characterize the binding profile as well as to notify the interaction of palmitic acid with metoprolol succinate at its binding site on albumin. Methods: The binding of metoprolol succinate to bovine serum albumin (BSA was studied by equilibrium dialysis method (ED at 27°C and pH 7.4, in order to have an insight in the binding chemistry of the drug to BSA in presence and absence of palmitic acid. The study was carried out using ranitidine as site-1 and diazepam as site-2 specific probe. Results: Different analysis of binding of metoprolol succinate to bovine serum albumin suggested two sets of association constants: high affinity association constant (k1 = 11.0 x 105 M-1 with low capacity (n1 = 2 and low affinity association (k2 = 4.0×105 M-1 constant with high capacity (n2 = 8 at pH 7.4 and 27°C. During concurrent administration of palmitic acid and metoprolol succinate in presence or absence of ranitidine or diazepam, it was found that palmitic acid displaced metoprolol succinate from its binding site on BSA resulting reduced binding of metoprolol succinate to BSA. The increment in free fraction of metoprolol succinate was from 26.27% to 55.08% upon the addition of increased concentration of palmitic acid at a concentration of 0×10-5 M to 16×10-5 M. In presence of ranitidine and diazepam, palmitic acid further increases the free fraction of metoprolol succinate from 33.05% to 66.95% and 40.68% to 72.88%, respectively. Conclusion: This data provided the evidence of interaction at higher concentration of palmitic acid at the binding sites on BSA, which might change the pharmacokinetic properties of metoprolol succinate.

  10. Ralph Ellison, critique de LeRoi Jones

    OpenAIRE

    Parent, Emmanuel

    2007-01-01

    On se propose ici de revenir sur la polémique ayant opposé Ralph Ellison à LeRoi Jones à l’occasion de la publication du Peuple du blues (1963). En restituant leur théorie respective du blues et du jazz, on montre comment Ellison essaie de dépasser tant le parti pris nationaliste qu’une histoire du jazz positive et progressiste qui célèbre l’avènement au cours du xxe siècle d’un véritable jazz dégagé des contraintes du folklore et du divertissement. En articulant d’une manière originale la mu...

  11. Patient-oriented interactive E-health tools on U.S. hospital Web sites.

    Science.gov (United States)

    Huang, Edgar; Chang, Chiu-Chi Angela

    2012-01-01

    The purpose of this study is to provide evidence for strategic planning regarding e-health development in U.S. hospitals. A content analysis of a representative sample of the U.S. hospital Web sites has revealed how U.S. hospitals have taken advantage of the 21 patient-oriented interactive tools identified in this study. Significant gaps between various types of hospitals have also been found. It is concluded that although the majority of the U.S. hospitals have adopted traditional functional tools, they need to make significant inroad in implementing the core e-business tools to serve their patients/users, making their Web sites more efficient marketing tools.

  12. Kinetic and docking studies of the interaction of quinones with the quinone reductase active site.

    Science.gov (United States)

    Zhou, Zhigang; Fisher, Derek; Spidel, Jared; Greenfield, Jodi; Patson, Brian; Fazal, Aleem; Wigal, Carl; Moe, Owen A; Madura, Jeffry D

    2003-02-25

    NAD(P)H/quinone acceptor oxidoreductase type 1 (QR1) protects cells from cytotoxic and neoplastic effects of quinones though two-electron reduction. Kinetic experiments, docking, and binding affinity calculations were performed on a series of structurally varied quinone substrates. A good correlation between calculated and measured binding affinities from kinetic determinations was obtained. The experimental and theoretical studies independently support a model in which quinones (with one to three fused aromatic rings) bind in the QR1 active site utilizing a pi-stacking interaction with the isoalloxazine ring of the FAD cofactor.

  13. How to awaken your nanomachines: Site-specific activation of focal adhesion kinases through ligand interactions

    KAUST Repository

    Walkiewicz, Katarzyna Wiktoria

    2015-06-17

    The focal adhesion kinase (FAK) and the related protein-tyrosine kinase 2-beta (Pyk2) are highly versatile multidomain scaffolds central to cell adhesion, migration, and survival. Due to their key role in cancer metastasis, understanding and inhibiting their functions are important for the development of targeted therapy. Because FAK and Pyk2 are involved in many different cellular functions, designing drugs with partial and function-specific inhibitory effects would be desirable. Here, we summarise recent progress in understanding the structural mechanism of how the tug-of-war between intramolecular and intermolecular interactions allows these protein ‘nanomachines’ to become activated in a site-specific manner.

  14. Humanin binds MPP8: mapping interaction sites of the peptide and protein.

    Science.gov (United States)

    Maximov, Vadim V; Martynenko, Alina V; Arman, Inga P; Tarantul, Vyacheslav Z

    2013-05-01

    Humanin (HN), a 24-amino acid peptide encoded by the mitochondrial 16S rRNA gene, was discovered by screening a cDNA library from the occipital cortex of a patient with Alzheimer's disease (AD) for a protection factor against AD-relevant insults. Earlier, using the yeast two-hybrid system, we have identified the M-phase phosphoprotein 8 (MPP8) as a binding partner for HN. In the present work, we further confirmed interaction of HN with MPP8 in co-immunoprecipitation experiments and localized an MPP8-binding site in the region between 5 and 12 aa. of HN. We have also shown that an MPP8 fragment (residues 431-560) is sufficient to bind HN. Further studies on functional consequences of the interaction between the potential oncopetide and the oncoprotein may elucidate some aspects of the molecular mechanisms of carcinogenesis. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.

  15. When Ernest Jones First Arrived in Toronto, or Reappraising the Bruce Letter.

    Science.gov (United States)

    Kuhn, Philip

    2018-04-16

    In July 1962, Toronto-based surgeon, Herbert Bruce, wrote a private and confidential letter to social worker and historian Cyril Greenland with some memories and impressions of Sigmund Freud's lifelong friend and biographer, Ernest Jones, in Toronto (1908-1913). In the letter, Bruce described Jones as a 'sexual pervert'. Despite Bruce's condemnation of Jones, historians and biographers have largely ignored this controversial aspect of Jones' impression in Toronto. The article traces how scholars have handled the existence of the Bruce letter, and the consequences for how this history has been understood. In the latter half of the article, the author considers how the existence of this letter offers insights into how the Toronto medical establishment regarded Ernest Jones.

  16. Efficient analysis using custom interactive visualization tools at a Superfund site

    Energy Technology Data Exchange (ETDEWEB)

    Williams, G. [Northwestern Univ., Evanston, IL (United States); Durham, L. [Argonne National Lab., IL (United States)

    1992-12-01

    Custom visualization analysis programs were developed and used to analyze contaminant transport calculations from a three-dimensional numerical groundwater flow model developed for a Department of Energy Superfund site. The site hydrogeology, which is highly heterogenous, includes both fractured limestone and dolomite and alluvium deposits. Three-dimensional interactive visualization techniques were used to understand and analyze the three-dimensional, double-porosity modeling results. A graphical object oriented programming environment was applied to efficiently develop custom visualization programs in a coarse-grained data structure language. Comparisons were made, using the results from the three-dimensional, finite-difference model, between traditional two-dimensional analyses (contour and vector plots) and interactive three-dimensional techniques. Subjective comparison areas include the accuracy of analysis, the ability to understand the results of three-dimensional contaminant transport simulation, and the capability to transmit the results of the analysis to the project management. In addition, a quantitative comparison was made on the time required to develop a thorough analysis of the modeling results. The conclusions from the comparative study showed that the visualization analysis provided an increased awareness of the contaminant transport mechanisms, provided new insights into contaminant migration, and resulted in a significant time savings.

  17. Efficient analysis using custom interactive visualization tools at a Superfund site

    International Nuclear Information System (INIS)

    Williams, G.; Durham, L.

    1992-01-01

    Custom visualization analysis programs were developed and used to analyze contaminant transport calculations from a three-dimensional numerical groundwater flow model developed for a Department of Energy Superfund site. The site hydrogeology, which is highly heterogenous, includes both fractured limestone and dolomite and alluvium deposits. Three-dimensional interactive visualization techniques were used to understand and analyze the three-dimensional, double-porosity modeling results. A graphical object oriented programming environment was applied to efficiently develop custom visualization programs in a coarse-grained data structure language. Comparisons were made, using the results from the three-dimensional, finite-difference model, between traditional two-dimensional analyses (contour and vector plots) and interactive three-dimensional techniques. Subjective comparison areas include the accuracy of analysis, the ability to understand the results of three-dimensional contaminant transport simulation, and the capability to transmit the results of the analysis to the project management. In addition, a quantitative comparison was made on the time required to develop a thorough analysis of the modeling results. The conclusions from the comparative study showed that the visualization analysis provided an increased awareness of the contaminant transport mechanisms, provided new insights into contaminant migration, and resulted in a significant time savings

  18. Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

    Science.gov (United States)

    Jian, Jhih-Wei; Elumalai, Pavadai; Pitti, Thejkiran; Wu, Chih Yuan; Tsai, Keng-Chang; Chang, Jeng-Yih; Peng, Hung-Pin; Yang, An-Suei

    2016-01-01

    Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from the three-dimensional probability density maps of interacting atoms, which were reconstructed on the query protein surfaces and were relatively insensitive to local conformational variations of the tentative ligand binding sites. The prediction accuracy of the ISMBLab-LIG predictors is comparable to that of the best LBS predictors benchmarked on several well-established testing datasets. More importantly, the ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models. As such, the method is particularly useful for predicting LBSs not only on experimental protein structures without known LBS templates in the database but also on computationally predicted model protein structures with structural uncertainties in the tentative ligand binding sites. PMID:27513851

  19. Nonlinear Time Domain Seismic Soil-Structure Interaction (SSI) Deep Soil Site Methodology Development

    International Nuclear Information System (INIS)

    Spears, Robert Edward; Coleman, Justin Leigh

    2015-01-01

    Currently the Department of Energy (DOE) and the nuclear industry perform seismic soil-structure interaction (SSI) analysis using equivalent linear numerical analysis tools. For lower levels of ground motion, these tools should produce reasonable in-structure response values for evaluation of existing and new facilities. For larger levels of ground motion these tools likely overestimate the in-structure response (and therefore structural demand) since they do not consider geometric nonlinearities (such as gaping and sliding between the soil and structure) and are limited in the ability to model nonlinear soil behavior. The current equivalent linear SSI (SASSI) analysis approach either joins the soil and structure together in both tension and compression or releases the soil from the structure for both tension and compression. It also makes linear approximations for material nonlinearities and generalizes energy absorption with viscous damping. This produces the potential for inaccurately establishing where the structural concerns exist and/or inaccurately establishing the amplitude of the in-structure responses. Seismic hazard curves at nuclear facilities have continued to increase over the years as more information has been developed on seismic sources (i.e. faults), additional information gathered on seismic events, and additional research performed to determine local site effects. Seismic hazard curves are used to develop design basis earthquakes (DBE) that are used to evaluate nuclear facility response. As the seismic hazard curves increase, the input ground motions (DBE's) used to numerically evaluation nuclear facility response increase causing larger in-structure response. As ground motions increase so does the importance of including nonlinear effects in numerical SSI models. To include material nonlinearity in the soil and geometric nonlinearity using contact (gaping and sliding) it is necessary to develop a nonlinear time domain methodology. This

  20. Vere-Jones' self-similar branching model

    International Nuclear Information System (INIS)

    Saichev, A.; Sornette, D.

    2005-01-01

    Motivated by its potential application to earthquake statistics as well as for its intrinsic interest in the theory of branching processes, we study the exactly self-similar branching process introduced recently by Vere-Jones. This model extends the ETAS class of conditional self-excited branching point-processes of triggered seismicity by removing the problematic need for a minimum (as well as maximum) earthquake size. To make the theory convergent without the need for the usual ultraviolet and infrared cutoffs, the distribution of magnitudes m ' of daughters of first-generation of a mother of magnitude m has two branches m ' ' >m with exponent β+d, where β and d are two positive parameters. We investigate the condition and nature of the subcritical, critical, and supercritical regime in this and in an extended version interpolating smoothly between several models. We predict that the distribution of magnitudes of events triggered by a mother of magnitude m over all generations has also two branches m ' ' >m with exponent β+h, with h=d√(1-s), where s is the fraction of triggered events. This corresponds to a renormalization of the exponent d into h by the hierarchy of successive generations of triggered events. For a significant part of the parameter space, the distribution of magnitudes over a full catalog summed over an average steady flow of spontaneous sources (immigrants) reproduces the distribution of the spontaneous sources with a single branch and is blind to the exponents β,d of the distribution of triggered events. Since the distribution of earthquake magnitudes is usually obtained with catalogs including many sequences, we conclude that the two branches of the distribution of aftershocks are not directly observable and the model is compatible with real seismic catalogs. In summary, the exactly self-similar Vere-Jones model provides an attractive new approach to model triggered seismicity, which alleviates delicate questions on the role of

  1. Reference interaction site model and optimized perturbation theories of colloidal dumbbells with increasing anisotropy.

    Science.gov (United States)

    Munaò, Gianmarco; Gámez, Francisco; Costa, Dino; Caccamo, Carlo; Sciortino, Francesco; Giacometti, Achille

    2015-06-14

    We investigate thermodynamic properties of anisotropic colloidal dumbbells in the frameworks provided by the Reference Interaction Site Model (RISM) theory and an Optimized Perturbation Theory (OPT), this latter based on a fourth-order high-temperature perturbative expansion of the free energy, recently generalized to molecular fluids. Our model is constituted by two identical tangent hard spheres surrounded by square-well attractions with same widths and progressively different depths. Gas-liquid coexistence curves are obtained by predicting pressures, free energies, and chemical potentials. In comparison with previous simulation results, RISM and OPT agree in reproducing the progressive reduction of the gas-liquid phase separation as the anisotropy of the interaction potential becomes more pronounced; in particular, the RISM theory provides reasonable predictions for all coexistence curves, bar the strong anisotropy regime, whereas OPT performs generally less well. Both theories predict a linear dependence of the critical temperature on the interaction strength, reproducing in this way the mean-field behavior observed in simulations; the critical density—that drastically drops as the anisotropy increases—turns to be less accurate. Our results appear as a robust benchmark for further theoretical studies, in support to the simulation approach, of self-assembly in model colloidal systems.

  2. Fast kinetic studies on the allosteric interactions between acetylcholine receptor and local anesthetic binding sites.

    Science.gov (United States)

    Heidmann, T; Changeux, J P

    1979-02-15

    Preincubation of receptor-rich membrane fragments from Torpedo marmorata with tertiary amine local anesthetics and several toxins such as histrionicotoxin, crotoxin and cerulotoxin, modifies the amplitude and time course of the relaxation processes monitored upon rapid mixing of the membrane fragments with the fluorescent agonist, Dns-C6-Cho. In particular, the amplitude of the rapid relaxation process, which is proportional to the fraction of acetylcholine receptor sites in a high-affinity state, increases; accordingly, the rate constant of the 'slow' and 'intermediate' relaxation processes also increases up to ten times (except with histrionicotoxin) whereas in a higher range of local anesthetic concentrations the rate constant of the 'rapid' relaxation process decreases. The data are accounted for by a two-state model of the acetylcholine regulator, assuming distinct binding sites for cholinergic agonists and local anesthetics and allosteric interactions between these two classes of sites; local anesthetics stabilize the regulator in a high-affinity state for agonists even in the absence of agonist, and modify the rate constants for th interconversions between the low-affinity and high-affinity states. The model accounts for the 'slow' fluorescence increase monitored upon addition of local anesthetics to a suspension of receptor-rich membranes supplemented with trace amounts of Dns-C6-Cho. The effect of local anesthetics on the apparent rate constant of the 'rapid' relaxation process can be accounted for on the basis of an additional low-affinity binding of local anesthetics to the acetylcholine receptor site. Finally the increase of the apparent rate constant of the 'intermediate' relaxation process can be simply accounted for by assuming the existence of a third state, corresponding to the 'active' state, to which local anesthetics bind and block ionic transport.

  3. El caso Marion Jones o el llanto de una reina

    Directory of Open Access Journals (Sweden)

    Juan A Martínez de Osaba y Goenega

    2008-03-01

    Full Text Available Con un somatotipo ideal esta atleta sobresalió en Sydney 2000. Se había propuesto obtener cinco medallas doradas en el hectómetro, los 200, relevos 4 por 100, 4 por 400 y salto largo. Tamaña proeza nunca la había logrado una mujer. Pero Marion llegó con el mundo a sus pies, preparada para la cima. Solo Jesse Owens, Carl Lewis y Fanny Blankers-Koen habían alcanzado cuatro. Otra cosa fue Paavo Nurmi en las carreras de resistencia, pues en París 1924 ganó cinco títulos, único hasta la fecha en el deporte rey.“Jones, Marion (1976. Considerada como la reina de los Juegos de la Olimpiada de Sydney 2000. Ganadora de cinco medallas durante esta lid; de ellas 3 de oro en: 200 (21,84 m y en 100 (10,75 m, y el relevo 4 x 400 metros planos, así como dos de bronce, en el relevo 4 x 100 metros planos y en el salto de longitud…”

  4. Interlayer interaction and mechanical properties in multi-layer graphene, Boron-Nitride, Aluminum-Nitride and Gallium-Nitride graphene-like structure: A quantum-mechanical DFT study

    Science.gov (United States)

    Ghorbanzadeh Ahangari, Morteza; Fereidoon, A.; Hamed Mashhadzadeh, Amin

    2017-12-01

    In present study, we investigated mechanical, electronic and interlayer properties of mono, bi and 3layer of Boron-Nitride (B-N), Aluminum-Nitride (Al-N) and Gallium-Nitride (Ga-N) graphene sheets and compared these results with results obtained from carbonic graphenes (C-graphenes). For reaching this purpose, first we optimized the geometrical parameters of these graphenes by using density functional theory (DFT) method. Then we calculated Young's modulus of graphene sheet by compressing and then elongating these sheets in small increment. Our results indicates that Young's modulus of graphenes didn't changed obviously by increasing the number of layer sheet. We also found that carbonic graphene has greatest Young's modulus among another mentioned sheets because of smallest equilibrium distance between its elements. Next we modeled the van der Waals interfacial interaction exist between two sheets with classical spring model by using general form of Lennard-Jones (L-J) potential for all of mentioned graphenes. For calculating L-J parameters (ε and σ), the potential energy between layers of mentioned graphene as a function of the separation distance was plotted. Moreover, the density of states (DOS) are calculated to understand the electronic properties of these systems better.

  5. Human platelets express CAR with localization at the sites of intercellular interaction

    Directory of Open Access Journals (Sweden)

    Othman Maha

    2011-09-01

    Full Text Available Abstract Adenovirus has a wide tissue tropism. The virus attaches to the surface of cells via the fiber protein knob binding to the Coxsackie and Adenovirus receptor known as CAR. Virus entry inside cells is facilitated by integrins αVβ3 and αVβ5. Mice platelets are shown to be the predominant Ad binding blood cell type and the virus is documented inside platelets. CAR was identified on human platelets in one study yet contradicted in another. The presence of CAR appears to be the most reasonable initial step for virus entry into platelets and is a key to the understanding of platelet adenovirus interaction. This study aimed to re investigate the presence of CAR on human platelets. Platelets were tested by indirect immune-fluorescence using rabbit H-300 polyclonal anti-CAR antibody and goat anti-rabbit IgG F(ab'2 Texas Red antibodies, alongside with CAR positive and negative controls. Platelets were found to express CAR on their surface and in contrast to the previous study only 3.5 ± 1.9% of the tested platelets did express CAR. In addition, CAR was seen within intracellular aggregates localized at the sites of cell-cell contacts indicating that CAR expression might be upregulated in response to platelet stimulation. We confirm the presence of CAR on human platelets, we provide explanation to some of the discrepancies in this regards and we add that this receptor is localized at the sites of intercellular interaction.

  6. Interactive marine spatial planning: siting tidal energy arrays around the Mull of Kintyre.

    Directory of Open Access Journals (Sweden)

    Karen A Alexander

    Full Text Available The rapid development of the offshore renewable energy sector has led to an increased requirement for Marine Spatial Planning (MSP and, increasingly, this is carried out in the context of the 'ecosystem approach' (EA to management. We demonstrate a novel method to facilitate implementation of the EA. Using a real-time interactive mapping device (touch-table and stakeholder workshops we gathered data and facilitated negotiation of spatial trade-offs at a potential site for tidal renewable energy off the Mull of Kintyre (Scotland. Conflicts between the interests of tidal energy developers and commercial and recreational users of the area were identified, and use preferences and concerns of stakeholders were highlighted. Social, cultural and spatial issues associated with conversion of common pool to private resource were also revealed. The method identified important gaps in existing spatial data and helped to fill these through interactive user inputs. The workshops developed a degree of consensus between conflicting users on the best areas for potential development suggesting that this approach should be adopted during MSP.

  7. Interactive marine spatial planning: siting tidal energy arrays around the Mull of Kintyre.

    Science.gov (United States)

    Alexander, Karen A; Janssen, Ron; Arciniegas, Gustavo; O'Higgins, Timothy G; Eikelboom, Tessa; Wilding, Thomas A

    2012-01-01

    The rapid development of the offshore renewable energy sector has led to an increased requirement for Marine Spatial Planning (MSP) and, increasingly, this is carried out in the context of the 'ecosystem approach' (EA) to management. We demonstrate a novel method to facilitate implementation of the EA. Using a real-time interactive mapping device (touch-table) and stakeholder workshops we gathered data and facilitated negotiation of spatial trade-offs at a potential site for tidal renewable energy off the Mull of Kintyre (Scotland). Conflicts between the interests of tidal energy developers and commercial and recreational users of the area were identified, and use preferences and concerns of stakeholders were highlighted. Social, cultural and spatial issues associated with conversion of common pool to private resource were also revealed. The method identified important gaps in existing spatial data and helped to fill these through interactive user inputs. The workshops developed a degree of consensus between conflicting users on the best areas for potential development suggesting that this approach should be adopted during MSP.

  8. Modeling Groundwater-Surface Water Interaction and Contaminant Transport of Chlorinated Solvent Contaminated Site

    Science.gov (United States)

    Yimer Ebrahim, Girma; Jonoski, Andreja; van Griensven, Ann; Dujardin, Juliette; Baetelaan, Okke; Bronders, Jan

    2010-05-01

    Chlorinated-solvent form one of the largest groups of environmental chemicals. Their use and misuse in industry have lead to a large entry of these chemicals into the environment, resulting in widespread dissemination and oftentimes environmental contamination. Chlorinated solvent contamination of groundwater resources has been widely reported. For instance, there has been much interest in the assessment of these contaminant levels and their evolutions with time in the groundwater body below the Vilvoorde-Machelen industrial area (Belgium). The long industrial history of the area has lead to complex patterns of pollution from multiple sources and the site has been polluted to the extent that individual plumes are not definable any more. Understanding of groundwater/surface water interaction is a critical component for determining the fate of contaminant both in streams and ground water due to the fact that groundwater and surface water are in continuous dynamic interaction in the hydrologic cycle. The interaction has practical consequences in the quantity and quality of water in either system in the sense that depletion and/or contamination of one of the system will eventually affect the other one. The transition zone between a stream and its adjacent aquifer referred to as the hyporheic zone plays a critical role in governing contaminant exchange and transformation during water exchange between the two water bodies. The hyporheic zone of Zenne River ( the main receptor ) is further complicated due to the fact that the river banks are artificially trained with sheet piles along its reach extending some 12 m below the surface. This study demonstrates the use of MODFLOW, a widely used modular three-dimensional block-centred finite difference, saturated flow model for simulating the flow and direction of movement of groundwater through aquifer and stream-aquifer interaction and the use of transport model RT3D, a three-dimensional multi-species reactive transport model

  9. Ly49-dependent NK cell licensing and effector inhibition involve the same interaction site on MHC ligands1

    Science.gov (United States)

    Choi, Taewoong; Ferris, Stephen T.; Matsumoto, Naoki; Poursine-Laurent, Jennifer; Yokoyama, Wayne M.

    2011-01-01

    NK cells become functionally competent to be triggered by their activation receptors through the interaction of NK cell inhibitory receptors with their cognate self-MHC ligands, an MHC-dependent educational process termed “licensing.” For example, Ly49A+ NK cells become licensed by the interaction of the Ly49A inhibitory receptor with its MHC class I ligand, H2Dd while Ly49C+ NK cells are licensed by H2Kb. Structural studies indicate that the Ly49A inhibitory receptor may interact with two sites, termed site 1 and site 2, on its H2Dd ligand. Site 2 encompasses the α1/α2/α3 domains of the H2Dd heavy chain and β2-microglobulin (β2m), and is the functional binding site for the Ly49A in effector inhibition. Ly49C functionally interacts with a similar site in H2Kb. However, it is currently unknown whether this same site is involved in Ly49A or Ly49C-dependent licensing. Herein, we produced transgenic C57BL/6 mice expressing wild type or site 2 mutant H2Dd molecules and studied whether or not Ly49A+ NK cells are licensed. We also investigated Ly49A and Ly49C-dependent NK licensing in murine β2m-deficient mice which are transgenic for human β2m which has species-specific amino acid substitutions in β2m. Our data from these transgenic mice indicate that site 2 on self-MHC is critical for Ly49A and Ly49C-dependent NK cell licensing. Thus, NK cell licensing through Ly49 involves specific interactions with its MHC ligand that are similar to those involved in effector inhibition. PMID:21335486

  10. The Jones polynomial as a new invariant of topological fluid dynamics

    International Nuclear Information System (INIS)

    Ricca, Renzo L; Liu, Xin

    2014-01-01

    A new method based on the use of the Jones polynomial, a well-known topological invariant of knot theory, is introduced to tackle and quantify topological aspects of structural complexity of vortex tangles in ideal fluids. By re-writing the Jones polynomial in terms of helicity, the resulting polynomial becomes then function of knot topology and vortex circulation, providing thus a new invariant of topological fluid dynamics. Explicit computations of the Jones polynomial for some standard configurations, including the Whitehead link and the Borromean rings (whose linking numbers are zero), are presented for illustration. In the case of a homogeneous, isotropic tangle of vortex filaments with same circulation, the new Jones polynomial reduces to some simple algebraic expression, that can be easily computed by numerical methods. This shows that this technique may offer a new setting and a powerful tool to detect and compute topological complexity and to investigate relations with energy, by tackling fundamental aspects of turbulence research. (paper)

  11. Development of a Model Protein Interaction Pair as a Benchmarking Tool for the Quantitative Analysis of 2-Site Protein-Protein Interactions.

    Science.gov (United States)

    Yamniuk, Aaron P; Newitt, John A; Doyle, Michael L; Arisaka, Fumio; Giannetti, Anthony M; Hensley, Preston; Myszka, David G; Schwarz, Fred P; Thomson, James A; Eisenstein, Edward

    2015-12-01

    A significant challenge in the molecular interaction field is to accurately determine the stoichiometry and stepwise binding affinity constants for macromolecules having >1 binding site. The mission of the Molecular Interactions Research Group (MIRG) of the Association of Biomolecular Resource Facilities (ABRF) is to show how biophysical technologies are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core technologies [such as biosensor, microcalorimetry, or analytic ultracentrifugation (AUC)]. In the present work, the MIRG has developed a robust model protein interaction pair consisting of a bivalent variant of the Bacillus amyloliquefaciens extracellular RNase barnase and a variant of its natural monovalent intracellular inhibitor protein barstar. It is demonstrated that this system can serve as a benchmarking tool for the quantitative analysis of 2-site protein-protein interactions. The protein interaction pair enables determination of precise binding constants for the barstar protein binding to 2 distinct sites on the bivalent barnase binding partner (termed binase), where the 2 binding sites were engineered to possess affinities that differed by 2 orders of magnitude. Multiple MIRG laboratories characterized the interaction using isothermal titration calorimetry (ITC), AUC, and surface plasmon resonance (SPR) methods to evaluate the feasibility of the system as a benchmarking model. Although general agreement was seen for the binding constants measured using solution-based ITC and AUC approaches, weaker affinity was seen for surface-based method SPR, with protein immobilization likely affecting affinity. An analysis of the results from multiple MIRG laboratories suggests that the bivalent barnase-barstar system is a suitable model for benchmarking new approaches for the quantitative characterization of complex biomolecular interactions.

  12. Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks

    Science.gov (United States)

    Bartoli, Lisa; Martelli, Pier Luigi; Rossi, Ivan; Fariselli, Piero; Casadio, Rita

    Most of the cellular functions are the result of the concerted action of protein complexes forming pathways and networks. For this reason, efforts were devoted to the study of protein-protein interactions. Large-scale experiments on whole genomes allowed the identification of interacting protein pairs. However residues involved in the interaction are generally not known and the majority of the interactions still lack a structural characterization. A crucial step towards the deciphering of the interaction mechanism of proteins is the recognition of their interacting surfaces, particularly in those structures for which also the most recent interaction network resources do not contain information. To this purpose, we developed a neural network-based method that is able to characterize protein complexes, by predicting amino acid residues that mediate the interactions. All the Protein Data Bank (PDB) chains, both in the unbound and in the complexed form, are predicted and the results are stored in a database of interaction surfaces (http://gpcr.biocomp.unibo.it/zenpatches). Finally, we performed a survey on the different computational methods for protein-protein interaction prediction and on their training/testing sets in order to highlight the most informative properties of protein interfaces.

  13. Environmental Assessment Bank Stabilization along St. Jones River Dover Air Force Base, Delaware

    Science.gov (United States)

    2008-12-01

    considered the implementation of all hard technologies such as riprap and gabions along the impacted 3,000 linear feet of banking. However, cost and...that ranges from 70 feet below ground surface to within a few feet near the St. Jones River. The groundwater generally flows southwest toward the St...high water table. 3.3.2 Stormwater Management The St. Jones River flows along the western boundary of Dover AFB. Pipe Elm Creek of the Little

  14. Regulatory restrictions and energy: The impact of the Jones Act on spot gasoline prices

    International Nuclear Information System (INIS)

    Gius, Mark

    2013-01-01

    The purpose of the present study is to estimate the effects of the Jones Act on spot gasoline prices. Although the Jones Act pertains to the domestic shipment of all types of goods, the present study will only focus on gasoline. The present study will use data obtained from the Energy Information Administration in order to determine if the price of gasoline declined during Jones Act waiver periods. Looking at daily prices, the results regarding the effects of the Jones Act on spot gasoline prices are mixed. When using a t-test, the results indicated either that there was no significant difference or that prices were actually higher during the waiver periods. When using a first-order autoregressive model, it was found that prices were lower during the 2005 waiver period but higher during the 2012 waiver. Given these inconclusive results, it is not possible to conclude that the Jones Act restrictions contribute to higher gasoline prices. - Highlights: • I examine the effect of the Jones Act on spot gasoline prices. • I use daily price data over a seven year period. • I find that the results are mixed. • For the Hurricane Katrina waiver, prices fell, but for the Hurricane Sandy waiver, prices rose

  15. Distinct parietal sites mediate the influences of mood, arousal, and their interaction on human recognition memory.

    Science.gov (United States)

    Greene, Ciara M; Flannery, Oliver; Soto, David

    2014-12-01

    The two dimensions of emotion, mood valence and arousal, have independent effects on recognition memory. At present, however, it is not clear how those effects are reflected in the human brain. Previous research in this area has generally dealt with memory for emotionally valenced or arousing stimuli, but the manner in which interacting mood and arousal states modulate responses in memory substrates remains poorly understood. We investigated memory for emotionally neutral items while independently manipulating mood valence and arousal state by means of music exposure. Four emotional conditions were created: positive mood/high arousal, positive mood/low arousal, negative mood/high arousal, and negative mood/low arousal. We observed distinct effects of mood valence and arousal in parietal substrates of recognition memory. Positive mood increased activity in ventral posterior parietal cortex (PPC) and orbitofrontal cortex, whereas arousal condition modulated activity in dorsal PPC and the posterior cingulate. An interaction between valence and arousal was observed in left ventral PPC, notably in a parietal area distinct from the those identified for the main effects, with a stronger effect of mood on recognition memory responses here under conditions of relative high versus low arousal. We interpreted the PPC activations in terms of the attention-to-memory hypothesis: Increased arousal may lead to increased top-down control of memory, and hence dorsal PPC activation, whereas positive mood valence may result in increased activity in ventral PPC regions associated with bottom-up attention to memory. These findings indicate that distinct parietal sites mediate the influences of mood, arousal, and their interplay during recognition memory.

  16. Quantification of site-city interaction effects on the response of structure under double resonance condition

    Science.gov (United States)

    Kumar, Neeraj; Narayan, Jay Prakash

    2018-01-01

    This paper presents the site-city interaction (SCI) effects on the response of closely spaced structures under double resonance condition (F_{02{{D}}}^{{S}} = F_{02{{D}}}^{{B}}), where F_{02{{D}}}^{{S}} and F_{02{{D}}}^{{B}} are fundamental frequencies of 2-D structure and 2-D basin, respectively. This paper also presents the development of empirical relations to predict the F_{02{{D}}}^{{B}} of elliptical and trapezoidal basins for both the polarizations of the S wave. Simulated results revealed that F_{02{{D}}}^{{B}} of a 2-D basin very much depends on its geometry, shape ratio and polarization of the incident S wave. The obtained spectral amplification factor (SAF) at F_{02{{D}}}^{{S}} of a standalone structure in a 2-D basin is greater than that in the 1-D case under double resonance condition. A considerable reduction of the fundamental resonance frequency of structures due to the SCI effects is observed for both the polarizations of the S wave. The SAFs at F_{02{{D}}}^{{S}} of closely spaced structures due to SCI effects is larger in the case of SV than SH waves. A splitting of the fundamental-mode frequency bandwidth along with the drastic decrease of SAF due to the SCI effects is obtained. The findings of this paper raise the question concerning the validity of the predicted response of standalone structure based on soil-structure interaction for the design of structures in a 2-D small basin, in an urban environment.

  17. Water-rock interaction modelling and uncertainties of mixing modelling. SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    Gimeno, Maria J.; Auque, Luis F.; Gomez, Javier B.; Acero, Patricia (Univ. of Zaragoza, Zaragoza (Spain))

    2009-01-15

    The overall objectives of hydrogeochemical description for Laxemar are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are the major driving force for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Laxemar site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and Univ. researchers with expertise in geochemistry

  18. Water-rock interaction modelling and uncertainties of mixing modelling. SDM-Site Laxemar

    International Nuclear Information System (INIS)

    Gimeno, Maria J.; Auque, Luis F.; Gomez, Javier B.; Acero, Patricia

    2009-01-01

    The overall objectives of hydrogeochemical description for Laxemar are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are the major driving force for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Laxemar site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and Univ. researchers with expertise in geochemistry, hydrochemistry

  19. Interatomic Coulombic Decay Effects in Theoretical DNA Recombination Systems Involving Protein Interaction Sites

    Science.gov (United States)

    Vargas, E. L.; Rivas, D. A.; Duot, A. C.; Hovey, R. T.; Andrianarijaona, V. M.

    2015-03-01

    DNA replication is the basis for all biological reproduction. A strand of DNA will ``unzip'' and bind with a complimentary strand, creating two identical strands. In this study, we are considering how this process is affected by Interatomic Coulombic Decay (ICD), specifically how ICD affects the individual coding proteins' ability to hold together. ICD mainly deals with how the electron returns to its original state after excitation and how this affects its immediate atomic environment, sometimes affecting the connectivity between interaction sites on proteins involved in the DNA coding process. Biological heredity is fundamentally controlled by DNA and its replication therefore it affects every living thing. The small nature of the proteins (within the range of nanometers) makes it a good candidate for research of this scale. Understanding how ICD affects DNA molecules can give us invaluable insight into the human genetic code and the processes behind cell mutations that can lead to cancer. Authors wish to give special thanks to Pacific Union College Student Senate in Angwin, California, for their financial support.

  20. Group tele-immersion:enabling natural interactions between groups at distant sites.

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Christine L. (Sandia National Laboratories, Livermore, CA); Stewart, Corbin (Sandia National Laboratories, Livermore, CA); Nashel, Andrew (University of North Carolina at Chapel Hill, Chapel Hill, NC)

    2005-08-01

    We present techniques and a system for synthesizing views for video teleconferencing between small groups. In place of replicating one-to-one systems for each pair of users, we create a single unified display of the remote group. Instead of performing dense 3D scene computation, we use more cameras and trade-off storage and hardware for computation. While it is expensive to directly capture a scene from all possible viewpoints, we have observed that the participants viewpoints usually remain at a constant height (eye level) during video teleconferencing. Therefore, we can restrict the possible viewpoint to be within a virtual plane without sacrificing much of the realism, and in cloning so we significantly reduce the number of required cameras. Based on this observation, we have developed a technique that uses light-field style rendering to guarantee the quality of the synthesized views, using a linear array of cameras with a life-sized, projected display. Our full-duplex prototype system between Sandia National Laboratories, California and the University of North Carolina at Chapel Hill has been able to synthesize photo-realistic views at interactive rates, and has been used to video conference during regular meetings between the sites.

  1. Interaction of radionuclides with argillite from the Eleana Formation on the Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    Dosch, R.G.; Lynch, A.W.

    1979-02-01

    Distribution coefficients have been determined for {sup 137}Cs, {sup 85}Sr, {sup 144}Ce, {sup 99}Tc, {sup 152}Eu, {sup 238}Pu, {sup 244}Cm, and {sup 243}Am between argillite from the Eleana Formation on the Nevada Test Site (NTS) and several aqueous phases. Radionuclide concentrations in the range of 1 to 0.001 {mu}Ci/ml were used with contact times of 14, 28, and 56 days. Reaction mechanism, concentration effects, exchange capacity, equilibration times, and particle size effects were addressed in a more comprehensive study of the interaction of argillite with Cs in deionized water. The experimental parameters used in the distribution coefficient measurements were based in part on this work. The aqueous phases included a simulated groundwater with composition based on the analysis of a NTS groundwater, the same simulant and deionized water which were pre-equilibrated with powdered argillite, and a groundwater simulant with approximately the same qualitative composition of the NTS simulant, but with a higher ionic strength. A system to provide continuous pH control by CO{sub 2} addition during equilibration of the argillite-solution mixtures was designed and assembled. Initial experiments were done with Cs and Eu and the effects of pH on their distribution coefficients are discussed.

  2. The effects of reading comprehension and launch site on frequency-predictability interactions during paragraph reading.

    Science.gov (United States)

    Whitford, Veronica; Titone, Debra

    2014-01-01

    We used eye movement measures of paragraph reading to examine whether word frequency and predictability interact during the earliest stages of lexical processing, with a specific focus on whether these effects are modulated by individual differences in reading comprehension or launch site (i.e., saccade length between the prior and currently fixated word--a proxy for the amount of parafoveal word processing). The joint impact of frequency and predictability on reading will elucidate whether these variables additively or multiplicatively affect the earliest stages of lexical access, which, in turn, has implications for computational models of eye movements during reading. Linear mixed effects models revealed additive effects during both early- and late-stage reading, where predictability effects were comparable for low- and high-frequency words. Moreover, less cautious readers (e.g., readers who engaged in skimming, scanning, mindless reading) demonstrated smaller frequency effects than more cautious readers. Taken together, our findings suggest that during extended reading, frequency and predictability exert additive influences on lexical and postlexical processing, and that individual differences in reading comprehension modulate sensitivity to the effects of word frequency.

  3. Using Transcranial Direct Current Stimulation to Enhance Creative Cognition: Interactions between Task, Polarity, and Stimulation Site

    Directory of Open Access Journals (Sweden)

    Adam B. Weinberger

    2017-05-01

    Full Text Available Creative cognition is frequently described as involving two primary processes, idea generation and idea selection. A growing body of research has used transcranial direct current stimulation (tDCS to examine the neural mechanisms implicated in each of these processes. This literature has yielded a diverse set of findings that vary depending on the location and type (anodal, cathodal, or both of electrical stimulation employed, as well as the task’s reliance on idea generation or idea selection. As a result, understanding the interactions between stimulation site, polarity and task demands is required to evaluate the potential of tDCS to enhance creative performance. Here, we review tDCS designs that have elicited reliable and dissociable enhancements for creative cognition. Cathodal stimulation over the left inferior frontotemporal cortex has been associated with improvements on tasks that rely primarily on idea generation, whereas anodal tDCS over left dorsolateral prefrontal cortex (DLPFC and frontopolar cortex has been shown to augment performance on tasks that impose high demands on creative idea selection. These results highlight the functional selectivity of tDCS for different components of creative thinking and confirm the dissociable contributions of left dorsal and inferior lateral frontotemporal cortex for different creativity tasks. We discuss promising avenues for future research that can advance our understanding of the effectiveness of tDCS as a method to enhance creative cognition.

  4. A cation-pi interaction in the binding site of the glycine receptor is mediated by a phenylalanine residue

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Millen, Kat S; Hanek, Ariele P

    2008-01-01

    Cys-loop receptor binding sites characteristically contain many aromatic amino acids. In nicotinic ACh and 5-HT3 receptors, a Trp residue forms a cation-pi interaction with the agonist, whereas in GABA(A) receptors, a Tyr performs this role. The glycine receptor binding site, however, contains...... of fluorinated Phe derivatives using unnatural amino acid mutagenesis. The data reveal a clear correlation between the glycine EC(50) value and the cation-pi binding ability of the fluorinated Phe derivatives at position 159, but not at positions 207 or 63, indicating a single cation-pi interaction between...

  5. Transcriptional stimulation via SC site of Bombyx sericin-1 gene through an interaction with a DNA binding protein SGF-3.

    Science.gov (United States)

    Matsuno, K; Takiya, S; Hui, C C; Suzuki, T; Fukuta, M; Ueno, K; Suzuki, Y

    1990-01-01

    Three protein binding sites have been identified in the upstream region of the sericin-1 gene. Two of them, SA and SC sites, have been known as putative cis-acting elements. Using synthetic oligonucleotides of these binding sites, it was found that silk gland factor-1 (SGF-1) binds to the SA site, and silk gland factor-3 (SGF-3) binds to the SC site but not to a mutated SC site, SCM. Tissue distribution of the two factors was different. SGF-3 is present abundantly in the middle silk gland (MSG) where the sericin-1 gene is transcribed specifically but is also present in other cell types, though in a much less concentration. SGF-1 is observed very abundantly in the two parts of silk gland, MSG and posterior silk gland (PSG), but not in other cells. Templates containing multimerized SA or SC sites at -39 of the sericin-1 gene promoter were tested in MSG nuclear extracts. The SC multimer strongly activated transcription, while the mutant SCM multimer did not. The SA multimer also gave a slight stimulation of transcription. These results suggest that SGF-3 stimulates transcription through an interaction with the SC site, and SGF-1 does so weakly through the SA site. Images PMID:2336359

  6. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes

    DEFF Research Database (Denmark)

    Cockburn, Darrell; Wilkens, Casper; Dilokpimol, Adiphol

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical...

  7. Screened Coulomb interactions in metallic alloys. II. Screening beyond the single-site and atomic-sphere approximations

    DEFF Research Database (Denmark)

    Ruban, Andrei; Simak, S.I.; Korzhavyi, P.A.

    2002-01-01

    -electron potential and energy. In the case of a random alloy such interactions can be accounted for only by lifting the atomic-sphere and single-site approximations, in order to include the polarization due to local environment effects. Nevertheless, a simple parametrization of the screened Coulomb interactions......A quantitative description of the configurational part of the total energy of metallic alloys with substantial atomic size difference cannot be achieved in the atomic-sphere approximation: It needs to be corrected at least for the multipole-moment interactions in the Madelung part of the one...

  8. Development of non-bonded interaction parameters between graphene and water using particle swarm optimization.

    Science.gov (United States)

    Bejagam, Karteek K; Singh, Samrendra; Deshmukh, Sanket A

    2018-05-05

    New Lennard-Jones parameters have been developed to describe the interactions between atomistic model of graphene, represented by REBO potential, and five commonly used all-atom water models, namely SPC, SPC/E, SPC/Fw, SPC/Fd, and TIP3P/Fs by employing particle swarm optimization (PSO) method. These new parameters were optimized to reproduce the macroscopic contact angle of water on a graphene sheet. The calculated line tension was in the order of 10 -11 J/m for the droplets of all water models. Our molecular dynamics simulations indicate the preferential orientation of water molecules near graphene-water interface with one OH bond pointing toward the graphene surface. Detailed analysis of simulation trajectories reveals the presence of water molecules with ≤∼1, ∼2, and ∼4 hydrogen bonds at the surface of air-water interface, graphene-water interface, and bulk region of the water droplet, respectively. Presence of water molecules with ≤∼1 and ∼2 hydrogen bonds suggest the existence of water clusters of different sizes at these interfaces. The trends observed in the libration, bending, and stretching bands of the vibrational spectra are closely associated with these structural features of water. The inhomogeneity in hydrogen bond network of water at the air-water and graphene-water interface is manifested by broadening of the peaks in the libration band for water present at these interfaces. The stretching band for the molecules in water droplet shows a blue shift as compared to the pure bulk water, which conjecture the presence of weaker hydrogen bond network in a droplet. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  9. Predicting the influence of a p2-symmetric substrate on molecular self-organization with an interaction-site model.

    Science.gov (United States)

    Rohr, Carsten; Balbás Gambra, Marta; Gruber, Kathrin; Höhl, Cornelia; Malarek, Michael S; Scherer, Lukas J; Constable, Edwin C; Franosch, Thomas; Hermann, Bianca A

    2011-02-14

    An interaction-site model can a priori predict molecular self-organisation on a new substrate in Monte Carlo simulations. This is experimentally confirmed with scanning tunnelling microscopy on Fréchet dendrons of a pentacontane template. Local and global ordering motifs, inclusion molecules and a rotated unit cell are correctly predicted.

  10. How Users Take Advantage of Different Forms of Interactivity on Online News Sites: Clicking, E-Mailing, and Commenting

    Science.gov (United States)

    Boczkowski, Pablo J.; Mitchelstein, Eugenia

    2012-01-01

    This study examines the uptake of multiple interactive features on news sites. It looks at the thematic composition of the most clicked, most e-mailed, and most commented stories during periods of heightened and routine political activity. Results show that (a) during the former period, the most commented stories were more likely to be focused on…

  11. Structural Mutations that Probe the Interactions between the Catalytic and Dianion Activation Sites at Triosephosphate Isomerase‡

    Science.gov (United States)

    Zhai, Xiang; Amyes, Tina L.; Wierenga, Rik K.; Loria, J. Patrick; Richard, John P.

    2013-01-01

    Triosephosphate isomerase (TIM) catalyzes the isomerization of dihydroxyacetone phosphate to form D-glyceraldehyde 3-phosphate. The effects of two structural mutations at TIM on the kinetic parameters for catalysis of the reaction of the truncated substrate glycolaldehyde (GA) and the activation of this reaction by phosphite dianion are reported. The P168A mutation results in similar 50-fold and 80-fold decreases, respectively, in (kcat/Km)E and (kcat/Km)E•HPi for deprotonation of GA catalyzed by free TIM and by the TIM•HPO32− complex. The mutation has little effect on the observed and intrinsic phosphite dianion binding energy, or on the magnitude of phosphite dianion activation of TIM for catalysis of deprotonation of GA. A loop 7 replacement mutant (L7RM) of TIM from chicken muscle was prepared by substitution of the archaeal sequence 208-TGAG for 208-YGGS. The L7RM exhibits a 25-fold decrease in (kcat/Km)E and a larger 170-fold decrease in (kcat/Km)E•HPi for reactions of GA. The mutation has little effect on the observed and intrinsic phosphodianion binding energy, and only a modest effect on phosphite dianion activation of TIM. The observation that both the P168A and loop 7 replacement mutations affect mainly the kinetic parameters for TIM-catalyzed deprotonation, but result in much smaller changes in the parameters for enzyme activation by phosphite dianion provide support for the conclusion that catalysis of proton transfer and dianion activation of TIM take place at separate, weakly interacting, sites in the protein catalyst. PMID:23909928

  12. Evaluation of anxiolytic activity of compound Valeriana jatamansi Jones in mice.

    Science.gov (United States)

    You, Jie-Shu; Peng, Min; Shi, Jin-Li; Zheng, Hu-Zhan; Liu, Yong; Zhao, Bao-Sheng; Guo, Jian-You

    2012-11-21

    Compound Valeriana jatamansi Jones is a formula for treating anxiety-related diseases in the clinic, which is composed of Valeriana jatamansi Rhizoma et Radix, Ziziphi Spinosae Semen, Albiziae Cortex and Junci Medulla. The purpose of this study was to explore the anxiolytic properties of this compound in mice. Male ICR mice were treated with compound Valerianae Jatamansi Jones (1.2 g/kg, 2.4 g/kg, 4.8 g/kg), saline, diazepam (2 mg/kg) orally for 10 days and then exposed to elevated maze-plus (EPM) and light-dark box (LDB). The effects of the compound on spontaneous activity were evaluated by locomotor activity test. We further investigated the mechanism of action underlying the anxiolytic-like effect of compound by pre-treating animals with antagonists of benzodiazepine (flumazenil, 3mg/kg) prior to evaluation using EPM and LDB. Compound Valerianae Jatamansi Jones (2.4, 4.8 g/kg, p.o.) significantly increased entries (P0.05). In addition, compound Valerianae Jatamansi Jones treatment didn't affect the spontaneous activity in mice (P> 0.05). The present study supports the hypothesis that compound Valeriana jatamansi Jones exert anxiolytic action but no sedative effects in mice and that this effect might be mediated by benzodiazepine receptors.

  13. Cephalometric effects of the Jones Jig appliance followed by fixed appliances in Class II malocclusion treatment.

    Science.gov (United States)

    Patel, Mayara Paim; Henriques, José Fernando Castanha; Freitas, Karina Maria Salvatore; Grec, Roberto Henrique da Costa

    2014-01-01

    The aim of this study was to cephalometrically assess the skeletal and dentoalveolar effects of Class II malocclusion treatment performed with the Jones Jig appliance followed by fixed appliances. The sample comprised 25 patients with Class II malocclusion treated with the Jones Jig appliance followed by fixed appliances, at a mean initial age of 12.90 years old. The mean time of the entire orthodontic treatment was 3.89 years. The distalization phase lasted for 0.85 years, after which the fixed appliance was used for 3.04 years. Cephalograms were used at initial (T1), post-distalization (T2) and final phases of treatment (T3). For intragroup comparison of the three phases evaluated, dependent ANOVA and Tukey tests were used. Jones Jig appliance did not interfere in the maxillary and mandibular component and did not change maxillomandibular relationship. Jones Jig appliance promoted distalization of first molars with anchorage loss, mesialization and significant extrusion of first and second premolars, as well as a significant increase in anterior face height at the end of treatment. The majority of adverse effects that occur during intraoral distalization are subsequently corrected during corrective mechanics. Buccal inclination and protrusion of mandibular incisors were identified. By the end of treatment, correction of overjet and overbite was observed. Jones Jig appliance promoted distalization of first molars with anchorage loss represented by significant mesial movement and extrusion of first and second premolars, in addition to a significant increase in anterior face height.

  14. Cephalometric effects of the Jones Jig appliance followed by fixed appliances in Class II malocclusion treatment

    Science.gov (United States)

    Patel, Mayara Paim; Henriques, José Fernando Castanha; de Freitas, Karina Maria Salvatore; Grec, Roberto Henrique da Costa

    2014-01-01

    Objective The aim of this study was to cephalometrically assess the skeletal and dentoalveolar effects of Class II malocclusion treatment performed with the Jones Jig appliance followed by fixed appliances. Methods The sample comprised 25 patients with Class II malocclusion treated with the Jones Jig appliance followed by fixed appliances, at a mean initial age of 12.90 years old. The mean time of the entire orthodontic treatment was 3.89 years. The distalization phase lasted for 0.85 years, after which the fixed appliance was used for 3.04 years. Cephalograms were used at initial (T1), post-distalization (T2) and final phases of treatment (T3). For intragroup comparison of the three phases evaluated, dependent ANOVA and Tukey tests were used. Results Jones Jig appliance did not interfere in the maxillary and mandibular component and did not change maxillomandibular relationship. Jones Jig appliance promoted distalization of first molars with anchorage loss, mesialization and significant extrusion of first and second premolars, as well as a significant increase in anterior face height at the end of treatment. The majority of adverse effects that occur during intraoral distalization are subsequently corrected during corrective mechanics. Buccal inclination and protrusion of mandibular incisors were identified. By the end of treatment, correction of overjet and overbite was observed. Conclusions Jones Jig appliance promoted distalization of first molars with anchorage loss represented by significant mesial movement and extrusion of first and second premolars, in addition to a significant increase in anterior face height. PMID:25162565

  15. Spectroscopic study of interaction between osthole and human serum albumin: Identification of possible binding site of the compound

    International Nuclear Information System (INIS)

    Bijari, Nooshin; Shokoohinia, Yalda; Ashrafi-Kooshk, Mohammad Reza; Ranjbar, Samira; Parvaneh, Shahram; Moieni-Arya, Maryam; Khodarahmi, Reza

    2013-01-01

    The studies on the interaction between human serum albumin (HSA) and drugs have been an interesting research field in life science, chemistry and clinical medicine. Osthole possesses a variety of pharmacological activities including anti-tumor, anti-inflammation, anti-seizure, anti-hyperlipidemic and anti-osteoporosis effects. The interaction of osthole with HSA and its binding site in HSA by spectroscopic methods is the subject of this work. By monitoring the intrinsic fluorescence of the single Trp 214 residue and performing site markers displacement measurements, the specific binding of osthole in the vicinity of Sudlow's site I of HSA has been clarified. The changes in the secondary structure of HSA after its complexation with ligand were studied with CD spectroscopy, which indicate that osthole induced only a slight decrease in the helix structural content of the protein. In addition, the mean distance between osthole and HSA fluorophores is estimated to be 4.96 nm using Föster's equation on the basis of the fluorescence energy transfer. Furthermore, the synchronous fluorescence spectra show that the microenvironment of the tryptophan residues does not have obvious changes. Osthole can quench the intrinsic fluorescence of HSA by dynamic quenching, and analysis of the thermodynamic parameters of binding showed that hydrophobic interactions play an important role in the stabilizing of the complex. Increase of protein surface hydrophobicity (PSH) was also observed upon the osthole binding. -- Highlights: • Hydrophobic interactions play an important role in osthole–HSA interaction. • Sudlow's I site is possible binding site of osthole. • Osthole inhibits esterase activity of HSA. • Osthole binding induces no gross protein structural changes

  16. Spectroscopic study of interaction between osthole and human serum albumin: Identification of possible binding site of the compound

    Energy Technology Data Exchange (ETDEWEB)

    Bijari, Nooshin [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Shokoohinia, Yalda [Department of Pharmacognosy and Biotechnology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Ashrafi-Kooshk, Mohammad Reza; Ranjbar, Samira; Parvaneh, Shahram [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Moieni-Arya, Maryam [Student Research Committee, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Khodarahmi, Reza, E-mail: rkhodarahmi@mbrc.ac.ir [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Department of Pharmacognosy and Biotechnology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)

    2013-11-15

    The studies on the interaction between human serum albumin (HSA) and drugs have been an interesting research field in life science, chemistry and clinical medicine. Osthole possesses a variety of pharmacological activities including anti-tumor, anti-inflammation, anti-seizure, anti-hyperlipidemic and anti-osteoporosis effects. The interaction of osthole with HSA and its binding site in HSA by spectroscopic methods is the subject of this work. By monitoring the intrinsic fluorescence of the single Trp{sub 214} residue and performing site markers displacement measurements, the specific binding of osthole in the vicinity of Sudlow's site I of HSA has been clarified. The changes in the secondary structure of HSA after its complexation with ligand were studied with CD spectroscopy, which indicate that osthole induced only a slight decrease in the helix structural content of the protein. In addition, the mean distance between osthole and HSA fluorophores is estimated to be 4.96 nm using Föster's equation on the basis of the fluorescence energy transfer. Furthermore, the synchronous fluorescence spectra show that the microenvironment of the tryptophan residues does not have obvious changes. Osthole can quench the intrinsic fluorescence of HSA by dynamic quenching, and analysis of the thermodynamic parameters of binding showed that hydrophobic interactions play an important role in the stabilizing of the complex. Increase of protein surface hydrophobicity (PSH) was also observed upon the osthole binding. -- Highlights: • Hydrophobic interactions play an important role in osthole–HSA interaction. • Sudlow's I site is possible binding site of osthole. • Osthole inhibits esterase activity of HSA. • Osthole binding induces no gross protein structural changes.

  17. Site investigation SFR. Water-rock interaction and mixing modelling in the SFR

    International Nuclear Information System (INIS)

    Gimeno, Maria J.; Auque, Luis F.; Gomez, Javier B.; Acero, Patricia

    2011-10-01

    the major geochemical processes controlling the behaviour of variables such as pH and Eh and, in general, all the parameters controlled by microbial or water-rock interaction processes. Thus, an integration of the mineralogical and microbiological data has also been performed. The other aim is to characterise the mixing processes that have affected the groundwaters over time. Thus, a statistical analysis has been performed with M3 in order to obtain a more quantitative approach to the mixing processes in the system, as well as to provide a mathematical basis to take into account all the variability of the system and to evaluate the reliability of the categorised groundwater types which are based on expert judgement (Nilsson et al. 2010). Therefore, this report should be considered as a supporting document to the final hydrogeochemical site description version 1.0 (Nilsson et al. 2011). Most of the main geochemical characters and trends observed in the SFR groundwaters are similar to those observed at Forsmark, especially if only groundwaters with marine contributions are compared. This applies to the carbonate, sulphate, silica and fluoride systems. No clear pH trend with depth has been found in these waters which may reflect the lateral heterogeneity of the groundwater system. The high and variable HCO 3 - values found in groundwaters with a marine signature seem to be the result of the biological activity during infiltration of marine waters through seabed sediments. Calcite equilibrium is the main pH controlling process, and its presence has been detected at all depths. Marine waters are the main source of sulphur, and neither heterogeneous reactions with sulphate minerals (undersaturated, in the case of gypsum or in equilibrium in the case of barite), nor sulphate reducing microbial activity have played an important role on the control of dissolved sulphate concentrations (conditioned, therefore, mainly by mixing). Dissolved silica and fluoride concentrations are

  18. Site investigation SFR. Water-rock interaction and mixing modelling in the SFR

    Energy Technology Data Exchange (ETDEWEB)

    Gimeno, Maria J.; Auque, Luis F.; Gomez, Javier B.; Acero, Patricia (University of Zaragoza (Spain))

    2011-10-15

    the major geochemical processes controlling the behaviour of variables such as pH and Eh and, in general, all the parameters controlled by microbial or water-rock interaction processes. Thus, an integration of the mineralogical and microbiological data has also been performed. The other aim is to characterise the mixing processes that have affected the groundwaters over time. Thus, a statistical analysis has been performed with M3 in order to obtain a more quantitative approach to the mixing processes in the system, as well as to provide a mathematical basis to take into account all the variability of the system and to evaluate the reliability of the categorised groundwater types which are based on expert judgement (Nilsson et al. 2010). Therefore, this report should be considered as a supporting document to the final hydrogeochemical site description version 1.0 (Nilsson et al. 2011). Most of the main geochemical characters and trends observed in the SFR groundwaters are similar to those observed at Forsmark, especially if only groundwaters with marine contributions are compared. This applies to the carbonate, sulphate, silica and fluoride systems. No clear pH trend with depth has been found in these waters which may reflect the lateral heterogeneity of the groundwater system. The high and variable HCO{sub 3}{sup -} values found in groundwaters with a marine signature seem to be the result of the biological activity during infiltration of marine waters through seabed sediments. Calcite equilibrium is the main pH controlling process, and its presence has been detected at all depths. Marine waters are the main source of sulphur, and neither heterogeneous reactions with sulphate minerals (undersaturated, in the case of gypsum or in equilibrium in the case of barite), nor sulphate reducing microbial activity have played an important role on the control of dissolved sulphate concentrations (conditioned, therefore, mainly by mixing). Dissolved silica and fluoride

  19. LCD panel characterization by measuring full Jones matrix of individual pixels using polarization-sensitive digital holographic microscopy.

    Science.gov (United States)

    Park, Jongchan; Yu, Hyeonseung; Park, Jung-Hoon; Park, YongKeun

    2014-10-06

    We present measurements of the full Jones matrix of individual pixels in a liquid-crystal display (LCD) panel. Employing a polarization-sensitive digital holographic microscopy based on Mach-Zehnder interferometry, the complex amplitudes of the light passing through individual LCD pixels are precisely measured with respect to orthogonal bases of polarization states, from which the full Jones matrix components of individual pixels are obtained. We also measure the changes in the Jones matrix of individual LCD pixels with respect to an applied bias. In addition, the complex optical responses of a LCD panel with respect to arbitrary polarization states of incident light were characterized from the measured Jones matrix.

  20. Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms

    Science.gov (United States)

    Tsai, Keng-Chang; Jian, Jhih-Wei; Yang, Ei-Wen; Hsu, Po-Chiang; Peng, Hung-Pin; Chen, Ching-Tai; Chen, Jun-Bo; Chang, Jeng-Yih; Hsu, Wen-Lian; Yang, An-Suei

    2012-01-01

    Non-covalent protein-carbohydrate interactions mediate molecular targeting in many biological processes. Prediction of non-covalent carbohydrate binding sites on protein surfaces not only provides insights into the functions of the query proteins; information on key carbohydrate-binding residues could suggest site-directed mutagenesis experiments, design therapeutics targeting carbohydrate-binding proteins, and provide guidance in engineering protein-carbohydrate interactions. In this work, we show that non-covalent carbohydrate binding sites on protein surfaces can be predicted with relatively high accuracy when the query protein structures are known. The prediction capabilities were based on a novel encoding scheme of the three-dimensional probability density maps describing the distributions of 36 non-covalent interacting atom types around protein surfaces. One machine learning model was trained for each of the 30 protein atom types. The machine learning algorithms predicted tentative carbohydrate binding sites on query proteins by recognizing the characteristic interacting atom distribution patterns specific for carbohydrate binding sites from known protein structures. The prediction results for all protein atom types were integrated into surface patches as tentative carbohydrate binding sites based on normalized prediction confidence level. The prediction capabilities of the predictors were benchmarked by a 10-fold cross validation on 497 non-redundant proteins with known carbohydrate binding sites. The predictors were further tested on an independent test set with 108 proteins. The residue-based Matthews correlation coefficient (MCC) for the independent test was 0.45, with prediction precision and sensitivity (or recall) of 0.45 and 0.49 respectively. In addition, 111 unbound carbohydrate-binding protein structures for which the structures were determined in the absence of the carbohydrate ligands were predicted with the trained predictors. The overall

  1. System of multifunctional Jones matrix tomography of phase anisotropy in diagnostics of endometriosis

    Science.gov (United States)

    Ushenko, V. O.; Koval, G. D.; Ushenko, Yu. O.; Pidkamin, L. Y.; Sidor, M. I.; Vanchuliak, O.; Motrich, A. V.; Gorsky, M. P.; Meglinskiy, I.

    2017-09-01

    The paper presents the results of Jones-matrix mapping of uterine wall histological sections with second-degree and third-degree endometriosis. The technique of experimental measurement of coordinate distributions of the modulus and phase values of Jones matrix elements is suggested. Within the statistical and cross-correlation approaches the modulus and phase maps of Jones matrix images of optically thin biological layers of polycrystalline films of plasma and cerebrospinal fluid are analyzed. A set of objective parameters (statistical and generalized correlation moments), which are the most sensitive to changes in the phase of anisotropy, associated with the features of polycrystalline structure of uterine wall histological sections with second-degree and third-degree endometriosis are determined.

  2. Observation of Two-Dimensional Localized Jones-Roberts Solitons in Bose-Einstein Condensates

    Science.gov (United States)

    Meyer, Nadine; Proud, Harry; Perea-Ortiz, Marisa; O'Neale, Charlotte; Baumert, Mathis; Holynski, Michael; Kronjäger, Jochen; Barontini, Giovanni; Bongs, Kai

    2017-10-01

    Jones-Roberts solitons are the only known class of stable dark solitonic solutions of the nonlinear Schrödinger equation in two and three dimensions. They feature a distinctive elongated elliptical shape that allows them to travel without change of form. By imprinting a triangular phase pattern, we experimentally generate two-dimensional Jones-Roberts solitons in a three-dimensional atomic Bose-Einstein condensate. We monitor their dynamics, observing that this kind of soliton is indeed not affected by dynamic (snaking) or thermodynamic instabilities, that instead make other classes of dark solitons unstable in dimensions higher than one. Our results confirm the prediction that Jones-Roberts solitons are stable solutions of the nonlinear Schrödinger equation and promote them for applications beyond matter wave physics, like energy and information transport in noisy and inhomogeneous environments.

  3. Lithosphere-biosphere interaction at a shallow-sea hydrothermal vent site; Hot Lake, Panarea, Italy

    Science.gov (United States)

    Huang, Chia-I.; Amann, Rudolf; Amend, Jan P.; Bach, Wolfgang; Brunner, Benjamin; Meyerdierks, Anke; Price, Roy E.; Schubotz, Florence; Summons, Roger; Wenzhöfer, Frank

    2010-05-01

    pore fluids geochemistry (anions, cations and stable isotope composition of water and sulfate) of depth profiles. DNA-fingerprinting techniques (DGGE, ARISA) revealed distinctly different bacterial 16S rRNA gene patterns for three separate sediment cores taken at Hot Lake. Intact polar lipid (IPL) biomarker analysis revealed a dominance of bacterial over archaeal biomass. The bacterial IPLs were mainly comprised of diether and diester phospholipids and ornithine lipids, indicative of viable thermophilic sulfate-reducing and acidophilic sulfide-oxidizing bacteria. Bacterial IPL abundance was highest in the sediment surface layer. Fluorescence in situ hybridization showed that with increasing depth and temperature, the abundance of archaea increased relative to that of bacteria. Comparative 16S rRNA gene analysis revealed a moderate diversity of bacteria, and a dominance of epsilonproteobacterial sequences. Cultured representatives of the detected epsilonproteobacterial classes are known to catalyze elemental sulfur reduction and oxidation reactions and to mediate the formation of iron-sulfides, including framboidal pyrite, which was found in sediment samples. We conclude that mixing between hydrothermal fluids and seawater leads to distinctly different temperature gradients and ecological niches in Hot Lake sediments. From the geochemical profiles and a preliminary characterization of the microbiological community, we found strong evidence of sulfur-related metabolism. Further investigation of certain clusters of bacteria and archaea as well as gene expression analysis will give us a deeper understanding of the interaction between geosphere and biosphere at this site in the future.

  4. Molecular interactions and thermal transport in ionic liquids with carbon nanomaterials.

    Science.gov (United States)

    França, João M P; Nieto de Castro, Carlos A; Pádua, Agílio A H

    2017-07-05

    We used molecular dynamics simulation to study the effect of suspended carbon nanomaterials, nanotubes and graphene sheets, on the thermal conductivity of ionic liquids, an issue related to understanding the properties of nanofluids. One important aspect that we developed is an atomistic model of the interactions between the organic ions and carbon nanomaterials, so we did not rely on existing force fields for small organic molecules or assume simple combining rules to describe the interactions at the liquid/material interface. Instead, we used quantum calculations with a density functional suitable for non-covalent interactions to parameterize an interaction model, including van der Waals terms and also atomic partial charges on the materials. We fitted a n-m interaction potential function with n values of 9 or 10 and m values between 5 and 8, so a 12-6 Lennard-Jones function would not fit the quantum calculations. For the atoms of ionic liquids and carbon nanomaterials interacting among themselves, we adopted existing models from the literature. We studied the imidazolium ionic liquids [C 4 C 1 im][SCN], [C 4 C 1 im][N(CN) 2 ], [C 4 C 1 im][C(CN) 3 ] and [C 4 C 1 im][(CF 3 SO 2 ) 2 N]. Attraction is stronger for cations (than for anions) above and below the π-system of the nanomaterials, whereas anions show stronger attraction for the hydrogenated edges. The ordering of ions around and inside (7,7) and (10,10) single-walled nanotubes, and near a stack of graphene sheets, was analysed in terms of density distribution functions. We verified that anions are found, as well as cations, in the first interfacial layer interacting with the materials, which is surprising given the interaction potential surfaces. The thermal conductivity of the ionic liquids and of composite systems containing one nanotube or one graphene stack in suspension was calculated using non-equilibrium molecular dynamics. Thermal conductivity was calculated along the axis of the nanotube and

  5. Generation of Earthquake Ground Motion Considering Local Site Effects and Soil-Structure Interaction Analysis of Ancient Structures

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jae Kwan; Lee, J. S.; Yang, T. S.; Cho, J. R.; R, H. [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1997-09-01

    In order to establish a correct correlation between them, mechanical characteristics of the ancient structures need to be investigated. Since sedimentary basins are preferred dwelling sites in ancient times, it is necessary to perform SSI analysis to derive correct correlation between the damage and ground motion intensity. Contents of Project are as follows: (1) Generation of stochastic earthquake ground motion considering source mechanism and site effects. (2) Analysis of seismic response of sedimentary basin. (3) Soil-structure interaction analysis of ancient structures (4) Investigation of dynamic response characteristics of ancient structure considering soil-structure interaction effects. A procedure is presented for generation of stochastic earthquake ground motion considering source mechanism and site effects. The simulation method proposed by Boore is used to generate the outcropping rock motion. The free field motion at the soil site is obtained by a convolution analysis. And for the study of wood structures, a nonlinear SDOF model is developed. The effects of soil-structure interaction on the behavior of the wood structures are found to be very minor. But the response can be significantly affected due to the intensity and frequency contents of the input motion. 13 refs., 6 tabs., 31 figs. (author)

  6. A strategy for interaction site prediction between phospho-binding modules and their partners identified from proteomic data.

    Science.gov (United States)

    Aucher, Willy; Becker, Emmanuelle; Ma, Emilie; Miron, Simona; Martel, Arnaud; Ochsenbein, Françoise; Marsolier-Kergoat, Marie-Claude; Guerois, Raphaël

    2010-12-01

    Small and large scale proteomic technologies are providing a wealth of potential interactions between proteins bearing phospho-recognition modules and their substrates. Resulting interaction maps reveal such a dense network of interactions that the functional dissection and understanding of these networks often require to break specific interactions while keeping the rest intact. Here, we developed a computational strategy, called STRIP, to predict the precise interaction site involved in an interaction with a phospho-recognition module. The method was validated by a two-hybrid screen carried out using the ForkHead Associated (FHA)1 domain of Rad53, a key protein of Saccharomyces cerevisiae DNA checkpoint, as a bait. In this screen we detected 11 partners, including Cdc7 and Cdc45, essential components of the DNA replication machinery. FHA domains are phospho-threonine binding modules and the threonines involved in both interactions could be predicted using the STRIP strategy. The threonines T484 and T189 in Cdc7 and Cdc45, respectively, were mutated and loss of binding could be monitored experimentally with the full-length proteins. The method was further tested for the analysis of 63 known Rad53 binding partners and provided several key insights regarding the threonines likely involved in these interactions. The STRIP method relies on a combination of conservation, phosphorylation likelihood, and binding specificity criteria and can be accessed via a web interface at http://biodev.extra.cea.fr/strip/.

  7. A Strategy for Interaction Site Prediction between Phospho-binding Modules and their Partners Identified from Proteomic Data*

    Science.gov (United States)

    Aucher, Willy; Becker, Emmanuelle; Ma, Emilie; Miron, Simona; Martel, Arnaud; Ochsenbein, Françoise; Marsolier-Kergoat, Marie-Claude; Guerois, Raphaël

    2010-01-01

    Small and large scale proteomic technologies are providing a wealth of potential interactions between proteins bearing phospho-recognition modules and their substrates. Resulting interaction maps reveal such a dense network of interactions that the functional dissection and understanding of these networks often require to break specific interactions while keeping the rest intact. Here, we developed a computational strategy, called STRIP, to predict the precise interaction site involved in an interaction with a phospho-recognition module. The method was validated by a two-hybrid screen carried out using the ForkHead Associated (FHA)1 domain of Rad53, a key protein of Saccharomyces cerevisiae DNA checkpoint, as a bait. In this screen we detected 11 partners, including Cdc7 and Cdc45, essential components of the DNA replication machinery. FHA domains are phospho-threonine binding modules and the threonines involved in both interactions could be predicted using the STRIP strategy. The threonines T484 and T189 in Cdc7 and Cdc45, respectively, were mutated and loss of binding could be monitored experimentally with the full-length proteins. The method was further tested for the analysis of 63 known Rad53 binding partners and provided several key insights regarding the threonines likely involved in these interactions. The STRIP method relies on a combination of conservation, phosphorylation likelihood, and binding specificity criteria and can be accessed via a web interface at http://biodev.extra.cea.fr/strip/. PMID:20733106

  8. Return to Play and Performance After Jones Fracture in National Basketball Association Athletes

    Science.gov (United States)

    Begly, John P.; Guss, Michael; Ramme, Austin J.; Karia, Raj; Meislin, Robert J.

    2015-01-01

    Background: Basketball players are at risk for foot injuries, including Jones fractures. It is unknown how this injury affects the future play and performance of athletes. Hypothesis: National Basketball Association (NBA) players who sustain Jones fractures of the base of the fifth metatarsal have high rates of return to play and do not experience a decrease in performance on return to competition when compared with preinjury and with control-matched peers. Study Design: Retrospective cohort study. Level of Evidence: Level 5. Methods: Data on 26 elite basketball players with Jones fractures over 19 NBA seasons (1994-1995 to 2012-2013) were obtained from injury reports, press releases, player profiles, and online public databases. Variables included age, body mass index (BMI), player position, experience, and surgical treatment. Individual season statistics pre- and postinjury were collected. Twenty-six controls were identified by matched player position, age, and performance statistics. Results: The mean age at the time of injury was 24.8 years, mean BMI was 24.7 kg/m2, and the mean experience prior to injury was 4.1 NBA seasons. Return to previous level of competition was achieved by 85% of athletes. There was no change in player efficiency rating (PER) when pre- and postinjury performance was compared. When compared with controls, no decline in PER measured performance was identified. Conclusion: The majority of NBA players sustaining a Jones fracture return to their preinjury level of competition. These elite athletes demonstrate no decrease in performance on their return to play. Clinical Relevance: Jones fractures are well-studied injuries in terms of etiology, diagnosis, and management. However, the effect of these injuries on future performance of athletes is unknown. Using the findings of our study, orthopaedic surgeons may be better prepared to counsel and educate elite athletes who sustain a Jones fracture. PMID:26627111

  9. Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site

    Science.gov (United States)

    Valley, Cary T.; Porter, Douglas F.; Qiu, Chen; Campbell, Zachary T.; Hall, Traci M. Tanaka; Wickens, Marvin

    2012-01-01

    mRNA control hinges on the specificity and affinity of proteins for their RNA binding sites. Regulatory proteins must bind their own sites and reject even closely related noncognate sites. In the PUF [Pumilio and fem-3 binding factor (FBF)] family of RNA binding proteins, individual proteins discriminate differences in the length and sequence of binding sites, allowing each PUF to bind a distinct battery of mRNAs. Here, we show that despite these differences, the pattern of RNA interactions is conserved among PUF proteins: the two ends of the PUF protein make critical contacts with the two ends of the RNA sites. Despite this conserved “two-handed” pattern of recognition, the RNA sequence is flexible. Among the binding sites of yeast Puf4p, RNA sequence dictates the pattern in which RNA bases are flipped away from the binding surface of the protein. Small differences in RNA sequence allow new modes of control, recruiting Puf5p in addition to Puf4p to a single site. This embedded information adds a new layer of biological meaning to the connections between RNA targets and PUF proteins. PMID:22467831

  10. A Hydrophobic Pocket in the Active Site of Glycolytic Aldolase Mediates Interactions with Wiskott-Aldrich Syndrome Protein

    Energy Technology Data Exchange (ETDEWEB)

    St-Jean,M.; Izard, T.; Sygusch, J.

    2007-01-01

    Aldolase plays essential catalytic roles in glycolysis and gluconeogenesis. However, aldolase is a highly abundant protein that is remarkably promiscuous in its interactions with other cellular proteins. In particular, aldolase binds to highly acidic amino acid sequences, including the C-terminus of the Wiskott-Aldrich syndrome protein, an actin nucleation promoting factor. Here we report the crystal structure of tetrameric rabbit muscle aldolase in complex with a C-terminal peptide of Wiskott-Aldrich syndrome protein. Aldolase recognizes a short, 4-residue DEWD motif (residues 498-501), which adopts a loose hairpin turn that folds about the central aromatic residue, enabling its tryptophan side chain to fit into a hydrophobic pocket in the active site of aldolase. The flanking acidic residues in this binding motif provide further interactions with conserved aldolase active site residues, Arg-42 and Arg-303, aligning their side chains and forming the sides of the hydrophobic pocket. The binding of Wiskott-Aldrich syndrome protein to aldolase precludes intramolecular interactions of its C-terminus with its active site, and is competitive with substrate as well as with binding by actin and cortactin. Finally, based on this structure a novel naphthol phosphate-based inhibitor of aldolase was identified and its structure in complex with aldolase demonstrated mimicry of the Wiskott-Aldrich syndrome protein-aldolase interaction. The data support a model whereby aldolase exists in distinct forms that regulate glycolysis or actin dynamics.

  11. Analysis of the interactions between GMF and Arp2/3 complex in two binding sites by molecular dynamics simulation.

    Science.gov (United States)

    Popinako, A; Antonov, M; Dibrova, D; Chemeris, A; Sokolova, O S

    2018-02-05

    The Arp2/3 complex plays a key role in nucleating actin filaments branching. The glia maturation factor (GMF) competes with activators for interacting with the Arp2/3 complex and initiates the debranching of actin filaments. In this study, we performed a comparative analysis of interactions between GMF and the Arp2/3 complex and identified new amino acid residues involved in GMF binding to the Arp2/3 complex at two separate sites, revealed by X-ray and single particle EM techniques. Using molecular dynamics simulations we demonstrated the quantitative and qualitative changes in hydrogen bonds upon binding with GMF. We identified the specific amino acid residues in GMF and Arp2/3 complex that stabilize the interactions and estimated the mean force profile for the GMF using umbrella sampling. Phylogenetic and structural analyses of the recently defined GMF binding site on the Arp3 subunit indicate a new mechanism for Arp2/3 complex inactivation that involves interactions between the Arp2/3 complex and GMF at two binding sites. Copyright © 2018 Elsevier Inc. All rights reserved.

  12. Regulation of xanthine oxidase activity by substrates at active sites via cooperative interactions between catalytic subunits: implication to drug pharmacokinetics.

    Science.gov (United States)

    Tai, L A; Hwang, K C

    2011-01-01

    Three xanthine oxidase substrates (i.e., xanthine, adenine, and 2-amino-4-hydroxypterin) show a "substrate inhibition" pattern (i.e., slower turnover rates at higher substrate concentrations), whereas another two substrates (i.e., xanthopterin and lumazine) show a "substrate activation" pattern (i.e., higher turnover rates at higher substrate concentrations). Binding of a 6-formylpterin at one of the two xanthine oxidase active sites slows down the turnover rate of xanthine at the adjacent active site from 17.0 s(-1) to 10.5 s(-1), and converts the V-[S] plot from "substrate inhibition" pattern to a classical Michaelis-Menten hyperbolic saturation pattern. In contrast, binding of xanthine at an active site accelerates the turnover rate of 6-formylpterin at the neighboring active site. The experimental results demonstrate that a substrate can regulate the activity of xanthine oxidase via binding at the active sites; or a xanthine oxidase catalytic subunit can simultaneously serve as a regulatory unit. Theoretical simulation based on the velocity equation derived from the extended Michaelis-Menten model shows that the substrate inhibition and the substrate activation behavior in the V-[S] plots could be obtained by introducing cooperative interactions between two catalytic subunits in homodimeric enzymes. The current work confirms that there exist very strong cooperative interactions between the two catalytic subunits of xanthine oxidase.

  13. Upper removable appliance or Jones Jig for distalizing first molars? A randomized clinical trial.

    Science.gov (United States)

    Paul, L D; O'Brien, K D; Mandall, N A

    2002-11-01

    To compare the effectiveness of two intra-oral methods of distalizing upper first permanent molars: an upper removable appliance (URA) and a Jones Jig. Twelve patients were randomly allocated to URA treatment and 11 patients to a Jones Jig. Upper study models were collected at the start of treatment and after 6 months of appliance wear. The amount of distal movement, tipping and rotation of the upper first permanent molars and mesial movement of the upper first permanent premolars was measured using a reflex metrograph. There were no statistically significant differences between the two treatment methods for any of the outcome measures (P Jig as a non-compliance appliance.

  14. Occurrence of pathotypes of Ascochyta pinodes (Jones in the Olsztyn district

    Directory of Open Access Journals (Sweden)

    Helena Furgał-Węgrzycka

    2013-12-01

    Full Text Available The causal agent of leaf and pods spot-pot of peas and field peas in the Olsztyn district was the fungus Ascochyta pinodes (Jones. Investigated isolates of A. pinoides different by macroscopic and microscopic features. From diseased leaves and pods of peas and field peas saprophytic fungi were also obtained. Among them Alternaria alternata, Cladosporium cladosporioides, Epicoccum purpurascens, Stemphylium botryosum, Sordaria fimicola and mycelia sterilia were dominant. In the study on the identification and distribution of pathotypes of A. pinodes (Jones six pathotypes were identified among which pathotypes 3 dominated. The identified pathotypes differed by macroscopic and microscopic features.

  15. Polarization-interference Jones-matrix mapping of biological crystal networks

    Science.gov (United States)

    Ushenko, O. G.; Dubolazov, O. V.; Pidkamin, L. Y.; Sidor, M. I.; Pavlyukovich, N.; Pavlyukovich, O.

    2018-01-01

    The paper consists of two parts. The first part presents short theoretical basics of the method of Jones-matrix mapping with the help of reference wave. It was provided experimentally measured coordinate distributions of modulus of Jones-matrix elements of polycrystalline film of bile. It was defined the values and ranges of changing of statistic moments, which characterize such distributions. The second part presents the data of statistic analysis of the distributions of matrix elements of polycrystalline film of urine of donors and patients with albuminuria. It was defined the objective criteria of differentiation of albuminuria.

  16. Algorithm for optimization of Viola–Jones object detection framework parameters

    Science.gov (United States)

    Egorov, A. D.

    2018-01-01

    The Viola-Jones algorithm is one of the most popular algorithms for objects recognition in an image. This research paper deals with the possibilities of parametric optimization of the Viola-Jones algorithm to achieve maximum efficiency of the algorithm in specific environmental conditions. It is shown that with the use of additional modifications it is possible to increase the speed of the algorithm in a particular image by 2-5 times with the loss of accuracy and completeness of work by not more than 3-5%.

  17. Structure, single-particle and many-particle coefficients of Lennard ...

    Indian Academy of Sciences (India)

    We investigate the effects of temperature and density on the single-particle and many-particle coefficients as well as on the structures of homogenous systems in which the particles are assumed to interact via a continuous soft sphere potential in the microcanonical ensemble. The pair distribution function and therefore the ...

  18. Better estimation of protein-DNA interaction parameters improve prediction of functional sites

    Directory of Open Access Journals (Sweden)

    O'Flanagan Ruadhan A

    2008-12-01

    Full Text Available Abstract Background Characterizing transcription factor binding motifs is a common bioinformatics task. For transcription factors with variable binding sites, we need to get many suboptimal binding sites in our training dataset to get accurate estimates of free energy penalties for deviating from the consensus DNA sequence. One procedure to do that involves a modified SELEX (Systematic Evolution of Ligands by Exponential Enrichment method designed to produce many such sequences. Results We analyzed low stringency SELEX data for E. coli Catabolic Activator Protein (CAP, and we show here that appropriate quantitative analysis improves our ability to predict in vitro affinity. To obtain large number of sequences required for this analysis we used a SELEX SAGE protocol developed by Roulet et al. The sequences obtained from here were subjected to bioinformatic analysis. The resulting bioinformatic model characterizes the sequence specificity of the protein more accurately than those sequence specificities predicted from previous analysis just by using a few known binding sites available in the literature. The consequences of this increase in accuracy for prediction of in vivo binding sites (and especially functional ones in the E. coli genome are also discussed. We measured the dissociation constants of several putative CAP binding sites by EMSA (Electrophoretic Mobility Shift Assay and compared the affinities to the bioinformatics scores provided by methods like the weight matrix method and QPMEME (Quadratic Programming Method of Energy Matrix Estimation trained on known binding sites as well as on the new sites from SELEX SAGE data. We also checked predicted genome sites for conservation in the related species S. typhimurium. We found that bioinformatics scores based on SELEX SAGE data does better in terms of prediction of physical binding energies as well as in detecting functional sites. Conclusion We think that training binding site detection

  19. Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Crichlow, G.; Lubetsky, J; Leng, L; Bucala, R; Lolis, E

    2009-01-01

    Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.

  20. Superfluid-insulator transition in a disordered two-dimensional quantum rotor model with random on-site interactions

    Science.gov (United States)

    An, Taeyang; Cha, Min-Chul

    2013-03-01

    We study the superfluid-insulator quantum phase transition in a disordered two-dimensional quantum rotor model with random on-site interactions in the presence of particle-hole symmetry. Via worm-algorithm Monte Carlo calculations of superfluid density and compressibility, we find the dynamical critical exponent z ~ 1 . 13 (2) and the correlation length critical exponent 1 / ν ~ 1 . 1 (1) . These exponents suggest that the insulating phase is a incompressible Mott glass rather than a Bose glass.

  1. Persistence of uranium groundwater plumes: Contrasting mechanisms at two DOE sites in the groundwater-river interaction zone

    Energy Technology Data Exchange (ETDEWEB)

    Zachara, John M.; Long, Philip E.; Bargar, John; Davis, James A.; Fox, Patricia M.; Fredrickson, Jim K.; Freshley, Mark D.; Konopka, Allan; Liu, Chongxuan; McKinley, James P.; Rockhold, Mark L.; Williams, Kenneth H.; Yabusaki, Steven B.

    2013-04-01

    We examine subsurface uranium (U) plumes at two U.S. Department of Energy sites that are located near large river systems and that are influenced by groundwater-river hydrologic interaction. Following surface excavation of contaminated materials, both sites were projected to naturally flush remnant uranium contamination to levels below regulatory limits (e.g., 30 µg/L or 0.126 µmol/L; U.S. EPA drinking water standard), with 10 years projected for the Hanford 300 Area (Columbia River) and 12 years for the Rifle site (Colorado River). The rate of observed uranium decrease was much lower than expected at both sites. While uncertainty remains, a comparison of current understanding suggests that the two sites have common, but also different mechanisms controlling plume persistence. At the Hanford 300 A, the persistent source is adsorbed U(VI) in the vadose zone that is released to the aquifer during spring water table excursions. The release of U(VI) from the vadose zone and its transport within the oxic, coarse-textured aquifer sediments is dominated by kinetically-limited surface complexation. Modeling implies that annual plume discharge volumes to the Columbia River are small (< one pore volume). At the Rifle site, slow oxidation of naturally reduced, contaminant U(IV) in the saturated zone and a continuous influx of U(VI) from natural, up-gradient sources influences plume persistence. Rate-limited mass transfer and surface complexation also control U(VI) migration velocity in the sub-oxic Rifle groundwater. Flux of U(VI) from the vadose zone at the Rifle site may be locally important, but it is not the dominant process that sustains the plume. A wide range in microbiologic functional diversity exists at both sites. Strains of Geobacter and other metal reducing bacteria are present at low natural abundance that are capable of enzymatic U(VI) reduction in localized zones of accumulated detrital organic carbon or after organic carbon amendment. Major differences

  2. Developing interactive course Web sites for distance education and characteristics of students enrolled in distance learning courses.

    Science.gov (United States)

    Diwakar, Vikas; Ertmer, Peggy A; Nour, Abdelfattah Y M

    2003-01-01

    The ubiquity of the Internet has made disseminating information across geographical boundaries a relatively easy task. Apart from text-based materials, the Internet provides an easy means to transmit images, sound, video, and other multimedia content to a global audience, making it an ideal medium for establishing distance learning programs. Two Internet-based distance learning courses were developed to teach animal physiology to veterinary technicians in the School of Veterinary Medicine at Purdue University. These distance learning course sites are designed to take advantage of multimedia technology to enhance students' learning experiences. Multimedia has been used in education to make the learning process more engaging and interactive. The two course sites have a number of multimedia features that complement the textual subject matter. This article describes the features of the course Web sites and summarizes our experiences in designing and conducting Web-based physiology courses to distance learners. In addition, we describe the characteristics of our distance learning students.

  3. Class II malocclusion treatment effects with Jones Jig and Distal Jet followed by fixed appliances.

    Science.gov (United States)

    Vilanova, Lorena; Henriques, José Fernando Castanha; Janson, Guilherme; Patel, Mayara Paim; Reis, Rachelle Simões; Aliaga-Del Castillo, Aron

    2018-01-01

    To compare the skeletal, dentoalveolar, and soft tissue changes in Class II malocclusion patients treated with Jones Jig and Distal Jet distalizers followed by fixed appliances. The experimental groups comprised 45 Class II malocclusion subjects divided into two groups. Group 1 consisted of 25 patients treated with the Jones Jig, and group 2 consisted of 20 patients treated with the Distal Jet. Group 3 comprised 19 untreated Class II subjects. Cephalograms were analyzed before and after orthodontic treatment. For intergroup comparisons, one-way analysis of variance and post hoc Tukey tests were performed. During treatment, the experimental groups exhibited significant increases in occlusal plane inclination and maxillary second molar mesial tipping. Additionally, the molar relationship improved and overjet decreased significantly in the experimental groups. The Jones Jig group showed greater mandibular incisor proclination and greater overbite reduction than the control group. No significant intergroup differences in nasolabial angle changes were found. Treatment protocols using the Jones Jig and Distal Jet followed by fixed appliances were effective in correcting Class II malocclusion by means of dentoalveolar changes without significant skeletal and soft tissue changes. The experimental groups showed occlusal plane clockwise rotation and greater mesial tipping of maxillary second molars when compared to the untreated group.

  4. Flexible equation of state for a hard sphere and Lennard–Jones fluid ...

    Indian Academy of Sciences (India)

    Equation of state; Lennard–Jones potential; hard-sphere potential; liquid mixture; computer simulation. ... deviation than Barker–Henderson BH2 for LJ fluids, and results are much closer to molecular dynamics (MD) simulations than expectations and reproduce the existing simulation data and present EoS for LJ potential, ...

  5. "Armastuse retsepti" tippkokk Zeta Jones ei oska muna keeta / Triin Tael

    Index Scriptorium Estoniae

    Tael, Triin

    2007-01-01

    Scott Hicksi romantiline komöödiafilm "Armastuse retsept" ("No Reservations"), mille peaosas Walesist pärit näitlejanna Catherine Zeta Jones. Näitlejanna muljeid oma rolliks ettevalmistustest, mille hulka käis ka praktika pärisrestoranis

  6. The Game TV Plays: Or, Why an English Teacher Came to Hate Barnaby Jones.

    Science.gov (United States)

    Shaw, Patrick W.

    The message of current popular television shows in which the hero is, or appears to be, a dumb clod (e.g., Archie Bunker, Fred Sanford, Columbo, and Barnaby Jones), apparently is that corruption may be equated with articulation, wealth, and education, while virtue may be equated with poverty and, often, illiteracy. Unfortunately, the effect of…

  7. Käsitsi tegemise võlu / David Jones ; intervjueerinud Kai Lobjakas

    Index Scriptorium Estoniae

    Jones, David, 1953-

    2010-01-01

    10. Kohila keraamikasümpoosionil osalenud briti keraamik ja teoreetik David Jones endast, rakutehnikast, huvist põletamisega seonduvate teemade vastu, Kohila sümpoosioni raames tehtust, keraamika õpetamisest Inglismaal, käsitöö ja keraamika positsioonist praegu ja tulevikus jm.

  8. Malaria and the Decline of Ancient Greece: Revisiting the Jones Hypothesis in an Era of Interdisciplinarity

    Science.gov (United States)

    Baron, Christopher; Hamlin, Christopher

    2015-01-01

    Between 1906 and 1909 the biologist Ronald Ross and the classicist W.H.S. Jones pioneered interdisciplinary research in biology and history in advancing the claim that malaria had been crucial in the decline of golden-age Greece (fourth century BCE). The idea had originated with Ross, winner of the Nobel Prize for demonstrating the importance of…

  9. Machine News and Volatility: The Dow Jones Industrial Average and the TRNA Sentiment Series

    NARCIS (Netherlands)

    D.E. Allen (David); A.K. Singh (Abhay)

    2014-01-01

    markdownabstract__Abstract__ This paper features an analysis of the relationship between the volatility of the Dow Jones Industrial Average (DJIA) Index and a sentiment news series using daily data obtained from the Thomson Reuters News Analytics (TRNA) provided by SIRCA (The Securities Industry

  10. Enhancing Undergraduates' Capabilities through Team-Based Competitions: The Edward Jones Challenge

    Science.gov (United States)

    Umble, Elisabeth J.; Umble, Michael; Artz, Kendall

    2008-01-01

    The Edward Jones Company recently initiated financial sponsorship of team-based competitions in six undergraduate business core classes at Baylor University. The challenges were chosen to take place in an introductory freshman business class, Managerial Accounting, Principles of Marketing, Corporate Finance, Operations Management, and Strategic…

  11. HIV-1 Nef interaction influences the ATP-binding site of the Src-family kinase, Hck

    Directory of Open Access Journals (Sweden)

    Pene-Dumitrescu Teodora

    2012-03-01

    Full Text Available Abstract Background Nef is an HIV-1 accessory protein essential for viral replication and AIDS progression. Nef interacts with a multitude of host cell signaling partners, including members of the Src kinase family. Nef preferentially activates Hck, a Src-family kinase (SFK strongly expressed in macrophages and other HIV target cells, by binding to its regulatory SH3 domain. Recently, we identified a series of kinase inhibitors that preferentially inhibit Hck in the presence of Nef. These compounds also block Nef-dependent HIV replication, validating the Nef-SFK signaling pathway as an antiretroviral drug target. Our findings also suggested that by binding to the Hck SH3 domain, Nef indirectly affects the conformation of the kinase active site to favor inhibitor association. Results To test this hypothesis, we engineered a "gatekeeper" mutant of Hck with enhanced sensitivity to the pyrazolopyrimidine tyrosine kinase inhibitor, NaPP1. We also modified the RT loop of the Hck SH3 domain to enhance interaction of the kinase with Nef. This modification stabilized Nef:Hck interaction in solution-based kinase assays, as a way to mimic the more stable association that likely occurs at cellular membranes. Introduction of the modified RT loop rendered Hck remarkably more sensitive to activation by Nef, and led to a significant decrease in the Km for ATP as well as enhanced inhibitor potency. Conclusions These observations suggest that stable interaction with Nef may induce Src-family kinase active site conformations amenable to selective inhibitor targeting.

  12. Soil structure interaction analysis for the Hanford Site 241-SY-101 double-shell waste storage tanks

    International Nuclear Information System (INIS)

    Giller, R.A.; Weiner, E.O.

    1991-09-01

    The 241-SY-101 tank is a double-shell waste storage tank buried in the 241-SY tank farm in the 200 West Area of the Hanford Site. This analysis addresses the effects of seismic soil-structure interaction on the tank structure and includes a parametric soil-structure interaction study addressing three configurations: two-dimensional soil structure, a two-dimensional structure-soil-structure, and a three-dimensional soil-structure interaction. This study was designed to determine an optimal method for addressing seismic-soil effects on underground storage tanks. The computer programs calculate seismic-soil pressures on the double-shell tank walls and and seismic acceleration response spectra in the tank. The results of this soil-structure interaction parametric study as produced by the computer programs are given in terms of seismic soil pressures and response spectra. The conclusions of this soil-structure interaction evaluation are that dynamically calculated soil pressures in the 241-SY-101 tank are significantly reduce from those using standard hand calculation methods and that seismic evaluation of underground double-shell waste storage tanks must consider soil-structure interaction effects in order to predict conservative structural response. Appendixes supporting this study are available in Volume 2 of this report

  13. Persistence of uranium groundwater plumes: Contrasting mechanisms at two DOE sites in the groundwater-river interaction zone

    Science.gov (United States)

    Zachara, John M.; Long, Philip E.; Bargar, John; Davis, James A.; Fox, Patricia; Fredrickson, Jim K.; Freshley, Mark D.; Konopka, Allan E.; Liu, Chongxuan; McKinley, James P.; Rockhold, Mark L.; Williams, Kenneth H.; Yabusaki, Steve B.

    2013-04-01

    We examine subsurface uranium (U) plumes at two U.S. Department of Energy sites that are located near large river systems and are influenced by groundwater-river hydrologic interaction. Following surface excavation of contaminated materials, both sites were projected to naturally flush remnant uranium contamination to levels below regulatory limits (e.g., 30 μg/L or 0.126 μmol/L; U.S. EPA drinking water standard), with 10 years projected for the Hanford 300 Area (Columbia River) and 12 years for the Rifle site (Colorado River). The rate of observed uranium decrease was much lower than expected at both sites. While uncertainty remains, a comparison of current understanding suggests that the two sites have common, but also different mechanisms controlling plume persistence. At the Hanford 300 A, the persistent source is adsorbed U(VI) in the vadose zone that is released to the aquifer during spring water table excursions. The release of U(VI) from the vadose zone and its transport within the oxic, coarse-textured aquifer sediments is dominated by kinetically-limited surface complexation. Modeling implies that annual plume discharge volumes to the Columbia River are small (oxidation of naturally reduced, contaminant U(IV) in the saturated zone and a continuous influx of U(VI) from natural, up-gradient sources influence plume persistence. Rate-limited mass transfer and surface complexation also control U(VI) migration velocity in the sub-oxic Rifle groundwater. Flux of U(VI) from the vadose zone at the Rifle site may be locally important, but it is not the dominant process that sustains the plume. A wide range in microbiologic functional diversity exists at both sites. Strains of Geobacter and other metal reducing bacteria are present at low natural abundance that are capable of enzymatic U(VI) reduction in localized zones of accumulated detrital organic carbon or after organic carbon amendment. Major differences between the sites include the geochemical nature of

  14. The interactive on-site inspection system: An information management system to support arms control inspections

    Energy Technology Data Exchange (ETDEWEB)

    DeLand, S.M.; Widney, T.W.; Horak, K.E.; Caudell, R.B.; Grose, E.M.

    1996-12-01

    The increasing use of on-site inspection (OSI) to meet the nation`s obligations with recently signed treaties requires the nation to manage a variety of inspection requirements. This document describes a prototype automated system to assist in the preparation and management of these inspections.

  15. Protein-protein interaction site prediction in Homo sapiens and E. coli using an interaction-affinity based membership function in fuzzy SVM.

    Science.gov (United States)

    Sriwastava, Brijesh Kumar; Basu, Subhadip; Maulik, Ujjwal

    2015-10-01

    Protein-protein interaction (PPI) site prediction aids to ascertain the interface residues that participate in interaction processes. Fuzzy support vector machine (F-SVM) is proposed as an effective method to solve this problem, and we have shown that the performance of the classical SVM can be enhanced with the help of an interaction-affinity based fuzzy membership function. The performances of both SVM and F-SVM on the PPI databases of the Homo sapiens and E. coli organisms are evaluated and estimated the statistical significance of the developed method over classical SVM and other fuzzy membership-based SVM methods available in the literature. Our membership function uses the residue-level interaction affinity scores for each pair of positive and negative sequence fragments. The average AUC scores in the 10-fold cross-validation experiments are measured as 79.94% and 80.48% for the Homo sapiens and E. coli organisms respectively. On the independent test datasets, AUC scores are obtained as 76.59% and 80.17% respectively for the two organisms. In almost all cases, the developed F-SVM method improves the performances obtained by the corresponding classical SVM and the other classifiers, available in the literature.

  16. Protein–Protein interaction site prediction in Homo sapiens and E ...

    Indian Academy of Sciences (India)

    2015-09-28

    Sep 28, 2015 ... point does not have the same significance to the decision surface. Consequently to solve this problem, .... there may exist some non-central interacting residues. This consideration is extremely important ..... S and Wang JT 2011a Computational intelligence and pattern analysis in biology informatics, p 20.

  17. DIBS: a repository of disordered binding sites mediating interactions with ordered proteins.

    Science.gov (United States)

    Schad, Eva; Fichó, Erzsébet; Pancsa, Rita; Simon, István; Dosztányi, Zsuzsanna; Mészáros, Bálint

    2018-02-01

    Intrinsically Disordered Proteins (IDPs) mediate crucial protein-protein interactions, most notably in signaling and regulation. As their importance is increasingly recognized, the detailed analyses of specific IDP interactions opened up new opportunities for therapeutic targeting. Yet, large scale information about IDP-mediated interactions in structural and functional details are lacking, hindering the understanding of the mechanisms underlying this distinct binding mode. Here, we present DIBS, the first comprehensive, curated collection of complexes between IDPs and ordered proteins. DIBS not only describes by far the highest number of cases, it also provides the dissociation constants of their interactions, as well as the description of potential post-translational modifications modulating the binding strength and linear motifs involved in the binding. Together with the wide range of structural and functional annotations, DIBS will provide the cornerstone for structural and functional studies of IDP complexes. DIBS is freely accessible at http://dibs.enzim.ttk.mta.hu/. The DIBS application is hosted by Apache web server and was implemented in PHP. To enrich querying features and to enhance backend performance a MySQL database was also created. dosztanyi@caesar.elte.hu or bmeszaros@caesar.elte.hu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

  18. Site characterization, evaluation and acceptance: Swiss policy and approaches for interaction with the public

    International Nuclear Information System (INIS)

    Issler, H.

    1993-01-01

    Despite the positive outcome of studies carried out by national and international organizations and experts, large sectors of the Swiss population still consider demonstrating the long-term safety of radioactive waste disposal to be an unsolved problem. This situation can be explained by the general perception of safety problems, which tends to be dominated by feelings of fear and anxiety - particularly in the case of radioactive waste. Additional problems of a sociological and political nature arise as part of the decision-making process relating to site characterization, site selection and construction and operation of waste repositories. In the following, the legal, organizational, political and technical boundary conditions pertaining to disposal of radioactive waste in Switzerland will be discussed, together with their implications for public relations programmes. Experience gained in communicating with the public will also be presented

  19. Interaction of mining activities and aquatic environment: A review from Greek mine sites.

    Science.gov (United States)

    Vasileiou, Eleni; Kallioras, Andreas

    2016-04-01

    In Greece a significant amount of mineral and ore deposits have been recorded accompanied by large industrial interest and a long mining history. Today many active and/or abandoned mine sites are scattered within the country; while mining activities take place in different sites for exploiting various deposits (clay, limestone, slate, gypsum, kaolin, mixed sulphide ores (lead, zinc, olivine, pozzolan, quartz lignite, nickel, magnesite, aluminum, bauxite, gold, marbles etc). The most prominent recent ones are: (i) the lignite exploitation that is extended in the area of Ptolemais (Western Macedonia) and Megalopolis (Central Peloponnese); and (ii) the major bauxite deposits located in central Greece within the Parnassos-Ghiona geotectonic zone and on Euboea Island. In the latter area, significant ores of magnesite were exploited and mixed sulphide ores. Centuries of intensive mining exploitation and metallurgical treatment of lead-silver deposits in Greece, have also resulted in significant abandoned sites, such as the one in Lavrion. Mining activities in Lavrio, were initiated in ancient times and continued until the 1980s, resulting in the production of significant waste stockpiles deposited in the area, crucial for the local water resources. Ιn many mining sites, environmental pressures are also recorded after the mine closure to the aquatic environment, as the surface waters flow through waste dump areas and contaminated soils. This paper aims to the geospatial visualization of the mining activities in Greece, in connection to their negative (surface- and/or ground-water pollution; overpumping due to extensive dewatering practices) or positive (enhanced groundwater recharge; pit lakes, improvement of water budget in the catchment scale) impacts on local water resources.

  20. Puromycin-rRNA interaction sites at the peptidyl transferase center

    DEFF Research Database (Denmark)

    Rodriguez-Fonseca, Christina; Phan, Hien; Long, Katherine Sarah

    2000-01-01

    of puromycin. They include A2439, G2505, and G2553 for E. coli, and G2058, A2503, G2505, and G2553 for Hf. gibbonsii (using the E. coli numbering system). Reproducible enhanced reactivities were also observed at A508 and A1579 within domains I and III, respectively, of E. coli 23S rRNA. In further experiments......The binding site of puromycin was probed chemically in the peptidyl-transferase center of ribosomes from Escherichia coli and of puromycin-hypersensitive ribosomes from the archaeon Haloferax gibbonsii. Several nucleotides of the 23S rRNAs showed altered chemical reactivities in the presence......, puromycin was shown to produce a major reduction in the UV-induced crosslinking of deacylated-(2N3A76)tRNA to U2506 within the P' site of E. coli ribosomes. Moreover, it strongly stimulated the putative UV-induced crosslink between a streptogramin B drug and m2A2503/psi2504 at an adjacent site in E. coli 23...

  1. p15PAF is an intrinsically disordered protein with nonrandom structural preferences at sites of interaction with other proteins.

    Science.gov (United States)

    De Biasio, Alfredo; Ibáñez de Opakua, Alain; Cordeiro, Tiago N; Villate, Maider; Merino, Nekane; Sibille, Nathalie; Lelli, Moreno; Diercks, Tammo; Bernadó, Pau; Blanco, Francisco J

    2014-02-18

    We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15(PAF), showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions. p15(PAF) is a 12 kDa nuclear protein that acts as a regulator of DNA repair during DNA replication. The p15(PAF) gene is overexpressed in several types of human cancer. The nearly complete NMR backbone assignment of p15(PAF) allowed us to measure 86 N-H(N) residual dipolar couplings. Our residual dipolar coupling analysis reveals nonrandom conformational preferences in distinct regions, including the proliferating-cell-nuclear-antigen-interacting protein motif (PIP-box) and the KEN-box (recognized by the ubiquitin ligase that targets p15(PAF) for degradation). In accordance with these findings, analysis of the (15)N R2 relaxation rates shows a relatively reduced mobility for the residues in these regions. The agreement between the experimental small angle x-ray scattering curve of p15(PAF) and that computed from a statistical coil ensemble corrected for the presence of local secondary structural elements further validates our structural model for p15(PAF). The coincidence of these transiently structured regions with protein-protein interaction and posttranslational modification sites suggests a possible role for these structures as molecular recognition elements for p15(PAF). Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  2. High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site

    Science.gov (United States)

    Chavan, Tanmay S.; Jang, Hyunbum; Khavrutskii, Lyuba; Abraham, Sherwin J.; Banerjee, Avik; Freed, Benjamin C.; Johannessen, Liv; Tarasov, Sergey G.; Gaponenko, Vadim; Nussinov, Ruth; Tarasova, Nadya I.

    2015-01-01

    Ras proteins are small GTPases that act as signal transducers between cell surface receptors and several intracellular signaling cascades. They contain highly homologous catalytic domains and flexible C-terminal hypervariable regions (HVRs) that differ across Ras isoforms. KRAS is among the most frequently mutated oncogenes in human tumors. Surprisingly, we found that the C-terminal HVR of K-Ras4B, thought to minimally impact the catalytic domain, directly interacts with the active site of the protein. The interaction is almost 100-fold tighter with the GDP-bound than the GTP-bound protein. HVR binding interferes with Ras-Raf interaction, modulates binding to phospholipids, and slightly slows down nucleotide exchange. The data indicate that contrary to previously suggested models of K-Ras4B signaling, HVR plays essential roles in regulation of signaling. High affinity binding of short peptide analogs of HVR to K-Ras active site suggests that targeting this surface with inhibitory synthetic molecules for the therapy of KRAS-dependent tumors is feasible. PMID:26682817

  3. Generalized theory on the mechanism of site-specific DNA-protein interactions

    Science.gov (United States)

    Niranjani, G.; Murugan, R.

    2016-05-01

    We develop a generalized theoretical framework on the binding of transcription factor proteins (TFs) with specific sites on DNA that takes into account the interplay of various factors regarding overall electrostatic potential at the DNA-protein interface, occurrence of kinetic traps along the DNA sequence, presence of other roadblock protein molecules along DNA and crowded environment, conformational fluctuations in the DNA binding domains (DBDs) of TFs, and the conformational state of the DNA. Starting from a Smolochowski type theoretical framework on site-specific binding of TFs we logically build our model by adding the effects of these factors one by one. Our generalized two-step model suggests that the electrostatic attractive forces present inbetween the positively charged DBDs of TFs and the negatively charged phosphate backbone of DNA, along with the counteracting shielding effects of solvent ions, is the core factor that creates a fluidic type environment at the DNA-protein interface. This in turn facilitates various one-dimensional diffusion (1Dd) processes such as sliding, hopping and intersegmental transfers. These facilitating processes as well as flipping dynamics of conformational states of DBDs of TFs between stationary and mobile states can enhance the 1Dd coefficient on a par with three-dimensional diffusion (3Dd). The random coil conformation of DNA also plays critical roles in enhancing the site-specific association rate. The extent of enhancement over the 3Dd controlled rate seems to be directly proportional to the maximum possible 1Dd length. We show that the overall site-specific binding rate scales with the length of DNA in an asymptotic way. For relaxed DNA, the specific binding rate will be independent of the length of DNA as length increases towards infinity. For condensed DNA as in in vivo conditions, the specific binding rate depends on the length of DNA in a turnover way with a maximum. This maximum rate seems to scale with the

  4. Site response - a critical problem in soil-structure interaction analyses for embedded structures

    International Nuclear Information System (INIS)

    Seed, H.B.; Lysmer, J.

    1986-01-01

    Soil-structure interaction analyses for embedded structures must necessarily be based on a knowledge of the manner in which the soil would behave in the absence of any structure - that is on a knowledge and understanding of the spatial distribution of motions in the ground within the depth of embedment of the structure. The nature of these spatial variations is discussed and illustrated by examples of recorded motions. It is shown that both the amplitude of peak acceleration and the form of the acceleration response spectrum for earthquake motions will necessarily vary with depth and failure to take these variations into account may introduce an unwarranted degree of conservatism into the soil-structure interaction analysis procedure

  5. Reserpine: interactions with batrachotoxin and brevetoxin sites on voltage-dependent sodium channels.

    Science.gov (United States)

    Flowers, Andrew; Onwueme, Kenolisa; Creveling, Cyrus R; Daly, John W

    2002-02-01

    Reserpine inhibited batrachotoxin-elicited sodium influx in guinea pig brain synaptoneurosomes with an IC50 of about 1 microM. In the presence of brevetoxin the IC50 increased to about 80 microM. Reserpine inhibited binding of batrachotoxinin-A [3H]benzoate ([3H]BTX-B) binding in a complex manner causing a partial inhibition from 0.001 to 0.08 microM, then a rebound stimulation from 0.1 to 0.8 microM, followed by complete inhibition by 80 microM. The stimulation was prevented by the presence of brevetoxin; reserpine then smoothly inhibited binding with an IC50 of about 1 microM. Reserpine at 1 microM slightly reduced the off-rate of [3H]BTX-B binding measured in the presence of veratridine, while at a concentration of 50 microM it enhanced the off-rate, presumably by an allosteric mechanism. Reserpine at 0.3-10 microM elicited a partial inhibition of the binding of [3H]brevetoxin-3. The local anesthetic dibucaine had effects similar to reserpine: It partially inhibited binding of [3H]brevetoxin. The presence of brevetoxin reduced the potency of dibucaine as an inhibitor of batrachotoxin-elicited sodium influx from an IC50 of about 2 microM to an IC50 of about 50 microM. The results suggest that reserpine binds at both a local anesthetic site to cause allosteric inhibition of batrachotoxin-binding and action, but that it also binds to another site causing, like brevetoxin, an enhancement of batrachotoxin-binding and action. Local anesthetics also may bind to the brevetoxin site.

  6. Solvent water interactions within the active site of the membrane type I matrix metalloproteinase.

    Science.gov (United States)

    Decaneto, Elena; Vasilevskaya, Tatiana; Kutin, Yuri; Ogata, Hideaki; Grossman, Moran; Sagi, Irit; Havenith, Martina; Lubitz, Wolfgang; Thiel, Walter; Cox, Nicholas

    2017-11-22

    Matrix metalloproteinases (MMP) are an important family of proteases which catalyze the degradation of extracellular matrix components. While the mechanism of peptide cleavage is well established, the process of enzyme regeneration, which represents the rate limiting step of the catalytic cycle, remains unresolved. This step involves the loss of the newly formed N-terminus (amine) and C-terminus (carboxylate) protein fragments from the site of catalysis coupled with the inclusion of one or more solvent waters. Here we report a novel crystal structure of membrane type I MMP (MT1-MMP or MMP-14), which includes a small peptide bound at the catalytic Zn site via its C-terminus. This structure models the initial product state formed immediately after peptide cleavage but before the final proton transfer to the bound amine; the amine is not present in our system and as such proton transfer cannot occur. Modeling of the protein, including earlier structural data of Bertini and coworkers [I. Bertini, et al., Angew. Chem., Int. Ed., 2006, 45, 7952-7955], suggests that the C-terminus of the peptide is positioned to form an H-bond network to the amine site, which is mediated by a single oxygen of the functionally important Glu240 residue, facilitating efficient proton transfer. Additional quantum chemical calculations complemented with magneto-optical and magnetic resonance spectroscopies clarify the role of two additional, non-catalytic first coordination sphere waters identified in the crystal structure. One of these auxiliary waters acts to stabilize key intermediates of the reaction, while the second is proposed to facilitate C-fragment release, triggered by protonation of the amine. Together these results complete the enzymatic cycle of MMPs and provide new design criteria for inhibitors with improved efficacy.

  7. Mathematical description of drug-target interactions: application to biologics that bind to targets with two binding sites.

    Science.gov (United States)

    Gibiansky, Leonid; Gibiansky, Ekaterina

    2018-02-01

    The emerging discipline of mathematical pharmacology occupies the space between advanced pharmacometrics and systems biology. A characteristic feature of the approach is application of advance mathematical methods to study the behavior of biological systems as described by mathematical (most often differential) equations. One of the early application of mathematical pharmacology (that was not called this name at the time) was formulation and investigation of the target-mediated drug disposition (TMDD) model and its approximations. The model was shown to be remarkably successful, not only in describing the observed data for drug-target interactions, but also in advancing the qualitative and quantitative understanding of those interactions and their role in pharmacokinetic and pharmacodynamic properties of biologics. The TMDD model in its original formulation describes the interaction of the drug that has one binding site with the target that also has only one binding site. Following the framework developed earlier for drugs with one-to-one binding, this work aims to describe a rigorous approach for working with similar systems and to apply it to drugs that bind to targets with two binding sites. The quasi-steady-state, quasi-equilibrium, irreversible binding, and Michaelis-Menten approximations of the model are also derived. These equations can be used, in particular, to predict concentrations of the partially bound target (RC). This could be clinically important if RC remains active and has slow internalization rate. In this case, introduction of the drug aimed to suppress target activity may lead to the opposite effect due to RC accumulation.

  8. Cooperative interaction between phosphorylation sites on PERIOD maintains circadian period in Drosophila.

    Directory of Open Access Journals (Sweden)

    David S Garbe

    Full Text Available Circadian rhythms in Drosophila rely on cyclic regulation of the period (per and timeless (tim clock genes. The molecular cycle requires rhythmic phosphorylation of PER and TIM proteins, which is mediated by several kinases and phosphatases such as Protein Phosphatase-2A (PP2A and Protein Phosphatase-1 (PP1. Here, we used mass spectrometry to identify 35 "phospho-occupied" serine/threonine residues within PER, 24 of which are specifically regulated by PP1/PP2A. We found that cell culture assays were not good predictors of protein function in flies and so we generated per transgenes carrying phosphorylation site mutations and tested for rescue of the per(01 arrhythmic phenotype. Surprisingly, most transgenes restore wild type rhythms despite carrying mutations in several phosphorylation sites. One particular transgene, in which T610 and S613 are mutated to alanine, restores daily rhythmicity, but dramatically lengthens the period to ~ 30 hrs. Interestingly, the single S613A mutation extends the period by 2-3 hours, while the single T610A mutation has a minimal effect, suggesting these phospho-residues cooperate to control period length. Conservation of S613 from flies to humans suggests that it possesses a critical clock function, and mutational analysis of residues surrounding T610/S613 implicates the entire region in determining circadian period. Biochemical and immunohistochemical data indicate defects in overall phosphorylation and altered timely degradation of PER carrying the double or single S613A mutation(s. The PER-T610A/S613A mutant also alters CLK phosphorylation and CLK-mediated output. Lastly, we show that a mutation at a previously identified site, S596, is largely epistatic to S613A, suggesting that S613 negatively regulates phosphorylation at S596. Together these data establish functional significance for a new domain of PER, demonstrate that cooperativity between phosphorylation sites maintains PER function, and support a model

  9. Contribution of factor VIII light-chain residues 2007-2016 to an activated protein C-interactive site.

    Science.gov (United States)

    Takeyama, Masahiro; Wakabayashi, Hironao; Fay, Philip J

    2013-02-01

    Although factor (F) VIIIa is inactivated by activated protein C (APC) through cleavages in the FVIII heavy chain-derived A1 (Arg(336)) and A2 subunits (Arg(562), the FVIII light chain (LC) contributes to catalysis by binding the enzyme. ELISA-based binding assays showed that FVIII and FVIII LC bound to immobilised active site-modified APC (DEGR-APC) (apparent K(d) ~270 nM and 1.0 μM, respectively). Fluid-phase binding studies using fluorescence indicated an estimated K(d) of ~590 nM for acrylodan-labelled LC binding to DEGR-APC. Furthermore, FVIII LC effectively competed with FVIIIa in blocking APC-catalysed cleavage at Arg(336) (K(i) = 709 nM). A binding site previously identified near the C-terminal end of the A3 domain (residues 2007-2016) of FVIII LC was subjected to Ala-scanning mutagenesis. FXa generation assays and western and dot blotting were employed to assess the contribution of these residues to FVIIIa interactions with APC. Virtually all variants tested showed reductions in the rates of APC-catalysed inactivation of the cofactor and cleavage at the primary inactivation site (Arg(336)), with maximal reductions in inactivation rates (~3-fold relative to WT) and cleavage rates (~3 to ~9-fold relative to WT) observed for the Met2010Ala, Ser2011Ala, and Leu2013Ala variants. Titration of FVIIIa substrate concentration monitoring cleavage by a dot blot assay indicated that these variants also showed ~3-fold increases relative to WT while a double mutant (Met2010Ala/Ser2011Ala) showed a >4-fold increase in K(m). These results show a contribution of a number of residues within the 2007-2016 sequence, and in particular residues Met2010, Ser2011, and Leu2013 to an APC-interactive site.

  10. Interaction of Carthamus tinctorius lignan arctigenin with the binding site of tryptophan-degrading enzyme indoleamine 2,3-dioxygenase☆

    Science.gov (United States)

    Temml, Veronika; Kuehnl, Susanne; Schuster, Daniela; Schwaiger, Stefan; Stuppner, Hermann; Fuchs, Dietmar

    2013-01-01

    Mediterranean Carthamus tinctorius (Safflower) is used for treatment of inflammatory conditions and neuropsychiatric disorders. Recently C. tinctorius lignans arctigenin and trachelogenin but not matairesinol were described to interfere with the activity of tryptophan-degrading enzyme indoleamine 2,3-dioxygenase (IDO) in peripheral blood mononuclear cells in vitro. We examined a potential direct influence of compounds on IDO enzyme activity applying computational calculations based on 3D geometry of the compounds. The interaction pattern analysis and force field-based minimization was performed within LigandScout 3.03, the docking simulation with MOE 2011.10 using the X-ray crystal structure of IDO. Results confirm the possibility of an intense interaction of arctigenin and trachelogenin with the binding site of the enzyme, while matairesinol had no such effect. PMID:24251110

  11. Biotic interactions mediate the influence of bird colonies on vegetation and soil chemistry at aggregation sites.

    Science.gov (United States)

    Natusch, Daniel James Deans; Lyons, Jessica Ann; Brown, Gregory P; Shine, Richard

    2017-02-01

    Colonial-nesting organisms can strongly alter the chemical and biotic conditions around their aggregation sites, with cascading impacts on other components of the ecosystem. In tropical Australia, Metallic Starlings (Aplonis metallica) nest in large colonies far above the forest canopy, in emergent trees. The ground beneath those trees is open, in stark contrast to the dense foliage all around. We surveyed the areas beneath 27 colony trees (and nearby randomly chosen trees lacking bird colonies) to quantify the birds' impacts on soil and vegetation characteristics, and to test alternative hypotheses about the proximate mechanisms responsible for the lack of live vegetation beneath colony trees. Nutrient levels were greatly elevated beneath colony trees (especially, those with larger colonies), potentially reaching levels toxic to older trees. However, seedlings thrived in the soil from beneath colony trees. The primary mechanism generating open areas beneath colony trees is disturbance by scavengers (feral pigs and native Turkeys) that are attracted in vast numbers to these nutrient hotspots. Seedlings flourished within exclosures inaccessible to vertebrate herbivores, but were rapidly consumed if unprotected. Our results contrast with previous studies of colonies of seabirds on remote islands, where a lack of large terrestrial herbivores results in bird colonies encouraging rather than eliminating vegetation in areas close to the nesting site. In our continental study system, scavengers may rapidly dilute the spatial heterogeneity generated by the massive nutrient subsidy from bird colonies. © 2016 by the Ecological Society of America.

  12. Ionic interactions in the water zone at oil well-sites

    Energy Technology Data Exchange (ETDEWEB)

    Kleven, R.

    1996-11-01

    The aim of this doctoral thesis has been to obtain a better understanding of ionic behaviour in a water zone of sedimentary rock exposed to sea-water based drilling fluid and completion fluid. Interaction processes addressed have been ion exchange on the surface of the reservoir rocks and precipitation of divalent cations with sulphate ions from the sea water. Clay minerals are focused on because of their ability to conduct electricity through ion-exchange reactions. The most important parameters that the distribution of ions around a borehole depends upon are suggested to be (1) the ability of the sedimentary rocks to sorb/desorb ions, (2) the effect of added solutions on the sorption/desorption processes, (3) the mobility of ions. The first of four enclosed papers studies ionic interaction, mainly on homo-ionic clay mineral - salt solution, in batch experiments under pH, ionic strength and temperature conditions likely to occur in the field. Paper II investigates the use of tritiated water as a reference tracer in miscible displacement processes in porous sandstone cores. Ionic interaction processes during drilling of oil wells with conventional KCl bentonite mud tagged with HTO were studied by means of measured ionic and HTO concentration of water sampled in the near well-bore region. A tracer method was developed and ``tracer diagrams`` illustrate sorption/desorption processes. The water analyses, sampling procedure, and tracer techniques are presented in the third paper. Paper IV compares the interpretation of laboratory data and field data. 173 refs., 47 figs., 22 tabs.

  13. Interaction of hookworm 14-3-3 with the forkhead transcription factor DAF-16 requires intact Akt phosphorylation sites

    Directory of Open Access Journals (Sweden)

    Hawdon John M

    2009-04-01

    Full Text Available Abstract Background Third-stage infective larvae (L3 of hookworms are in an obligatory state of developmental arrest that ends upon entering the definitive host, where they receive a signal that re-activates development. Recovery from the developmentally arrested dauer stage of Caenorhabditis elegans is analogous to the resumption of development during hookworm infection. Insulin-like signaling (ILS mediates recovery from arrest in C. elegans and activation of hookworm dauer L3. In C. elegans, phosphorylation of the forkhead transcription factor DAF-16 in response to ILS creates binding cites for the 14-3-3 protein Ce-FTT-2, which translocates DAF-16 out of the nucleus, resulting in resumption of reproductive development. Results To determine if hookworm 14-3-3 proteins play a similar role in L3 activation, hookworm FTT-2 was identified and tested for its ability to interact with A. caninum DAF-16 in vitro. The Ac-FTT-2 amino acid sequence was 91% identical to the Ce-FTT-2, and was most closely related to FTT-2 from other nematodes. Ac-FTT-2 was expressed in HEK 293T cells, and was recognized by an antibody against human 14-3-3β isoform. Reciprocal co-immunoprecipitations using anti-epitope tag antibodies indicated that Ac-FTT-2 interacts with Ac-DAF-16 when co-expressed in serum-stimulated HEK 293T cells. This interaction requires intact Akt consensus phosphorylation sites at serine107 and threonine312, but not serine381. Ac-FTT-2 was undetectable by Western blot in excretory/secretory products from serum-stimulated (activated L3 or adult A. caninum. Conclusion The results indicate that Ac-FTT-2 interacts with DAF-16 in a phosphorylation-site dependent manner, and suggests that Ac-FTT-2 mediates activation of L3 by binding Ac-DAF-16 during hookworm infection.

  14. Two distinct sites in sonic Hedgehog combine for heparan sulfate interactions and cell signaling functions

    DEFF Research Database (Denmark)

    Chang, Shu-Chun; Mulloy, Barbara; Magee, Anthony I

    2011-01-01

    had reduced signaling activity compared with wild type hShh or a control mutation (K74S). In addition, the mutant hShh proteins supported reduced proliferation and invasion of PANC1 cells compared with control hShh proteins, following endogenous hShh depletion by RNAi knockdown. The data correlated...... with reduced Shh multimerization where the Lys-37/38 and/or Lys-178 mutations were examined. These studies provide a new insight into the functional roles of hShh interactions with HSPGs, which may allow targeting this aspect of hShh biology in, for example, pancreatic ductal adenocarcinoma....

  15. Water-rock interaction modelling and uncertainties of mixing modelling. SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Gimeno, Maria J.; Auque, Luis F.; Gomez, Javier B.; Acero, Patricia (Univ. of Zaragoza, Zaragoza (Spain))

    2008-08-15

    The overall objectives of the hydrogeochemical description for Forsmark are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are one of the major driving forces for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes behind of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Forsmark site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and university researchers with expertise

  16. Water-rock interaction modelling and uncertainties of mixing modelling. SDM-Site Forsmark

    International Nuclear Information System (INIS)

    Gimeno, Maria J.; Auque, Luis F.; Gomez, Javier B.; Acero, Patricia

    2008-08-01

    The overall objectives of the hydrogeochemical description for Forsmark are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are one of the major driving forces for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes behind of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Forsmark site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and university researchers with expertise in

  17. A Four-Site Molecular Model for Simulations of Liquid Methanol and Water-Methanol Mixtures: MeOH-4P.

    Science.gov (United States)

    Martínez-Jiménez, Manuel; Saint-Martin, Humberto

    2018-04-17

    In this work, we present a new four-site potential for methanol, MeOH-4P, fitted to reproduce the dielectric constant ε, the surface tension γ s , and the liquid density ρ of the pure liquid at T = 298.15 K and p = 1 bar. The partial charges on each site were taken from the OPLS/2016 model with the only difference of putting the negative charge on the fourth site ( M) instead of on the O atom, as done in four-site water models. The original Lennard-Jones (LJ) parameters of OPLS/2016 for the methyl moiety (Me) were modified for the fitting of ρ and γ s , whereas the parameters of the TIP4P-FB water model were used for the O atom without change. Taking into account the energetic cost of the enhanced dipole relative to the isolated molecule, the results from simulations with this model showed good agreement with experiments for ρ, α p , κ T , C p , and Δ H v- l . Also, the temperature dependence of γ s and ε is satisfactory in the interval between 260 and 360 K, and the critical point description is similar to that of OPLS/2016. It is shown that orientational correlations, described by the Kirkwood factor G k , play a prominent role in the appropriate description of dielectric constants in existing models; unfortunately, the enhancement of the dipole moment produced a low diffusion coefficient D MeOH ; thus, a compromise was required between a good reproduction of ε and an acceptable D MeOH . The use of a fourth site resulted in a significant improvement for water-methanol mixtures described with TIP4P-FB and MeOH-4P, respectively, but required the modification of the LJ geometric combination rule to allow a good description of the methanol molar-fraction dependence of ρ, ε, and methanol (water) diffusion coefficients D MeOH ( D H 2 O ) and excess volume of mixing Δ V mix in the entire range of composition. The resulting free energy of hydration Δ G hyd shows excellent agreement with experiments in the interval between 280 and 360 K.

  18. Geochemical Characterization of Rock-Water Interaction in Groundwater at the KURT Site

    International Nuclear Information System (INIS)

    Ryu, Ji Hun; Kwon, Jang Soon; Kim, Geon Young; Koh, Yong Kwon

    2012-01-01

    Geochemical composition of fracture filling minerals and groundwater was investigated to characterize geochemical characteristics of groundwater system at the KURT site. Minerals such as calcite, illite, laumontite, chlorite, epidote, montmorillonite, and kaolinite, as well as I/S mixed layer minerals were detected in the minerals extracted from the fracture surfaces of the core samples. The groundwater from the DB-1, YS-1 and YS-4 boreholes showed alkaline conditions with pH of higher than 8. The electrical conductivity (EC) values of the groundwater samples were around 200 μS/cm, except for the YS-1 borehole. Dissolved oxygen was almost zero in the DB-1 borehole indicating highly reduced conditions. The Cl- concentration was estimated around 5 mg/L and showed homogeneous distribution along depths at the KURT site. It might indicate the mixing between shallow groundwater and deep groundwater. The shallow groundwater from boreholes showed Ca-HCO 3 type, whereas deep groundwater below 300 m from the surface indicated Na-HCO3 type. The isotopic values observed in the groundwater ranged from -10.4 to -8.2% for δ 18 O and from -71.3 to -55.0 % for δD. In addition, the isotope-depleted water contained higher fluoride concentration. The oxygen and hydrogen isotopic values of deep groundwater were more depleted compared to the shallow groundwater. The results from age dating analysis using 14 C indicated relatively younger (2000-6000yr old) groundwater compared to other european granitic groundwaters such as Stripa (Sweden).

  19. Theory of site-specific interactions of the combinatorial transcription factors with DNA

    International Nuclear Information System (INIS)

    Murugan, R

    2010-01-01

    We derive a functional relationship between the mean first passage time associated with the concurrent binding of multiple transcription factors (TFs) at their respective combinatorial cis-regulatory module sites (CRMs) and the number n of TFs involved in the regulation of the initiation of transcription of a gene of interest. Our results suggest that the overall search time τ s that is required by the n TFs to locate their CRMs which are all located on the same DNA chain scales with n as τ s ∼n α where α ∼ (2/5). When the jump size k that is associated with the dynamics of all the n TFs along DNA is higher than that of the critical jump size k c that scales with the size of DNA N as k c ∼ N 2/3 , we observe a similar power law scaling relationship and also the exponent α. When k c , α shows a strong dependence on both n and k. Apparently there is a critical number of combinatorial TFs n c ∼ 20 that is required to efficiently regulate the initiation of transcription of a given gene below which (2/5) 1. These results seem to be independent of the initial distances between the TFs and their corresponding CRMs and also suggest that the maximum number of TFs involved in a given combinatorial regulation of the initiation of transcription of a gene of interest seems to be restricted by the degree of condensation of the genomic DNA. The optimum number m opt of roadblock protein molecules per genome at which the search time associated with these n TFs to locate their binding sites is a minimum seems to scale as m opt ∼Ln α/2 where L is the sliding length of TFs whose maximum value seems to be such that L ≤ 10 4 bps for the E. coli bacterial genome.

  20. Volatility Transmission between Dow Jones Stock Index and Emerging Bond Index

    Directory of Open Access Journals (Sweden)

    Amir Saadaoui

    2016-04-01

    Full Text Available In this paper, we use a bivariate GARCH model to estimate simultaneously of the mean and the conditional variance between the Dow Jones stock index and some emerging bond indices. We used the DCC-GARCH model to graphically demonstrate the peaks of the volatility transmission. We examined this transmission using daily returns between July, 30, 2009 and January, 18, 2011 extracted from Datastream. Our results demonstrate that there is a significant transmission of shocks and volatility between the Dow Jones stock index and bond indices of the emerging countries. The results also confirm the idea that the crisis was transmitted from the United States to the emerging countries due to foreign investment made in these countries.

  1. Jones-matrix tomography of biological tissues phase anisotropy in the diagnosis of uterus wall prolapse

    Science.gov (United States)

    Trifonyuk, L.; Baranovsky, V.; Dubolazov, O. V.; Ushenko, V. O.; Ushenko, O. G.; Zhytaryuk, V. G.; Prydiy, O. G.; Vanchulyak, O.

    2018-01-01

    The work consists of two parts. In the first part - we mapped a distribution of optical activity and birefringence in polycrystalline networks of biological tissues. The Jones-matrix formalism is used for accessible quantitative description of these types of optical anisotropy. We demonstrate that differentiation of polycrystalline networks of biological tissues can be performed based on the statistical analysis of distribution of rotation angles and phase shifts associated with the optical activity and birefringence, respectively. In the second part we defined - practical operational characteristics, such as sensitivity, specificity and accuracy of Jones-matrix reconstruction of optical anisotropy were identified with the special emphasis on biomedical application, specifically for differentiation of two types of pathology: prolapse and albuminuria.

  2. Mapping of polycrystalline films of biological fluids utilizing the Jones-matrix formalism

    Science.gov (United States)

    Ushenko, Vladimir A.; Dubolazov, Alexander V.; Pidkamin, Leonid Y.; Sakchnovsky, Michael Yu; Bodnar, Anna B.; Ushenko, Yuriy A.; Ushenko, Alexander G.; Bykov, Alexander; Meglinski, Igor

    2018-02-01

    Utilizing a polarized light approach, we reconstruct the spatial distribution of birefringence and optical activity in polycrystalline films of biological fluids. The Jones-matrix formalism is used for an accessible quantitative description of these types of optical anisotropy. We demonstrate that differentiation of polycrystalline films of biological fluids can be performed based on a statistical analysis of the distribution of rotation angles and phase shifts associated with the optical activity and birefringence, respectively. Finally, practical operational characteristics, such as sensitivity, specificity and accuracy of the Jones-matrix reconstruction of optical anisotropy, were identified with special emphasis on biomedical application, specifically for differentiation of bile films taken from healthy donors and from patients with cholelithiasis.

  3. Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site

    Energy Technology Data Exchange (ETDEWEB)

    Trehan, I.; Beadle, B.M.; Shoichet, B.K. (NWU)

    2010-03-08

    {beta}-Lactamases hydrolyze {beta}-lactam antibiotics, including penicillins and cephalosporins; these enzymes are the most widespread resistance mechanism to these drugs and pose a growing threat to public health. {beta}-Lactams that contain a bulky 6(7){alpha} substituent, such as imipenem and moxalactam, actually inhibit serine {beta}-lactamases and are widely used for this reason. Although mutant serine {beta}-lactamases have arisen that hydrolyze {beta}-lactamase resistant {beta}-lactams (e.g., ceftazidime) or avoid mechanism-based inhibitors (e.g., clavulanate), mutant serine {beta}-lactamases have not yet arisen in the clinic with imipenemase or moxalactamase activity. Structural and thermodynamic studies suggest that the 6(7){alpha} substituents of these inhibitors form destabilizing contacts within the covalent adduct with the conserved Asn152 in class C {beta}-lactamases (Asn132 in class A {beta}-lactamases). This unfavorable interaction may be crucial to inhibition. To test this destabilization hypothesis, we replaced Asn152 with Ala in the class C {beta}-lactamase AmpC from Escherichia coli and examined the mutant enzyme's thermodynamic stability in complex with imipenem and moxalactam. Consistent with the hypothesis, the Asn152 {yields} Ala substitution relieved 0.44 and 1.10 kcal/mol of strain introduced by imipenem and moxalactam, respectively, relative to the wild-type complexes. However, the kinetic efficiency of AmpC N152A was reduced by 6300-fold relative to that of the wild-type enzyme. To further investigate the inhibitor's interaction with the mutant enzyme, the X-ray crystal structure of moxalactam in complex with N152A was determined to a resolution of 1.83 {angstrom}. Moxalactam in the mutant complex is significantly displaced from its orientation in the wild-type complex; however, moxalactam does not adopt an orientation that would restore competence for hydrolysis. Although Asn152 forces {beta}-lactams with 6(7){alpha

  4. Screw fixation diameter for fifth metatarsal jones fracture: a cadaveric study.

    Science.gov (United States)

    Scott, Ryan T; Hyer, Christopher F; DeMill, Shyler L

    2015-01-01

    The fifth metatarsal Jones fracture is a well-documented injury occurring at the proximal diaphyseal-metaphyseal junction. Conservative versus surgical intervention has been discussed in published studies for the management of Jones fractures. Solid intramedullary fixation relies on accurate matching of the screw diameter to the intraosseous diameter. The purpose of the present cadaveric study was to determine the average intraosseous diameter of the proximal fifth metatarsal as it relates to screw size selection for Jones fracture stabilization. Twenty fresh-frozen cadaver legs were used for examination. The fifth metatarsal was completely dissected. A transverse osteotomy was performed from laterally to medially along the midline of the metatarsal. A digital caliper was used to measure the diameter of the medullary canal of the fifth metatarsal. The measurement was taken at the narrowest portion of the medullary canal just distal to the proximal metaphysis. The mean dorsal to plantar diameter of the fifth metatarsal was 6.475 ± 1.54 (range 4 to 12) mm and the mean medial to lateral diameter was 4.6 ± 0.85 (range 3 to 6) mm. Intramedullary screw fixation has shown beneficial results in the treatment protocol of fifth metatarsal Jones fractures. Our study has demonstrated that a 4.5-mm cannulated screw is the narrowest diameter screw that can be used in the average fifth metatarsal and still obtain adequate intraosseous purchase. When selecting the appropriate screw, the surgeon must be comfortable selecting the largest screw that will achieve the maximal interface with the dense cortical bone in both the medial to lateral and dorsal to plantar plane. Copyright © 2015 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

  5. Optimal Fixation of Jones Fractures Sacrifices the Peroneal Brevis Tendon Insertion andthe Plantar Fascia

    OpenAIRE

    van Dijk, Pim A.d.; Breuking, Sofie; Vopat, Bryan G.; Guss, Daniel; Johnson, Anne H.; Hosseini, Ali; DiGiovanni, Christopher

    2017-01-01

    Objectives: Patients with Jones fractures (JF) frequently undergo operative management with intramedullary screw fixation. Screw insertion through the base of the fifth metatarsal potentially compromises attachment points of the plantar fascia (PF) and peroneal brevis tendon (PB), and appropriate screw length and diameter remains controversial. The aim of this study was to define the anatomy of the fifth metatarsal bone using CT modeling in order to provide better guidance regarding optimized...

  6. Enzyme-ligand interactions that drive active site rearrangements in the Helicobacter pylori 5´-methylthioadenosine/S-adenosylhomocysteine nucleosidase

    Energy Technology Data Exchange (ETDEWEB)

    Ronning, Donald R; Iacopelli, Natalie M; Mishra, Vidhi [Toledo

    2012-03-15

    The bacterial enzyme 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) plays a central role in three essential metabolic pathways in bacteria: methionine salvage, purine salvage, and polyamine biosynthesis. Recently, its role in the pathway that leads to the production of autoinducer II, an important component in quorum-sensing, has garnered much interest. Because of this variety of roles, MTAN is an attractive target for developing new classes of inhibitors that influence bacterial virulence and biofilm formation. To gain insight toward the development of new classes of MTAN inhibitors, the interactions between the Helicobacter pylori-encoded MTAN and its substrates and substrate analogs were probed using X-ray crystallography. The structures of MTAN, an MTAN-Formycin A complex, and an adenine bound form were solved by molecular replacement and refined to 1.7, 1.8, and 1.6 Å, respectively. The ribose-binding site in the MTAN and MTAN-adenine cocrystal structures contain a tris[hydroxymethyl]aminomethane molecule that stabilizes the closed form of the enzyme and displaces a nucleophilic water molecule necessary for catalysis. This research gives insight to the interactions between MTAN and bound ligands that promote closing of the enzyme active site and highlights the potential for designing new classes of MTAN inhibitors using a link/grow or ligand assembly development strategy based on the described H. pylori MTAN crystal structures.

  7. Mutability and Deformity: Models of the Body and the Art of Edward Burne-Jones

    Directory of Open Access Journals (Sweden)

    Caroline Arscott

    2008-10-01

    Full Text Available This essay discusses the alternatives that emerged in the Victorian period to a perfect and regular neoclassical conception of the heroic male body. It charts the evolving fascination with mutable forms, whether heroic or monstrous, imagined first of all in the 1850s in terms of a body conceived of as bolted together or modified by the fusion of organic and inorganic substances. The early work of Burne-Jones is discussed in relation to investigations of cell structure and mechanical inventions in the Great Exhibition of 1851 such as the 'Expanding Model of a Man' invented by Count Dunin. Arscott also discusses the cybernetic implications of Burne-Jones's gouache, 'The Merciful Knight' (1863. Later works of Burne-Jones, in particular 'Perseus and the Graiae' (1878 and the reworked composition 'Love Among the Ruins' (1894, are discussed in terms of a turn towards a sense of the spread and mutation of organic being through and beyond the self. Arscott considers this alongside contemporary investigations of the role of bacilli in disease, looking at leprosy and the heroisation of the Leper Priest of Molokai, Father Damien in the 1880s and 1890s. In the late-Victorian period, Arscott concludes, monstrous distortion was imagined as the unpredictable and unruly proliferation of the organic by the organism in both its vital and morbid states.

  8. Pendeteksian Bagian Tubuh Manusia untuk Filter Pornografi dengan Metode Viola-Jones

    Directory of Open Access Journals (Sweden)

    Benny Senjaya

    2012-06-01

    Full Text Available Information Technology does help people to get information promptly anytime and anywhere. Unfortunately, the information gathered from the Internet does not always come out positive. Some information can be destructive, such as porn images. To mitigate this problem, the study aims to create a desktop application that could detect parts of human body which can be expanded in the future to become an image filter application for pornography. The detection methodology in this study is Viola-Jones method which provides a complete framework for extracting and recognizing image features. A combination of Viola-Jones method with Haar-like features, integral image, boosting algorithm, and cascade classifier provide a robust detector for the application. First, several parts of the human body are chosen to be detected as the data training using the Viola-Jones method. Then, another set of images (similar body parts but different images are run through the application to be recognized. The result shows 86.25% of successful detection. The failures are identified and show that the inputted data are completely different with the data training.

  9. Interactions of 2'-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site.

    Directory of Open Access Journals (Sweden)

    Maciej Jasiński

    Full Text Available Synthetic oligonucleotides targeting functional regions of the prokaryotic rRNA could be promising antimicrobial agents. Indeed, such oligonucleotides were proven to inhibit bacterial growth. 2'-O-methylated (2'-O-Me oligoribonucleotides with a sequence complementary to the decoding site in 16S rRNA were reported as inhibitors of bacterial translation. However, the binding mode and structures of the formed complexes, as well as the level of selectivity of the oligonucleotides between the prokaryotic and eukaryotic target, were not determined. We have analyzed three 2'-O-Me oligoribonucleotides designed to hybridize with the models of the prokaryotic rRNA containing two neighboring aminoglycoside binding pockets. One pocket is the paromomycin/kanamycin binding site corresponding to the decoding site in the small ribosomal subunit and the other one is the close-by hygromycin B binding site whose dynamics has not been previously reported. Molecular dynamics (MD simulations, as well as isothermal titration calorimetry, gel electrophoresis and spectroscopic studies have shown that the eukaryotic rRNA model is less conformationally stable (in terms of hydrogen bonds and stacking interactions than the corresponding prokaryotic one. In MD simulations of the eukaryotic construct, the nucleotide U1498, which plays an important role in correct positioning of mRNA during translation, is flexible and spontaneously flips out into the solvent. In solution studies, the 2'-O-Me oligoribonucleotides did not interact with the double stranded rRNA models but all formed stable complexes with the single-stranded prokaryotic target. 2'-O-Me oligoribonucleotides with one and two mismatches bound less tightly to the eukaryotic target. This shows that at least three mismatches between the 2'-O-Me oligoribonucleotide and eukaryotic rRNA are required to ensure target selectivity. The results also suggest that, in the ribosome environment, the strand invasion is the

  10. Bacillus thuringiensis Cry34Ab1/Cry35Ab1 interactions with western corn rootworm midgut membrane binding sites.

    Directory of Open Access Journals (Sweden)

    Huarong Li

    Full Text Available BACKGROUND: Bacillus thuringiensis (Bt Cry34Ab1/Cry35Ab1 are binary insecticidal proteins that are co-expressed in transgenic corn hybrids for control of western corn rootworm, Diabrotica virgifera virgifera LeConte. Bt crystal (Cry proteins with limited potential for field-relevant cross-resistance are used in combination, along with non-transgenic corn refuges, as a strategy to delay development of resistant rootworm populations. Differences in insect midgut membrane binding site interactions are one line of evidence that Bt protein mechanisms of action differ and that the probability of receptor-mediated cross-resistance is low. METHODOLOGY/PRINCIPAL FINDINGS: Binding site interactions were investigated between Cry34Ab1/Cry35Ab1 and coleopteran active insecticidal proteins Cry3Aa, Cry6Aa, and Cry8Ba on western corn rootworm midgut brush border membrane vesicles (BBMV. Competitive binding of radio-labeled proteins to western corn rootworm BBMV was used as a measure of shared binding sites. Our work shows that (125I-Cry35Ab1 binds to rootworm BBMV, Cry34Ab1 enhances (125I-Cry35Ab1 specific binding, and that (125I-Cry35Ab1 with or without unlabeled Cry34Ab1 does not share binding sites with Cry3Aa, Cry6Aa, or Cry8Ba. Two primary lines of evidence presented here support the lack of shared binding sites between Cry34Ab1/Cry35Ab1 and the aforementioned proteins: 1 No competitive binding to rootworm BBMV was observed for competitor proteins when used in excess with (125I-Cry35Ab1 alone or combined with unlabeled Cry34Ab1, and 2 No competitive binding to rootworm BBMV was observed for unlabeled Cry34Ab1 and Cry35Ab1, or a combination of the two, when used in excess with (125I-Cry3Aa, or (125I-Cry8Ba. CONCLUSIONS/SIGNIFICANCE: Combining two or more insecticidal proteins active against the same target pest is one tactic to delay the onset of resistance to either protein. We conclude that Cry34Ab1/Cry35Ab1 are compatible with Cry3Aa, Cry6Aa, or Cry8Ba

  11. Interaction of Pseudolaric Acid B with The Colchicine Site of Tubulin

    Science.gov (United States)

    Sarkar, Taradas; Nguyen, Tam Luong; Su, Zhi-Wei; Hao, Jun; Bai, Ruoli; Gussio, Rick; Qiu, Samuel X.; Hamel, Ernest

    2012-01-01

    We purified pseudolaric acid B (PAB) from the root and stem bark of Pseudolarix kaempferi (Lindl.) Gorden. Confirming previous findings, we found that the compound had high nanomolar IC50 antiproliferative effects in several cultured cell lines, causing mitotic arrest and the disappearance of intracellular microtubules. PAB strongly inhibited tubulin assembly (IC50, 1.1 μM) but weakly inhibited the binding of colchicine to tubulin, as demonstrated by fluorescence and with [3H]colchicine. Kinetic analysis demonstrated that the mechanism of inhibition was competitive, with an apparent Ki of 12-15 μM. Indirect studies demonstrated that PAB bound rapidly to tubulin and dissociated more rapidly from tubulin than the colchicine analog 2-methoxy-5-(2′,3′,4′-trimethoxyphenyl)tropone, whose complex with tubulin is known to have a half-life of 17 s at 37 °C. We modeled PAB into the colchicine site of tubulin, using the crystal structure 1SA0 that contains two αβ-tubulin heterodimers, both bound to a colchicinoid and to a stathmin fragment. The binding model of PAB revealed common pharmacophoric features between PAB and colchicinoids, not readily apparent from their chemical structures. PMID:22634405

  12. The effects of World Heritage Sites on domestic tourism: a spatial interaction model for Italy

    Science.gov (United States)

    Patuelli, Roberto; Mussoni, Maurizio; Candela, Guido

    2013-07-01

    Culture is gaining increasing importance in the modern tourism industry and represents a significant force of attraction for tourists (both domestic and international). Cultural tourism allows destinations and regions to expand their customer base, diversify their offer, extend the stay of the tourist, and reduce seasonality. Great efforts are made, by national governments and regions, in order to obtain official designation regarding the relevance of their historical/cultural attractions, for example through UNESCO's World Heritage Sites (WHS) list. Such an aspect seems particularly relevant for a country like Italy, which has a high number of entries in the WHS list and where regions take an active role in promoting tourism. Using an 12-year panel of domestic tourism flows, we investigate the importance of the regional endowment in terms of WHS from two perspectives: (a) by separately estimating the effects, on tourism flows, of WHS located in the residence region of tourists and in the destination region; and (b) by taking into account potential spatial substitution/complementarity effects between regions due to their WHS endowment. Finally, a sensitivity analysis is offered to evaluate the spatial extent of the latter.

  13. Initial success of native grasses is contingent on multiple interactions among exotic grass competition, temporal priority, rainfall and site effects.

    Science.gov (United States)

    Young, Truman P; Zefferman, Emily P; Vaughn, Kurt J; Fick, Stephen

    2014-12-05

    Ecological communities are increasingly being recognized as the products of contemporary drivers and historical legacies that are both biotic and abiotic. In an attempt to unravel multiple layers of ecological contingency, we manipulated (i) competition with exotic annual grasses, (ii) the timing of this competition (temporal priority in arrival/seeding times) and (iii) watering (simulated rainfall) in a restoration-style planting of native perennial grasses. In addition, we replicated this experiment simultaneously at three sites in north-central California. Native perennial grasses had 73-99 % less cover when planted with exotic annuals than when planted alone, but this reduction was greatly ameliorated by planting the natives 2 weeks prior to the exotics. In a drought year, irrigation significantly reduced benefits of early planting so that these benefits resembled those observed in a non-drought year. There were significant differences across the three sites (site effects and interactions) in (i) overall native cover, (ii) the response of natives to competition, (iii) the strength of the temporal priority effect and (iv) the degree to which supplemental watering reduced priority effects. These results reveal the strong multi-layered contingency that underlies even relatively simple communities. Published by Oxford University Press on behalf of the Annals of Botany Company.

  14. Mainekas teadlane soovitab Eestil enam väliskapitali ligi meelitada / Simon Jones ; interv. Aleksei Günter

    Index Scriptorium Estoniae

    Jones, Simon

    2005-01-01

    Pärnus telekommunikatsiooni- ja infofoorumil viibiv innovatsiooniekspert vastab küsimustele, mis puudutavad tema hinnangut Eesti teadus- ja arendustegevusele, tehnoloogia kasutamist sotsiaalprobleemide lahendamisel ning Eesti varustamist tasuta internetiühendusega. Lisa: Simon Jones

  15. Scaled effective on-site Coulomb interaction in the DFT+U method for correlated materials

    Science.gov (United States)

    Nawa, Kenji; Akiyama, Toru; Ito, Tomonori; Nakamura, Kohji; Oguchi, Tamio; Weinert, M.

    2018-01-01

    The first-principles calculation of correlated materials within density functional theory remains challenging, but the inclusion of a Hubbard-type effective on-site Coulomb term (Ueff) often provides a computationally tractable and physically reasonable approach. However, the reported values of Ueff vary widely, even for the same ionic state and the same material. Since the final physical results can depend critically on the choice of parameter and the computational details, there is a need to have a consistent procedure to choose an appropriate one. We revisit this issue from constraint density functional theory, using the full-potential linearized augmented plane wave method. The calculated Ueff parameters for the prototypical transition-metal monoxides—MnO, FeO, CoO, and NiO—are found to depend significantly on the muffin-tin radius RMT, with variations of more than 2-3 eV as RMT changes from 2.0 to 2.7 aB. Despite this large variation in Ueff, the calculated valence bands differ only slightly. Moreover, we find an approximately linear relationship between Ueff(RMT) and the number of occupied localized electrons within the sphere, and give a simple scaling argument for Ueff; these results provide a rationalization for the large variation in reported values. Although our results imply that Ueff values are not directly transferable among different calculation methods (or even the same one with different input parameters such as RMT), use of this scaling relationship should help simplify the choice of Ueff.

  16. Interaction between nucleotide binding sites on chloroplast coupling factor 1 during ATP hydrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Leckband, D.; Hammes, G.G.

    1987-04-21

    The initial hydrolysis of radioactively-labelled CaATP by chloroplast coupling factor 1 was studied with the quenched-flow method. The time course of hydrolysis can be described as a first-order conversion of the enzyme to an active form followed by steady-state formation of product. The rate constant for the first-order process is independent of substrate concentration but increased hyperbolically to a limiting value of 0.43 s/sup -1/ with increasing concentrations of free Ca/sup 2 +/. A mechanism involving a Ca/sup 2 +/-triggered conversion to an active form of the enzyme is consistent with the data. The steady-state rate varied sigmoidally with the CaATP concentration. Initial exchange of tightly bound ADP is complex: approx. 50% of the bound nucleotide is lost within 30 s, with complete exchange requiring several minutes. The first-order rate constant characterizing the rapid phase of the reaction increases hyperbolically to a limiting value of 0.26 s/sup -1/ as the concentration of CaATP is increased, indicating that the binding of CaATP to the enzyme promotes the exchange process. Modification of the quenched-flow apparatus permitted measurement of the rate of nucleotide exchange during steady-state catalysis. The value of the first-order rate constant characterizing this process is similar to the catalytic rate constant determined under identical conditions. When MgATP is tightly bound to the enzyme, none of the kinetic properties of the enzyme described above were significantly changes. The results obtained suggest a mechanism in which two sites on the enzyme participate in catalysis. Several possible mechanisms consistent with the data are discussed.

  17. [Interaction of plasma selenium levels and D12S304 gene site in the pathogenesis of Kashin-Beck disease analyzed by multifactor dimensionality reduction software].

    Science.gov (United States)

    Ping, Zhiguang; Liu, Li; Guo, Xiong

    2011-07-01

    To explore the interaction of plasma selenium levels and D12S304 gene site in the pathogenesis of Kashin-Beck disease (KBD). Case-control design was taken to compare the difference of plasma selenium levels and genotype of D12S304 between KBD patients and non-patients, and the interactions were analyzed by MDR software. Plasma selenium levels was lower in the case group than in the control group, while the D12S304 gene site was not different between the two groups, and no interaction between plasma selenium and genotype was observed. There was no interaction between plasma selenium and genotype at D12S304. Enlarging sample size or selecting another gene site might be needed in exploring the gene-environment interactions in the pathogenesis of KBD.

  18. "No interest in human anatomy as such": Frederic Wood Jones dissects anatomical investigation in the United States in the 1920s.

    Science.gov (United States)

    Jones, Ross L

    2014-03-01

    In 1926, Frederic Wood Jones, professor of Anatomy at the University of Adelaide and a leading figure in the British anatomical world, took a Rockefeller Foundation funded trip to the United States in order to inspect anatomy programmes and medical museums and to meet leading figures in the anatomical and anthropological world. His later reflections paint a picture of a discipline in transition. Physical anthropology and gross anatomy were coming to a crisis point in the United States, increasingly displaced by research in histology, embryology and radiological anatomy. Meanwhile, in Britain and its colonial outposts, anatomists such as Wood Jones were attempting to re-invigorate the discipline in the field, studying biological specimens as functional and active agents in their particular milieus, but with human dissection at the core. Thus, an examination of this trip allows us to see how the interaction between two traditions in anatomy informed the process of the development of human biology in this critical period. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Cholinesterases: structure of the active site and mechanism of the effect of cholinergic receptor blockers on the rate of interaction with ligands

    Energy Technology Data Exchange (ETDEWEB)

    Antokhin, A M; Gainullina, E T; Taranchenko, V F [Federal State Agency ' 27 Scientific Centre of Ministry of Defence of the Russian Federation' (Russian Federation); Ryzhikov, S B; Yavaeva, D K [Department of Physics, M.V.Lomonosov Moscow State University (Russian Federation)

    2010-10-19

    Modern views on the structure of cholinesterase active sites and the mechanism of their interaction with organophosphorus inhibitors are considered. The attention is focused on the mechanism of the effect of cholinergic receptor blockers, acetylcholine antagonists, on the rate of interaction of acetylcholine esterase with organophosphorus inhibitors.

  20. Nuclear Protein Sam68 Interacts with the Enterovirus 71 Internal Ribosome Entry Site and Positively Regulates Viral Protein Translation.

    Science.gov (United States)

    Zhang, Hua; Song, Lei; Cong, Haolong; Tien, Po

    2015-10-01

    Enterovirus 71 (EV71) recruits various cellular factors to assist in the replication and translation of its genome. Identification of the host factors involved in the EV71 life cycle not only will enable a better understanding of the infection mechanism but also has the potential to be of use in the development of antiviral therapeutics. In this study, we demonstrated that the cellular factor 68-kDa Src-associated protein in mitosis (Sam68) acts as an internal ribosome entry site (IRES) trans-acting factor (ITAF) that binds specifically to the EV71 5' untranslated region (5'UTR). Interaction sites in both the viral IRES (stem-loops IV and V) and the heterogeneous nuclear ribonucleoprotein K homology (KH) domain of Sam68 protein were further mapped using an electrophoretic mobility shift assay (EMSA) and biotin RNA pulldown assay. More importantly, dual-luciferase (firefly) reporter analysis suggested that overexpression of Sam68 positively regulated IRES-dependent translation of virus proteins. In contrast, both IRES activity and viral protein translation significantly decreased in Sam68 knockdown cells compared with the negative-control cells treated with short hairpin RNA (shRNA). However, downregulation of Sam68 did not have a significant inhibitory effect on the accumulation of the EV71 genome. Moreover, Sam68 was redistributed from the nucleus to the cytoplasm and interacts with cellular factors, such as poly(rC)-binding protein 2 (PCBP2) and poly(A)-binding protein (PABP), during EV71 infection. The cytoplasmic relocalization of Sam68 in EV71-infected cells may be involved in the enhancement of EV71 IRES-mediated translation. Since Sam68 is known to be a RNA-binding protein, these results provide direct evidence that Sam68 is a novel ITAF that interacts with EV71 IRES and positively regulates viral protein translation. The nuclear protein Sam68 is found as an additional new host factor that interacts with the EV71 IRES during infection and could potentially

  1. Consideration of external hazards and multi-source interactions in the USNRC's site level 3 PSA project

    International Nuclear Information System (INIS)

    Siu, N.; Stutzke, M.; Drouin, M.; Tobin, K.; Coyne, K.; Kuritzky, A.

    2014-01-01

    U.S.NRC launched a project in September 2011 to evaluate the total risk at a selected reference NPP (the Vogtle plant) according to the entire initiators, including external hazards. The scope of this risk evaluation was given as 'reactor in all operational modes, including full power, low power and shutdown modes, spent fuel pool and dry cask storage, where all the internal and external hazards are considered'. As part of this study, an Integrated Site Risk Analysis (ISRA) addressing the combinations of and interactions between the different sources of radiological risk (reactors, spent fuel pool (SFP), dry casks) is underway. A number of modeling and implementation challenges were identified. The former include the problem of combinatorial explosion associated with the need to treat multiple sources over extended periods of time

  2. Interactions among the A and T units of an ECF-type biotin transporter analyzed by site-specific crosslinking.

    Directory of Open Access Journals (Sweden)

    Olivia Neubauer

    Full Text Available Energy-coupling factor (ECF transporters are a huge group of micronutrient importers in prokaryotes. They are composed of a substrate-specific transmembrane protein (S component and a module consisting of a moderately conserved transmembrane protein (T component and two ABC ATPase domains (A components. Modules of A and T units may be dedicated to a specific S component or shared by many different S units in an organism. The mode of subunit interactions in ECF transporters is largely unknown. BioMNY, the focus of the present study, is a biotin transporter with a dedicated AT module. It consists of the S unit BioY, the A unit BioM and the T unit BioN. Like all T units, BioN contains two three-amino-acid signatures with a central Arg residue in a cytoplasmic helical region. Our previous work had demonstrated a central role of the two motifs in T units for stability and function of BioMNY and other ECF transporters. Here we show by site-specific crosslinking of pairs of mono-cysteine variants that the Ala-Arg-Ser and Ala-Arg-Gly signatures in BioN are coupling sites to the BioM ATPases. Analysis of 64 BioN-BioM pairs uncovered interactions of both signatures predominantly with a segment of ~13 amino acid residues C-terminal of the Q loop of BioM. Our results further demonstrate that portions of all BioN variants with single Cys residues in the two signatures are crosslinked to homodimers. This finding may point to a dimeric architecture of the T unit in BioMNY complexes.

  3. Interactions among the A and T Units of an ECF-Type Biotin Transporter Analyzed by Site-Specific Crosslinking

    Science.gov (United States)

    Neubauer, Olivia; Reiffler, Christin; Behrendt, Laura; Eitinger, Thomas

    2011-01-01

    Energy-coupling factor (ECF) transporters are a huge group of micronutrient importers in prokaryotes. They are composed of a substrate-specific transmembrane protein (S component) and a module consisting of a moderately conserved transmembrane protein (T component) and two ABC ATPase domains (A components). Modules of A and T units may be dedicated to a specific S component or shared by many different S units in an organism. The mode of subunit interactions in ECF transporters is largely unknown. BioMNY, the focus of the present study, is a biotin transporter with a dedicated AT module. It consists of the S unit BioY, the A unit BioM and the T unit BioN. Like all T units, BioN contains two three-amino-acid signatures with a central Arg residue in a cytoplasmic helical region. Our previous work had demonstrated a central role of the two motifs in T units for stability and function of BioMNY and other ECF transporters. Here we show by site-specific crosslinking of pairs of mono-cysteine variants that the Ala-Arg-Ser and Ala-Arg-Gly signatures in BioN are coupling sites to the BioM ATPases. Analysis of 64 BioN-BioM pairs uncovered interactions of both signatures predominantly with a segment of ∼13 amino acid residues C-terminal of the Q loop of BioM. Our results further demonstrate that portions of all BioN variants with single Cys residues in the two signatures are crosslinked to homodimers. This finding may point to a dimeric architecture of the T unit in BioMNY complexes. PMID:22216173

  4. Xalpha-DVM investigation of double water molecule interactions with active sites of alpha- and beta-subunits of hemoglobin

    Science.gov (United States)

    Yuryeva, Elmira I.

    In this work, the results of Xalpha-discrete variation method calculations of the electronic structure and interatomic parameters of chemical bonding between iron (II) and oxygen molecule with and without extra electrons and protons in active site (AS) of alpha- and beta-subunits of oxyhemoglobin are presented. The Skulachev model of O2 molecule existing in respiration medium in the 2H2O form was used. The introduction of extra electrons does not change considerably the interaction of the iron atom with the O2 oxygen molecule, but strengthens the repulsion in the Fe bond N bonds. In this case, the estimated effective charge of the iron atom is +1.8/1.5e for AS of alpha-/beta-subunits of oxyhemoglobin, and the magnetic moment of iron atoms becomes zero. The deoxygenation effect of the AS of the alpha- and beta-subunits of oxyhemoglobin is due to the ability of extra protons to break down covalent attraction between the iron atom and the nearest oxygen atom and also to weakening of the repulsive component of the covalent Fe bond N interactions.

  5. Staging Henry Fielding: The Author-Narrator in Tom Jones On Screen

    Directory of Open Access Journals (Sweden)

    Eli Løfaldli

    2017-06-01

    Full Text Available As recent adaptation theory has shown, classic-novel adaptation typically sets issues connected to authorship and literal and figurative ownership into play. This key feature of such adaptations is also central to the screen versions of Henry Fielding’s Tom Jones (1749. In much of Fielding’s fiction, the narrator, typically understood as an embodiment of Fielding himself, is a particularly prominent presence. The author-narrator in Tom Jones is no exception: not only is his presence strongly felt throughout the novel, but through a variety of means, ‘The History of Tom Jones, A Foundling’ is also distinctly marked as being under his control and ownership. The two adaptations of Fielding’s novel, a 1963 film and a 1997 television series, both retain the figure of the author-narrator, but differ greatly in their handling of this device and its consequent thematic ramifications. Although the 1963 film de-emphasises Henry Fielding’s status as proprietor of the story, the author-narrator as represented in the film’s voiceover commentary is a figure of authority and authorial control. In contrast, the 1997 adaptation emphasises Fielding’s ownership of the narrative and even includes the author-narrator as a character in the series, but this ownership is undermined by the irreverent treatment to which he is consistently subjected. The representations of Henry Fielding in the form of the author-narrator in both adaptations are not only indicative of shifting conceptions of authorship, but also of the important interplay between authorship, ownership and adaptation more generally.

  6. Replica exchange molecular simulation of Lennard–Jones particles in a two-dimensional confined system

    Directory of Open Access Journals (Sweden)

    Hideo Doi

    2017-05-01

    Full Text Available Confined systems exhibit interesting properties that are applied to the fields of lubrication, adhesion and nanotechnology. The replica exchange molecular simulation method was applied to calculate the phase equilibrium points of Lennard–Jones particles in a two-dimensional confined system. The liquid–solid phase equilibrium points and the solid structure with a dependency of the slit width were determined and the order parameter of the solid structure was analyzed. Such confined systems are shown to be favorable for manipulation of the phase equilibrium points.

  7. Fairy tales? Marion Jones, C.J. Hunter and the framing of doping in American newspapers

    DEFF Research Database (Denmark)

    Pfister, Gertrud Ursula; Gems, Gerald

    2015-01-01

    convicted of doping. The material consists of sport reports about the 2000 Olympic Games in three American newspapers. These Games proved controversial due to the allegations and inquiries of the media (both national and international) regarding doping issues and the prominence of the American athletes...... under suspicion. At the same time, the 2000 Olympics can be considered a watershed in American anti-doping policy. The media portrayed Jones and Hunter as the Beauty and the Beast or Svengali and his victim, using a famous fairy tale and a well-known novel to capture attention, label the protagonists...

  8. Does polar interaction influence medium viscosity? A computer ...

    Indian Academy of Sciences (India)

    Abstract. Molecular dynamics simulations of model liquids interacting via Lennard–Jones (L–J) and. Stockmayer (SM) interactions have been carried out to explore the effects of the longer-ranged dipole–dipole interaction on solvent viscosity and diffusion. Switching on of the dipolar interaction at a fixed density and tem-.

  9. Optmizied random phase approximation for the phase diagram of C ...

    African Journals Online (AJOL)

    Our perturbation/variational approach for the Helmholtz free energy of the C60 molecules is based on the Lennard-Jones intermolecular interaction. We observe that higher accuracy is obtainable by treating all the grid points within the exclusion hole of the pair distribution function as independent variables. Our numerical ...

  10. Molecular beam scattering experiments with polar molecules. 1. Differential elastic scattering of H2+NH3 and H2+H2O

    International Nuclear Information System (INIS)

    Bickes, R.W. Jr.; Scoles, G.; Smith, K.M.

    1974-01-01

    Differential elastic scattering cross sections with well resolved quantum oscillations have been measuremed for the systems H 2 +NH 3 and H 2 +H 2 O. Assuming a spherically symmetric interaction the data show that a simple spherical potential (i.e. Lennard-Jones) does not properly describe the scattering

  11. Application of the cluster variation method to ordering in an interstitital solid solution

    DEFF Research Database (Denmark)

    Pekelharing, Marjon I.; Böttger, Amarante; Somers, Marcel A. J.

    1999-01-01

    The tetrahedron approximation of the cluster variation method (CVM) was applied to describe the ordering on the fcc interstitial sublattice of gamma-Fe[N] and gamma'-Fe4N1-x. A Lennard-Jones potential was used to describe the dominantly strain-induced interactions, caused by misfitting of the N a...

  12. A Computational Study of Rare Gas Clusters: Stepping Stones to the Solid State

    Science.gov (United States)

    Glendening, Eric D.; Halpern, Arthur M.

    2012-01-01

    An upper-level undergraduate or beginning graduate project is described in which students obtain the Lennard-Jones 6-12 potential parameters for Ne[subscript 2] and Ar[subscript 2] from ab initio calculations and use the results to express pairwise interactions between the atoms in clusters containing up to N = 60 atoms. The students use simulated…

  13. Line Tension and Wettability of Nanodrops on Curved Surfaces

    NARCIS (Netherlands)

    Maheshwari, Shantanu; van der Hoef, Martin Anton; Lohse, Detlef

    2016-01-01

    In this work we study the formation of nanodrops on curved surfaces (both convex and concave) by means of molecular dynamics simulations, where the particles interact via a Lennard-Jones potential. We find that the contact angle is not affected by the curvature of the substrate, in agreement with

  14. Peculiarities of the interaction of the restriction endonuclease BspD6I with DNA containing its recognition site.

    Science.gov (United States)

    Abrosimova, Liudmila A; Kubareva, Elena A; Migur, Anzhela Yu; Gavshina, Aleksandra V; Ryazanova, Aleksandra Yu; Norkin, Maxim V; Perevyazova, Tatiana A; Wende, Wolfgang; Hianik, Tibor; Zheleznaya, Liudmila A; Oretskaya, Tatiana S

    2016-09-01

    Nicking endonucleases are enzymes that recognize specific sites in double-stranded DNA and cleave only one strand at a predetermined position. These enzymes are involved in DNA replication and repair; they can also function as subunits of bacterial heterodimeric restriction endonucleases. One example of such a proteins is the restriction endonuclease BspD6I (R.BspD6I) from Bacillus species strain D6, which consists of the large subunit - nicking endonuclease BspD6I (Nt.BspD6I), and the small subunit (ss.BspD6I). Nt.BspD6I can function independently. Similar enzymes are now widely used in numerous biotechnological applications. The aim of this study was to investigate the fundamental properties of two subunits of R.BspD6I and their interdependence in the course of R.BspD6I activity. The binding and hydrolysis of DNA duplexes by R.BspD6I are primary analyzed by gel electrophoresis. To elucidate the difference between Nt.BspD6I interaction with the substrate and product of hydrolysis, the thickness shear mode acoustic method is used. The thermodynamic and kinetic parameters of the Nt.BspD6I interaction with DNA are determined. For the first time we demonstrated that Nt.BspD6I bends the DNA during complex formation. Nt.BspD6I is able to form complexes with the product nicked in the top strand and ss.BspD6I cleaves the bottom strand of the DNA consecutively. Furthermore, the influence of dA methylation in the R.BspD6I recognition site on ss.BspD6I activity is analyzed. The obtained results provide evidence that Nt.BspD6I coordinates the activity of R.BspD6I by strictly coupling of the bottom strand cleavage by ss.BspD6I to the top strand cleavage. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Characterization of the interactions between the active site of a protein tyrosine kinase and a divalent metal activator

    Directory of Open Access Journals (Sweden)

    Ayrapetov Marina K

    2005-11-01

    Full Text Available Abstract Background Protein tyrosine kinases are important enzymes for cell signalling and key targets for anticancer drug discovery. The catalytic mechanisms of protein tyrosine kinase-catalysed phosphorylation are not fully understood. Protein tyrosine kinase Csk requires two Mg2+ cations for activity: one (M1 binds to ATP, and the other (M2 acts as an essential activator. Results Experiments in this communication characterize the interaction between M2 and Csk. Csk activity is sensitive to pH in the range of 6 to 7. Kinetic characterization indicates that the sensitivity is not due to altered substrate binding, but caused by the sensitivity of M2 binding to pH. Several residues in the active site with potential of binding M2 are mutated and the effect on metal activation studied. An active mutant of Asn319 is generated, and this mutation does not alter the metal binding characteristics. Mutations of Glu236 or Asp332 abolish the kinase activity, precluding a positive or negative conclusion on their role in M2 coordination. Finally, the ability of divalent metal cations to activate Csk correlates to a combination of ionic radius and the coordination number. Conclusion These studies demonstrate that M2 binding to Csk is sensitive to pH, which is mainly responsible for Csk activity change in the acidic arm of the pH response curve. They also demonstrate critical differences in the metal activator coordination sphere in protein tyrosine kinase Csk and a protein Ser/Thr kinase, the cAMP-dependent protein kinase. They shed light on the physical interactions between a protein tyrosine kinase and a divalent metal activator.

  16. A quantitative test of Jones NTC beaming theory using CLUSTER constellation

    Directory of Open Access Journals (Sweden)

    S. Grimald

    2007-03-01

    Full Text Available Non-thermal continuum (NTC radiation is, with auroral kilometric radiation (AKR, one of the two electromagnetic emissions generated within the Earth's magnetosphere and radiated into space. The location of the source of NTC has been sought for several decades, with only limited success. The constellation formed by the four CLUSTER spacecraft provides the possibility of triangulation in the vicinity of the source, thus allowing progress in source localisation, while simultaneously revealing the beaming properties of NTC radio sources.

    We present a case event showing two beams localised on opposite sides of the magnetic equator. At any selected frequency, triangulation points to a single region source of small size. Its position is compatible with the range of possible loci of sources predicted by the radio window theory of Jones (1982 in a frame of constraints relaxed from the simple sketch proposed in early works. The analysis of similar observations from the Dynamics Explorer 1 by Jones et al. (1987 enabled the authors to claim validation of the radio window theory. CLUSTER observations, however, reveal a large beaming cone angle projected onto the ecliptic plane, a feature unobservable by Dynamics Explorer which had a different spin axis orientation. According to the radio window theory, such a large observed cone angle can only be formed by a series of point sources, each beaming in a narrow cone angle. This study demonstrates the difficulty of validating NTC linear generation mechanisms using global beaming properties alone.

  17. Safe aftercare following foot ankle surgery: Doing less is more: The Jones dressing cast, part 2.

    Science.gov (United States)

    Gottlieb, Tonio; Klaue, Kaj

    2018-04-01

    There is no universal approach to surgery aftercare among foot and ankle surgeons. Although infections following foot and ankle surgery are rare, soft tissue healing can be jeopardized after extensive and multiple approaches. We defined a precise fixation technique of the foot and ankle in the immediate post-operative phase using what we call "the Jones dressing cast". This technique is a modification of the Jones dressing bandage. In a previous study we compared two groups of patients (N=20/23) who underwent similar reconstructive surgery with the application of the described cast for one week and without. At the two-month follow-up we observed that the group treated with the cast required less pain relief, spent less time in hospital and achieved faster autonomy using crutches (Gottlieb and Klaue, 2013). In this study we considered a group of 45 patients who underwent similar reconstructive procedures to those in the first study and who were treated with the cast for two weeks post-operatively. There was no visual check of the soft tissues before removal of the cast. Unlike the earlier study, the results from this second study were more significant. Revision surgery occurred far less frequently in the group wearing the cast for two weeks. The reduced strain to the soft tissue around the foot due to the cast and less manipulation of the wound dressing decrease complications in the post-operative period. Copyright © 2017 European Foot and Ankle Society. Published by Elsevier Ltd. All rights reserved.

  18. Idiopathic gingival fibromatosis associated with progressive hearing loss: A nonfamilial variant of Jones syndrome

    Directory of Open Access Journals (Sweden)

    Bagavad Gita

    2014-01-01

    Full Text Available Gingival fibromatosis is characterized by gingival tissue overgrowth of a firm and fibrotic nature. The growth is slow and progressive and is drug-induced, idiopathic, or hereditary in etiology. It occurs isolated or frequently as a component of various syndromes. Our patient presented with the complaint of gingival enlargement associated with progressive deafness, characteristic of Jones syndrome. This case report is important and unique since it is the first known one to have a Jones syndrome-like presentation without a family history. A male patient aged 14 years reported with the chief complaint of swelling of gums and progressive hearing loss in both ears for the past one year. There was no family history or history of drug intake. Enlargement was generalized, fibrotic and bulbous, involving the free and attached gingiva, extending up to the middle 1/3 rd of the crown. Investigations such as pure tone audiogram, impedance audiometry, and Tone decay test concluded that there was severe right and moderate left sensorineural hearing loss. The case was diagnosed to be idiopathic, generalized gingival fibromatosis with progressive hearing loss. The gingival overgrowth was managed by gingivectomy and periodic review. The patient was advised to use high occlusion computer generated hearing aids for his deafness as it was not treatable by medicines or surgery. This unique case report once again emphasizes the heterogeneity of gingival fibromatosis, which can present in an atypical manner.

  19. The interactions of 9,10-phenanthrenequinone with glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a potential site for toxic actions.

    Science.gov (United States)

    Rodriguez, Chester E; Fukuto, Jon M; Taguchi, Keiko; Froines, John; Cho, Arthur K

    2005-06-30

    Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the oxidative phosphorylation of glyceraldehyde 3-phosphate to 1,3-diphosphoglycerate, one of the precursors for glycolytic ATP biosynthesis. The enzyme contains an active site cysteine thiolate, which is critical for its catalytic function. As part of a continuing study of the interactions of quinones with biological systems, we have examined the susceptibility of GAPDH to inactivation by 9,10-phenanthrenequinone (9,10-PQ). In a previous study of quinone toxicity, this quinone, whose actions have been exclusively attributed to reactive oxygen species (ROS) generation, caused a reduction in the glycolytic activity of GAPDH under aerobic and anaerobic conditions, indicating indirect and possible direct actions on this enzyme. In this study, the effects of 9,10-PQ on GAPDH were examined in detail under aerobic and anaerobic conditions so that the role of oxygen could be distinguished from the direct effects of the quinone. The results indicate that, in the presence of the reducing agent DTT, GAPDH inhibition by 9,10-PQ under aerobic conditions was mostly indirect and comparable to the direct actions of exogenously-added H2O2 on this enzyme. GAPDH was also inhibited by 9,10-PQ anaerobically, but in a somewhat more complex manner. This quinone, which is not considered an electrophile, inhibited GAPDH in a time-dependent manner, consistent with irreversible modification and comparable to the electrophilic actions of 1,4-benzoquinone (1,4-BQ). Analysis of the anaerobic inactivation kinetics for the two quinones revealed comparable inactivation rate constants (k(inac)), but a much lower inhibitor binding constant (K(i)) for 1,4-BQ. Protection and thiol titration studies suggest that these quinones bind to the NAD+ binding site and modify the catalytic thiol from this site. Thus, 9,10-PQ inhibits GAPDH by two distinct mechanisms: through ROS generation that results in the oxidization of GAPDH thiols, and by an

  20. Probing Interactions of N-Donor Molecules with Open Metal Sites within Paramagnetic Cr-MIL-101: A Solid-State NMR Spectroscopic and Density Functional Theory Study.

    Science.gov (United States)

    Wittmann, Thomas; Mondal, Arobendo; Tschense, Carsten B L; Wittmann, Johannes J; Klimm, Ottokar; Siegel, Renée; Corzilius, Björn; Weber, Birgit; Kaupp, Martin; Senker, Juergen

    2018-02-14

    Understanding host-guest interactions is one of the key requirements for adjusting properties in metal-organic frameworks (MOFs). In particular, systems with coordinatively unsaturated Lewis acidic metal sites feature highly selective adsorption processes. This is attributed to strong interactions with Lewis basic guest molecules. Here we show that a combination of 13 C MAS NMR spectroscopy with state-of-the-art density functional theory (DFT) calculations allows one to unravel the interactions of water, 2-aminopyridine, 3-aminopyridine, and diethylamine with the open metal sites in Cr-MIL-101. The 13 C MAS NMR spectra, obtained with ultrafast magic-angle spinning, are well resolved, with resonances distributed over 1000 ppm. They present a clear signature for each guest at the open metal sites. Based on competition experiments this leads to the following binding preference: water open metal sites, the NMR data offer additional information about the guest and framework dynamics. We expect that our strategy has the potential for probing the binding situation of adsorbate mixtures at the open metal sites of MOFs in general and thus accesses the microscopic interaction mechanisms for this important material class, which is essential for deriving structure-property relationships.

  1. Dietary fat and fiber interactively modulate apoptosis and mitochondrial bioenergetic profiles in mouse colon in a site-specific manner.

    Science.gov (United States)

    Fan, Yang-Yi; Vaz, Frederic M; Chapkin, Robert S

    2017-07-01

    We have demonstrated that the combination of bioactive components generated by fish oil (containing n-3 polyunsaturated fatty acids) and fermentable fiber (leading to butyrate production) act coordinately to protect against colon cancer. This is, in part, the result of an enhancement of apoptosis at the base of the crypt across all stages (initiation, promotion, and progression) of colon tumorigenesis. As mitochondria are key organelles capable of regulating the intrinsic apoptotic pathway and mediating programmed cell death, we investigated the effects of diet on mitochondrial function by measuring mucosal cardiolipin composition, mitochondrial respiratory parameters, and apoptosis in isolated crypts from the proximal and distal colon. C57BL/6 mice (n=15/treatment) were fed one of two dietary fats (corn oil and fish oil) and two fibers (pectin and cellulose) for 4 weeks in a 2×2 factorial design. In general, diet modulated apoptosis and the mucosal bioenergetic profiles in a site-specific manner. The fish/pectin diet promoted a more proapoptotic phenotype - for example, increased proton leak (Pinteraction=0.002) - compared with corn/cellulose (control) only in the proximal colon. With respect to the composition of cardiolipin, a unique phospholipid localized to the mitochondrial inner membrane where it mediates energy metabolism, fish oil feeding indirectly influenced its molecular species with a combined carbon number of C68 or greater, suggesting compensatory regulation. These data indicate that dietary fat and fiber can interactively modulate the mitochondrial metabolic profile and thereby potentially modulate apoptosis and subsequent colon cancer risk.

  2. Multi-band scattering of two atoms in a one-dimensional lattice with on-site interactions

    Science.gov (United States)

    Rittenhouse, Seth; Giannakeas, Panagiotis; Mehta, Nirav

    2017-04-01

    We examine a system of two-particles confined to a one-dimensional lattice described by a multi-band Hubbard model with on-site interactions. Asymptotically the two particles are relegated to remain in bands that are energetically accessible. However, when the particles occupy the same state, they can virtually scatter into bands that are energetically closed. We incorporate this virtual scattering by solving the Lippmann-Schwinger equation for the reactance matrix (K-matrix) using a lattice Green's operator. The resulting formula for the K-matrix for open band scattering bears a striking similarity to that which arrises from channel closing formulas in standard multi-channel scattering theory. We then apply this formula for two-body scattering in the lowest and first excited bands within a two band approximation. Within this approximation, virtual scattering into closed bands can create scattering resonances in the presence of bound states attached to closed bands in analogy to Feshbach or confinement induced resonances. This work was partially funded by Grants from the NSF and a the Research Corporation for Science Advancement.

  3. Holocene environmental and parasequence development of the St. Jones Estuary, Delaware (USA): Foraminiferal proxies of natural climatic and anthropogenic change

    Science.gov (United States)

    Leorri, E.; Martin, R.; McLaughlin, P.

    2006-01-01

    The benthic foraminiferal record of marshes located along western Delaware Bay (St. Jones Estuary, USA) reflects the response of estuaries to sea-level and paleoclimate change during the Holocene. System tracts are recognized and within them parasequences based on sedimentological and foraminiferal assemblages identification. The parasequences defined by foraminiferal assemblages appear correlative with rapid Holocene climate changes that are of worldwide significance: 6000-5000, 4200-3800, 3500-2500, 1200-1000, and 600??cal years BP. Following postglacial sea-level rise, modern subestuaries and marshes in the region began to develop between 6000 and 4000??years BP, depending on their proximity to the mouth of Delaware Bay and coastal geomorphology. Initial sediments were fluvial in origin, with freshwater marshes established around 4000??years BP. The subsequent sea-level transgression occurred sufficiently slowly that freshwater marshes alternated with salt marshes at the same sites to around 3000??years BP. Locally another two transgressions are identified at 1800 and 1000??years BP respectively. Marine influence increased in the estuaries until 600??years BP (Little Ice Age), when regression occurred. Sea-level began to rise again during the mid-19th Century at the end of the Little Ice Age, when marshes became established. The presence of a sand lens in the upper and middle estuary and the reduction in the number of tests in the top samples in cores from the same area also suggest an anthropogenic influence. The estuary infill resulted in a sharp transgressive sequence, represented by salt marsh foraminiferal assemblages in the upper part of the cores. The increase in marsh foraminifera in both areas suggests an increase in marine influence that might be due to the transgression beginning at the end of the Little Ice Age about 150-180??years ago coupled with anthropogenic straightening of the channel in 1913. ?? 2006 Elsevier B.V. All rights reserved.

  4. Identification of the site of human mannan-binding lectin involved in the interaction with its partner serine proteases: the essential role of Lys55

    DEFF Research Database (Denmark)

    Teillet, F; Lacroix, M; Thiel, Steffen

    2007-01-01

    Mannan-binding lectin (MBL) is an oligomeric lectin that binds neutral carbohydrates on pathogens, forms complexes with MBL-associated serine proteases (MASP)-1, -2, and -3 and 19-kDa MBL-associated protein (MAp19), and triggers the complement lectin pathway through activation of MASP-2. To ident...... centered on residue Lys(55), which may form an ionic bond representing the major component of the MBL-MASP interaction. The binding sites for MASP-2/MAp19 and MASP-1/3 have common features but are not strictly identical........ To identify the MASP binding site(s) of human MBL, point mutants targeting residues C-terminal to the hinge region were produced and tested for their interaction with the MASPs and MAp19 using surface plasmon resonance and functional assays. Mutation Lys(55)Ala abolished interaction with the MASPs and MAp19...... and prevented formation of functional MBL-MASP-2 complexes. Mutations Lys(55)Gln and Lys(55)Glu abolished binding to MASP-1 and -3 and strongly inhibited interaction with MAp19. Conversely, mutation Lys(55)Arg abolished interaction with MASP-2 and MAp19, but only weakened interaction with MASP-1 and -3...

  5. Nephrotoxicity of Bence-Jones proteins: correlation with endocytosis by BHK cells and intracellular movement

    Directory of Open Access Journals (Sweden)

    Ana Lucia Nicastri

    2001-06-01

    Full Text Available The aim of this investigation was to evaluate the endocytosis of two Bence-Jones proteins by renal cells in order to elucidate the interference of their physical and chemical characteristics on nephrotoxicity. Bence-Jones proteins (AK and GL were purified and isolated from the urine of two patients with multiple myeloma. The isotype of both proteins was characterised as being human monoclonal lambda light chain. The AK protein presented mainly an Ip>7.0, a high content of galactose and a low amount of sialic acid molecules. On the other hand, the GL protein presented a single band with an Ip of 4.3, a higher level of sialic acid and a reduced amount of galactose, in comparison with the AK protein. Baby Hamster Kidney (BHK cells were maintained in culture in bottles at 37ºC, using DMEM culture media supplemented with 10% of calf serum with a pH of 7.4. Once the monolayer was observed to be confluent, the BHK cells were incubated with the two proteins, dissolved in a serum-free medium for 1, 5, 15, 30, 60 minutes and 24 hours. Control cells were established omitting the incubation with Bence-Jones proteins, but maintaining all of the other conditions. After, this the cells were washed, trypsinised, centrifuged and fixed in a solution of 4% paraformaldehyde and 0.5% glutaraldehyde on a 0.1 M, pH 7.4 phosphate buffer. Cells were processed for immunocytochemical reactions by using protein A coupled with colloidal gold and further silver enhancement. Semi-thin sections of the pellets were obtained and submitted to the cytochemical reactions. Detection of labelling was made by using light microscopy. It was observed that GL protein tended to be directed towards a perinuclear position, whereas the AK protein tended to suffer lysosomal deviation, suggesting that there is a direct contribution of physical and chemical characteristics on intracellular direction taken by Bence-Jones proteins.O objetivo deste trabalho foi avaliar a endocitose de duas prote

  6. Interaction of alpha-conotoxin ImII and its analogs with nicotinic receptors and acetylcholine-binding proteins: additional binding sites on Torpedo receptor

    NARCIS (Netherlands)

    Kasheverov, I.E.; Zhmak, M.N.; Fish, A.; Rucktooa, P.; Khruschov, A.Y.; Osipov, A.V.; Ziganshin, R.H.; D'Hoedt, D.; Bertrand, D.; Sixma, T.K.; Smit, A.B.; Tsetlin, V.I.

    2009-01-01

    α-Conotoxins interact with nicotinic acetylcholine receptors (nAChRs) and acetylcholine-binding proteins (AChBPs) at the sites for agonists/competitive antagonists. α-Conotoxins blocking muscle-type or α7 nAChRs compete with α-bungarotoxin. However, α-conotoxin ImII, a close homolog of the α7

  7. Reference interaction site model investigation of homonuclear hard dumbbells under simple fluid theory closures: comparison with Monte Carlo simulations.

    Science.gov (United States)

    Munaò, G; Costa, D; Caccamo, C

    2009-04-14

    We revisit the thermodynamic and structural properties of fluids of homonuclear hard dumbbells in the framework provided by the reference interaction site model (RISM) theory of molecular fluids. Besides the previously investigated Percus-Yevick (PY) approximation, we test the accuracy of other closures to the RISM equations, imported from the theory of simple fluids; specifically, we study the hypernetted chain (HNC), the modified HNC (MHNC) and, less extensively, the Verlet approximations. We implement our approach for models characterized by several different elongations, up to the case of tangent diatomics, and investigate the whole fluid density range. The theoretical predictions are assessed against Monte Carlo simulations, either available from literature or newly generated by us. The HNC and PY equations of state, calculated via different routes, share on the whole the same level of accuracy. The MHNC is applied by enforcing an internal thermodynamic consistency constraint, leading to good predictions for the equation of state as the elongation of the dumbbell increases. As for the radial distribution function, the MHNC appears superior to other theories, especially for tangent diatomics in the high density limit; the PY approximation is better than the HNC and Verlet closures in the high density or elongation regime. Our structural analysis is supplemented by an accurate inversion procedure to reconstruct from Monte Carlo data and RISM the "exact" direct correlation function. In agreement with such calculations and consistent with the forecast of rigorous diagrammatic analysis, all theories predict the occurrence in the direct correlation function of a first cusp inside the dumbbell core and (with the obvious exception of the PY) of a second cusp outside; the cusps' heights are also qualitatively well reproduced by the theories, except at high densities.

  8. Differential denaturation of a crystalline Bence-Jones type cryoprotein as monitored by fluorescence.

    Science.gov (United States)

    Finazzi Agrò, A; Crifò, C; Natali, P G; Chersi, A

    1978-01-01

    1) A Bence-Jones type protein (Cryo-Ver) showing the cold precipitation phenomenon has an extremely low intrinsic fluorescence when excited at 280-295 nm. 2) This fluorescence increases considerably upon denaturation of the molecule by heat or guanidine hydrochloride. Guanidine is about twice as effective as heat in terms of fluorescence yield. 3) The heat-denatured protein is still reactive with anti-cryoVer antibodies, at variance with the guanidine-treated samples. 4) Since the protein contains two tryptophans per mole, one in the constant portion of the molecule, the other in the variable region, it is proposed that heat treatment affects only the variable region, which seems involved in the cryoprecipitation phenomenon.

  9. The Value of Multivariate Model Sophistication: An Application to pricing Dow Jones Industrial Average options

    DEFF Research Database (Denmark)

    Rombouts, Jeroen V.K.; Stentoft, Lars; Violante, Francesco

    innovation for a Laplace innovation assumption improves the pricing in a smaller way. Apart from investigating directly the value of model sophistication in terms of dollar losses, we also use the model condence set approach to statistically infer the set of models that delivers the best pricing performance.......We assess the predictive accuracy of a large number of multivariate volatility models in terms of pricing options on the Dow Jones Industrial Average. We measure the value of model sophistication in terms of dollar losses by considering a set 248 multivariate models that differer...... in their specification of the conditional variance, conditional correlation, and innovation distribution. All models belong to the dynamic conditional correlation class which is particularly suited because it allows to consistently estimate the risk neutral dynamics with a manageable computational effort in relatively...

  10. John Paul Jones: An Overlooked Autopsy Finding that May Explain His Terminal Illness.

    Science.gov (United States)

    Hamrell, Burt B

    2016-03-01

    A finding in the autopsy of John Paul Jones, the American Revolutionary War naval hero, may explain his terminal illness. During his last 2 years, he had a persistent productive cough and dyspnea. Ten days before death, he developed rapidly progressive dependent edema and ascites. He died in France in 1792. His body, preserved in alcohol in a lead coffin, was, in 1905, removed to the United States. Glomerulonephritis was noted on an autopsy, performed in France, but there was no comment then or since about ventricular wall thickness being the same in both ventricles at 5-6 mm. Hypertrophy and dilatation with biventricular failure followed by tissue shrinkage during 113 years in alcohol could have resulted in these ventricular wall findings. Systemic hypertension and left ventricular failure are consistent with his respiratory symptoms complicated perhaps by pulmonary emboli, right ventricular failure with tricuspid regurgitation, peripheral congestion, and jaundice. © 2015 American Academy of Forensic Sciences.

  11. Sufism in Writings: Mysticism and Spirituality in the Love Poems of Salleh Ben Joned

    Directory of Open Access Journals (Sweden)

    Nadiah Abdol Ghani

    2013-07-01

    Full Text Available Salleh Ben Joned is seen as a notorious figure in the Malaysian literary scene as a result of his use of profanities and vulgarities, interlacing them into ideas or texts that are seen to be sacred by the society. He is most infamously known for his vivid descriptions of carnal images and sex and its vicissitudes in his poems, thus earning the accusations of being an apostate and his works to be blasphemous. This essay is an attempt at reappraising his love poetry, by explicating the poems using the doctrine of Sufism and its central theme of love and the Beloved/Divine. My view is that his poems are not just describing the ‘profane’ act of sexual copulation, but rather would be more apt in describing a devotee’s spiritual journey towards finding his Beloved or the Divine.

  12. The mechanisms of substrates interaction with the active site of Mycobacterium tuberculosis tyrosyl-tRNA synthetase studied by molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Mykuliak V. V.

    2014-03-01

    Full Text Available Aim. To study the mechanisms of substrates interaction with the active site of Mycobacterium tuberculosis tyrosyl-tRNA synthetase (MtTyrRS. Methods. Complexes of MtTyrRS with tyrosine, ATP and tyrosyl adenylate were constructed by superposition of the MtTyrRS structure and crystallographic structures of bacterial TyrRS. All complexes of MtTyrRS with substrates were investigated by molecular dynamics (MD simulations in solution. Results. It was shown the formation of network of hydrogen bonds between substrates and the MtTyrRS active center, which were stable in the course of MD simulations. ATP binds in the active site both by hydrogen bonds and via electrostatic interactions with Lys231 and Lys234 of catalytic KFGKS motif. Conclusions. The L-tyrosine binding site in the enzyme active site is negatively charged, whereas the ATP binding site contains positive Lys231 and Lys234 residues of catalytic KFGKS motif. The occupancy of H-bonds between substrates and the enzyme evidences a significant conformational mobility of the active site.

  13. 77 FR 17530 - Order Granting an Application of Edward Jones & Co. LLP Exemption From Exchange Act Section 11(d...

    Science.gov (United States)

    2012-03-26

    ...'') requested that the Securities and Exchange Commission (``Commission'') issue to Edward Jones an exemption... subject to the conditions contained in this order, is exempt from the new issue lending restriction of... SECURITIES AND EXCHANGE COMMISSION [Release No. 34-66624] Order Granting an Application of Edward...

  14. An entropy based analysis of the relationship between the DOW JONES Index and the TRNA Sentiment series

    NARCIS (Netherlands)

    D.E. Allen (David); M.J. McAleer (Michael); A.K. Singh (Abhay)

    2016-01-01

    textabstractThis paper features an analysis of the relationship between the DOW JONES Industrial Average Index (DJIA) and a sentiment news series using daily data obtained from the Thomson Reuters News Analytics (TRNA)1 provided by SIRCA (The Securities Industry Research Centre of the Asia Pacic).

  15. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions...... including puppetry and dance. However, the aesthetics of these traditions vary across cultures and carry different associative and interpretive meanings. Puppetry offers a useful frame for understanding the relationship between abstract and imitative gestures and behavior, and instantiates the complex...... interaction between a human operator and an artificial actor or agent. We can apply insights from puppetry to develop culturally-aware robots. Here we describe the development of a robotic marionette theatre wherein robotic controllers assume the role of human puppeteers. The system has been built, tested...

  16. Interactions

    DEFF Research Database (Denmark)

    The main theme of this anthology is the unique interaction between mathematics, physics and philosophy during the beginning of the 20th century. Seminal theories of modern physics and new fundamental mathematical structures were discovered or formed in this period. Significant physicists such as ......The main theme of this anthology is the unique interaction between mathematics, physics and philosophy during the beginning of the 20th century. Seminal theories of modern physics and new fundamental mathematical structures were discovered or formed in this period. Significant physicists...... such as Lorentz and Einstein as well as mathematicians such as Poincare, Minkowski, Hilbert and Weyl contributed to this development. They created the new physical theories and the mathematical disciplines that play such paramount roles in their mathematical formulations. These physicists and mathematicians were...... also key figures in the philosophical discussions of nature and science - from philosophical tendencies like logical empiricism via critical rationalism to various neo-Kantian trends....

  17. Studies of infiltration and lead-soil interactions at the Radioactive Waste Management Site in Area 5 of the Nevada Test Site

    International Nuclear Information System (INIS)

    Case, C.M.; Davis, J.O.; Heidker, J.C.; Whitbeck, M.R.

    1992-07-01

    Several studies were conducted to investigate the possibility of buried lead being transported by water in the unsaturated zone at the Area 5 Radioactive Waste Management Site (RWMS) on the Nevada Test Site. All involved soil from a 37-m soil core collected at the RWMS. The core consisted primarily of sand and small pebbles, with occasional layers of loose rocks. Few buried soil horizons were observed, and the core showed no evidence of a carbonate layer that would act as a barrier to infiltration. Samples chosen from various depths in the soil core were analyzed chemically. Calcium and sulfate occurred in a prominent layer about 5 m below the surface. The concentration of soluble carbonate increased gradually with depth, while chloride concentrations decreased. Lead concentrations ranged from 1 to 2 mg/kg. Additional data from the soil core were combined with results of earlier field infiltration studies at two sites near the RWMS to estimate flow velocities for water in the unsaturated zone. Under normal (dry) conditions, the degree of saturation is so small that gravity drainage does not occur; water moves by vapor transport and capillary action. Significant water movement occurs only if the soil is at or near saturation. The results suggest that even continuously ponded water at the RWMS would take several months to infiltrate to the water table. Seven samples from the soil core were tested for their ability to adsorb lead. All took up lead with about the same intensity and capacity. Adsorption of lead by insoluble carbonate minerals and precipitation of lead by soluble carbonate in the soil at the RWMS should provide a barrier to lead migration. Finally, measurements were made of the corrosion rates of lead and steel in contact with soil samples from the core. Corrosion rates generally increased with increasing soil saturation at all depths. Under ambient soil conditions at the RWMS, corrosion rates would be low

  18. Frustration in an exactly solvable mixed-spin Ising model with bilinear and three-site four-spin interactions on a decorated square lattice

    Energy Technology Data Exchange (ETDEWEB)

    Jaščur, M., E-mail: michal.jascur@upjs.sk [Department of Theoretical Physics and Astrophysics, Institute of Physics, P.J. Šafárik University in Košice, Park Angelinum 9, 040 01 Košice (Slovakia); Štubňa, V., E-mail: viliamstubna@yahoo.com [Department of Theoretical Physics and Astrophysics, Institute of Physics, P.J. Šafárik University in Košice, Park Angelinum 9, 040 01 Košice (Slovakia); Szałowski, K., E-mail: kszalowski@uni.lodz.pl [Department of Solid State Physics, Faculty of Physics and Applied Informatics, University of Łódź, ul. Pomorska 149/153, 90-236 Łódź (Poland); Balcerzak, T., E-mail: tadeusz.balcerzak@gmail.com [Department of Solid State Physics, Faculty of Physics and Applied Informatics, University of Łódź, ul. Pomorska 149/153, 90-236 Łódź (Poland)

    2016-11-01

    Competitive effects of so-called three-site four-spin interactions, single ion anisotropy and bilinear interactions is studied in the mixed spin-1/2 and spin-1 Ising model on a decorated square lattice. Exploring the decoration–iteration transformation, we have obtained exact closed-form expressions for the partition function and other thermodynamic quantities of the model. From these relations, we have numerically determined ground-state and finite-temperature phase diagrams of the system. We have also investigated temperature variations of the correlation functions, internal energy, entropy, specific heat and Helmholtz free energy of the system. From the physical point of view, the most interesting result represents our observation of a partially ordered ferromagnetic or phase in the system with zero bilinear interactions. It is remarkable, that due to strong frustrations disordered spins survive in the system even at zero temperature, so that the ground state of the system becomes macroscopically degenerate with non-zero entropy. Introduction of arbitrarily small bilinear interaction completely removes degeneracy and the entropy always goes to zero at the ground state. - Highlights: • Mixed-spin Ising model with three-site four-spin interactions has been studied. • Original phases have been observed in the system with pure multi-spin interactions. • Non-zero entropy has been found at zero absolute temperature.

  19. Analysis of multi-site drug-protein interactions by high-performance affinity chromatography: Binding by glimepiride to normal or glycated human serum albumin.

    Science.gov (United States)

    Matsuda, Ryan; Li, Zhao; Zheng, Xiwei; Hage, David S

    2015-08-21

    High-performance affinity chromatography (HPAC) was used in a variety of formats to examine multi-site interactions between glimepiride, a third-generation sulfonylurea drug, and normal or in vitro glycated forms of the transport protein human serum albumin (HSA). Frontal analysis revealed that glimepiride interacts with normal HSA and glycated HSA at a group of high affinity sites (association equilibrium constant, or Ka, 9.2-11.8×10(5)M(-1) at pH 7.4 and 37°C) and a group of lower affinity regions (Ka, 5.9-16×10(3)M(-1)). Zonal elution competition studies were designed and carried out in both normal- and reversed-role formats to investigate the binding by this drug at specific sites. These experiments indicated that glimepiride was interacting at both Sudlow sites I and II. Allosteric effects were also noted with R-warfarin at Sudlow site I and with tamoxifen at the tamoxifen site on HSA. The binding at Sudlow site I had a 2.1- to 2.3-fold increase in affinity in going from normal HSA to the glycated samples of HSA. There was no significant change in the affinity for glimepiride at Sudlow site II in going from normal HSA to a moderately glycated sample of HSA, but a slight decrease in affinity was seen in going to a more highly glycated HSA sample. These results demonstrated how various HPAC-based methods can be used to profile and characterize multi-site binding by a drug such as glimepiride to a protein and its modified forms. The information obtained from this study should be useful in providing a better understanding of how drug-protein binding may be affected by glycation and of how separation and analysis methods based on HPAC can be employed to study systems with complex interactions or that involve modified proteins. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Competitive interaction of agonists and antagonists with 5-HT3 recognition sites in membranes of neuroblastoma cells labelled with [3H]ICS 205-930

    International Nuclear Information System (INIS)

    Hoyer, D.; Neijt, H.C.; Karpf, A.

    1989-01-01

    [3H]ICS 205-930 labelled 5-HT3 recognition sites in membranes prepared from murine neuroblastoma N1E-115 cells. Binding was rapid, reversible, saturable and stereoselective to an apparently homogeneous population of sites. Kinetic studies revealed that agonists and antagonists produced a monophasic dissociation reaction of [3H]ICS 205-930 from its recognition sites. The dissociation rate constant of the radioligand was similar whether the dissociation was induced by an agonist or an antagonist. Competition studies carried out with agonists and antagonists also suggested the presence of a homogeneous population of [3H]ICS 205-930 recognition sites. Competition curves were best fit for a 1 site model. [3H]ICS 205-930 binding sites displayed the pharmacological profile of a 5-HT3 receptor. The interactions of agonists and antagonists with [3H]ICS 205-930 recognition sites were apparently competitive in nature, as demonstrated in kinetic and equilibrium experiments. In saturation experiments carried out with [3H]ICS 205-930 in the presence and the absence of unlabelled agonists and antagonists, apparent Bmax values were not reduced whereas apparent Kd values were increased in the presence of competing ligands. There was a good agreement between apparent pKB values calculated for the competing ligands in saturation experiments and pKd values calculated from competition experiments. The present data demonstrate that [3H]ICS 205-930 labels a homogeneous population of sites at which agonists and antagonists interact competitively

  1. Genotype-environment interaction and the number of test sites for the genetic improvement of rubber trees (Hevea in São Paulo State, Brazil

    Directory of Open Access Journals (Sweden)

    Costa Reginaldo Brito da

    2000-01-01

    Full Text Available The present study quantifies the possible genotype-environment interactions and determines the ideal number of test sites for rubber trees [Hevea brasiliensis (Willd ex Adr. de Juss. Muell Arg] in the plateau region of São Paulo State. The study was based on the genetic correlation among progenies at three different sites and on estimates of genetic gains with indirect selection of rubber trees. Twenty-two half-sib progenies were planted at the Jaú, Pindorama and Votuporanga experimental stations using random blocks with five replications and 10 plants per plot. At three years of age, the plants were evaluated for their total number of latex ring vessels (NR, rubber production (RP, bark thickness (BT and girth (SG. There was significant genetic variability in the characters RP, SG and BT, mainly among progenies from Pindorama and Votuporanga. The effects of genotype-site interactions were significant for RP and SG. The finding of significant interactions was not a complicating factor because of the large genetic correlation detected. These results indicate that the use of two sites is more profitable when the gains in efficiency of selection are greater than 10%. Thus, Pindorama and Votuporanga will satisfactorily attend the studied region.

  2. Vadose zone attenuation of organic compounds at a crude oil spill site - Interactions between biogeochemical reactions and multicomponent gas transport

    Science.gov (United States)

    Molins, S.; Mayer, K.U.; Amos, R.T.; Bekins, B.A.

    2010-01-01

    Contaminant attenuation processes in the vadose zone of a crude oil spill site near Bemidji, MN have been simulated with a reactive transport model that includes multicomponent gas transport, solute transport, and the most relevant biogeochemical reactions. Dissolution and volatilization of oil components, their aerobic and anaerobic degradation coupled with sequential electron acceptor consumption, ingress of atmospheric O2, and the release of CH4 and CO2 from the smear zone generated by the floating oil were considered. The focus of the simulations was to assess the dynamics between biodegradation and gas transport processes in the vadose zone, to evaluate the rates and contributions of different electron accepting processes towards vadose zone natural attenuation, and to provide an estimate of the historical mass loss. Concentration distributions of reactive (O2, CH4, and CO2) and non-reactive (Ar and N2) gases served as key constraints for the model calibration. Simulation results confirm that as of 2007, the main degradation pathway can be attributed to methanogenic degradation of organic compounds in the smear zone and the vadose zone resulting in a contaminant plume dominated by high CH4 concentrations. In accordance with field observations, zones of volatilization and CH4 generation are correlated to slightly elevated total gas pressures and low partial pressures of N2 and Ar, while zones of aerobic CH4 oxidation are characterized by slightly reduced gas pressures and elevated concentrations of N2 and Ar. Diffusion is the most significant transport mechanism for gases in the vadose zone; however, the simulations also indicate that, despite very small pressure gradients, advection contributes up to 15% towards the net flux of CH4, and to a more limited extent to O2 ingress. Model calibration strongly suggests that transfer of biogenically generated gases from the smear zone provides a major control on vadose zone gas distributions and vadose zone carbon

  3. Life on the edge in eastern Alaska: Basal Ordovician(Tremadocian), platform-margin faunas of the Jones Ridge Formation

    Science.gov (United States)

    Taylor, J. F.; Allen, T. J.; Repetski, John E.; Strauss, J. V.; Irwin, S. J.

    2015-01-01

    As the most fossiliferous and least deformed succession of unequivocally Laurentian lower Paleozoic strata in Alaska, the Jones Ridge Limestone has provided critical data for numerous stratigraphic studies (e. g. Palmer 1968; Harris et al. 1995; Dumoulin et al. 2002; Dumoulin and Harris 2012) focused on the Cambrian and Ordovician of northwestern North America/northeastern Laurentia (Figure 1). The Jones Ridge faunas are also significant in having provided the type material for some of the widespread and biostratigraphically useful latest Furongian and (perhaps) earliest Tremadocian species described by Kobayashi (1936) and Palmer (1968). Unfortunately, some of those taxa were based on very limited material for which, in the earlier study in particular, no detailed information regarding locality or stratigraphic horizon was provided. The limited amount of information and material available for study from Jones Ridge results largely from its remote location on the Yukon-Alaska boundary approximately 25km north of Eagle, Alaska, which renders it accessible only by helicopter. Parts of three field seasons (2010, 2011, and 2014) were invested in re-description and intensive sampling of the type section of the Jones Ridge Formation in order to produce an integrated and greatly refined set of biostratigraphic, chemostratigraphic, and sedimentological data. The new data support the interpretation offered by Palmer (1968) of the Jones Ridge strata as the product of deposition in outermost platform to upper slope environments offered by Palmer (1968) on the basis of taxonomic content of the faunas and close proximity of deep water units of equivalent age a very short distance to the southwest.

  4. Family-site interaction in Pinus radiata: implications for progeny testing strategy and regionalised breeding in New Zealand.

    Science.gov (United States)

    G.R. Johnson; R.D. Brudon

    1990-01-01

    A progeny test of 170 open-pollinated families from second-generation plus trees of Pinus radiata was established on four sites in New Zealand in 1981. Two test sites were on volcanic purnice soils in the Central North Island region and two were on phosphate-retentive clay soils in the Northland region.Assessments of volume growth, stem straightness, mal-...

  5. A combined spectroscopic and molecular docking study on site selective binding interaction of Toluidine blue O with Human and Bovine serum albumins

    Energy Technology Data Exchange (ETDEWEB)

    Selva Sharma, Arumugam [Department of Chemistry, Bharathiar University, Coimbatore 641046 (India); Anandakumar, Shanmugam [Department of Bioinformatics, Bharathiar University, Coimbatore 641046 (India); Ilanchelian, Malaichamy, E-mail: chelian73@yahoo.com [Department of Chemistry, Bharathiar University, Coimbatore 641046 (India)

    2014-07-01

    In the present investigation the interaction of a biologically active photodynamic therapeutic agent Toluidine blue O (TBO) with Serum albumins viz Human serum albumin (HSA) and Bovine serum albumin (BSA) was studied using absorption, emission, circular dichroism spectroscopy and molecular docking experiments. The emission titration experiments between HSA/BSA and TBO revealed the existence of strong interactions between TBO and the proteins. The site competitive experiment of HSA and BSA showed that the primary binding site of TBO is located in site I of HSA/BSA involving hydrophobic, hydrogen bonding and electrostatic interaction. To ascertain the results of site competitive experiments, molecular docking was utilized to characterize the binding models of TBO–HSA/BSA complexes. From the molecular docking studies, free energy calculations were undertaken to examine the energy contributions and the role of various amino acid residues of HSA/BSA in TBO binding. The existence of Forster Resonance Energy Transfer (FRET) between the ligand and the protein was utilized to calculate the donor–acceptor distance of TBO and protein. The TBO induced conformational changes of HSA/BSA was established using synchronous emission, three dimensional emission and circular dichroism studies. - Highlights: • Site selective binding interaction of TBO with HSA and BSA were investigated. • TBO quenches the intrinsic fluorescence of HSA/BSA by static quenching process. • Computational studies of TBO with HSA/BSA substantiate the experimental findings. • 3D and CD spectral studies of TBO–HSA/BSA revealed structural changes in protein. • The distance (r) between TBO and HSA/BSA were estimated from FRET theory.

  6. Properties of a soft-core model of methanol: An integral equation theory and computer simulation study

    Science.gov (United States)

    Huš, Matej; Munaò, Gianmarco; Urbic, Tomaz

    2014-01-01

    Thermodynamic and structural properties of a coarse-grained model of methanol are examined by Monte Carlo simulations and reference interaction site model (RISM) integral equation theory. Methanol particles are described as dimers formed from an apolar Lennard-Jones sphere, mimicking the methyl group, and a sphere with a core-softened potential as the hydroxyl group. Different closure approximations of the RISM theory are compared and discussed. The liquid structure of methanol is investigated by calculating site-site radial distribution functions and static structure factors for a wide range of temperatures and densities. Results obtained show a good agreement between RISM and Monte Carlo simulations. The phase behavior of methanol is investigated by employing different thermodynamic routes for the calculation of the RISM free energy, drawing gas-liquid coexistence curves that match the simulation data. Preliminary indications for a putative second critical point between two different liquid phases of methanol are also discussed. PMID:25362323

  7. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions...... including puppetry and dance. However, the aesthetics of these traditions vary across cultures and carry different associative and interpretive meanings. Puppetry offers a useful frame for understanding the relationship between abstract and imitative gestures and behavior, and instantiates the complex...

  8. Identification of binding sites in Huntingtin for the Huntingtin Interacting Proteins HIP14 and HIP14L.

    Directory of Open Access Journals (Sweden)

    Shaun S Sanders

    Full Text Available Huntington disease is an adult onset neurodegenerative disease characterized by motor, cognitive, and psychiatric dysfunction, caused by a CAG expansion in the HTT gene. Huntingtin Interacting Protein 14 (HIP14 and Huntingtin Interacting Protein 14-like (HIP14L are palmitoyl acyltransferases (PATs, enzymes that mediate the post-translational addition of long chain fatty acids to proteins in a process called palmitoylation. HIP14 and HIP14L interact with and palmitoylate HTT and are unique among PATs as they are the only two that have an ankyrin repeat domain, which mediates the interaction between HIP14 and HTT. These enzymes show reduced interaction with and palmitoylation of mutant HTT, leading to increased mutant HTT inclusion formation and toxicity. The interaction between HIP14 and HTT goes beyond that of only an enzyme-substrate interaction as HTT is essential for the full enzymatic activity of HIP14. It is important to further understand and characterize the interactions of HTT with HIP14 and HIP14L to guide future efforts to target and enhance this interaction and increase enzyme activity to remediate palmitoylation of HTT and their substrates, as well as to understand the relationship between the three proteins. HIP14 and HIP14L have been previously shown to interact with HTT amino acids 1-548. Here the interaction of HIP14 and HIP14L with N- and C-terminal HTT 1-548 deletion mutations was assessed. We show that HTT amino acids 1-548 were sufficient for full interaction of HTT with HIP14 and HIP14L, but partial interaction was also possible with HTT 1-427 and HTT 224-548. To further characterize the binding domain we assessed the interaction of HIP14-GFP and HIP14L-GFP with 15Q HTT 1-548Δ257-315. Both enzymes showed reduced but not abolished interaction with 15Q HTT 1-548Δ257-315. This suggests that two potential binding domains exist, one around residues 224 and the other around 427, for the PAT enzymes HIP14 and HIP14L.

  9. How does litter quality and site heterogeneity interact on decomposer food webs of a semi-natural forest?

    DEFF Research Database (Denmark)

    Strandmark, Lisa Bjørnlund; Christensen, Søren

    2005-01-01

    The relative importance of litter quality and site heterogeneity on population dynamics of decomposer food webs was investigated in a semi-natural mixed deciduous forest in Denmark. Litterbags containing beech or ash leaves were placed in four plots. Plots were located within gaps and under closed...... at the end of the study period. At the first sampling, where bacterial activity prevailed, the relative abundance of the two dominant bacterial-feeders, Rhabditidae (fast growing) and Plectus spp. (slower growing), depended more on site than litter type. At the second sampling where fungal activity became...... in the decomposer food web, site effects were also detected and nematode functional groups responded more to site than to litter quality early on in the decomposition process....

  10. Interactions of a new alpha-aminophosphinic derivative inside the active site of TLN (thermolysin): a model for zinc-metalloendopeptidase inhibition.

    Science.gov (United States)

    Selkti, Mohamed; Tomas, Alain; Gaucher, Jean-François; Prangé, Thierry; Fournié-Zaluski, Marie-Claude; Chen, Huixiong; Roques, Bernard-Pierre

    2003-07-01

    A new alpha-aminophosphinic compound able to inhibit both zinc-containing exopeptidases and endopeptidases has been crystallized with TLN as a model in order to investigate the mode of zinc recognition by the phosphinic moiety and to evaluate the potential role of the free alpha-amino group in the formation of enzyme-inhibitor complexes. In addition to the main interactions between the backbone of the inhibitor and the enzyme active site, it is observed that the phosphinic group acts as a distorted bidentate ligand for the zinc ion, while the free alpha-amino function does not directly participate in interactions within the active site. Association of the present data and the K(i) values of various analogues of the inhibitor towards TLN and neprilysin suggests differences in the hydrophobicity of the S(1)-S(2) domains of the enzymes. This could be taken into account in the design of selective inhibitors.

  11. The importance of the on-site electron-electron interaction for the magnetic coupling in the zigzag spin-chain compound In2VO5

    KAUST Repository

    Wang, Hao

    2010-09-27

    We present first-principles electronic structure calculations for the zigzag spin-chain compound In2VO5 using the generalized gradient approximation both with and without inclusion of an on-site Coulomb interaction. It has been proposed that In2VO5 is characterized by itinerant V 3d electrons at high temperature and localized electrons at low temperature. Consequently, it is to be expected that electronic correlations play an important role for the magnetic transition from ferromagnetic to antiferromagnetic exchange around 120 K. In this context, we study the electronic and magnetic properties of a set of possible spin configurations. Our calculations show that inclusion of an on-site Coulomb interaction in fact changes the ground state from ferromagnetic to antiferromagnetic. © 2010 IOP Publishing Ltd.

  12. The involvement of coordinative interactions in the binding of dihydrolipoamide dehydrogenase to titanium dioxide-Localization of a putative binding site.

    Science.gov (United States)

    Dayan, Avraham; Babin, Gilad; Ganoth, Assaf; Kayouf, Nivin Samir; Nitoker Eliaz, Neta; Mukkala, Srijana; Tsfadia, Yossi; Fleminger, Gideon

    2017-08-01

    Titanium (Ti) and its alloys are widely used in orthodontic and orthopedic implants by virtue to their high biocompatibility, mechanical strength, and high resistance to corrosion. Biointegration of the implants with the tissue requires strong interactions, which involve biological molecules, proteins in particular, with metal oxide surfaces. An exocellular high-affinity titanium dioxide (TiO 2 )-binding protein (TiBP), purified from Rhodococcus ruber, has been previously studied in our lab. This protein was shown to be homologous with the orthologous cytoplasmic rhodococcal dihydrolipoamide dehydrogenase (rhDLDH). We have found that rhDLDH and its human homolog (hDLDH) share the TiO 2 -binding capabilities with TiBP. Intrigued by the unique TiO 2 -binding properties of hDLDH, we anticipated that it may serve as a molecular bridge between Ti-based medical structures and human tissues. The objective of the current study was to locate the region and the amino acids of the protein that mediate the protein-TiO 2 surface interaction. We demonstrated the role of acidic amino acids in the nonelectrostatic enzyme/dioxide interactions at neutral pH. The observation that the interaction of DLDH with various metal oxides is independent of their isoelectric values strengthens this notion. DLDH does not lose its enzymatic activity upon binding to TiO 2 , indicating that neither the enzyme undergoes major conformational changes nor the TiO 2 binding site is blocked. Docking predictions suggest that both rhDLDH and hDLDH bind TiO 2 through similar regions located far from the active site and the dimerization sites. The putative TiO 2 -binding regions of both the bacterial and human enzymes were found to contain a CHED (Cys, His, Glu, Asp) motif, which has been shown to participate in metal-binding sites in proteins. Copyright © 2017 John Wiley & Sons, Ltd.

  13. iRPIS-PseNNC: identifying RNA-protein interaction sites by incorporating the position-specific dinucleotide propensity into ensemble random forest approach

    Science.gov (United States)

    Li, Long; Chen, Guojin; Jin, Tingdu

    2017-06-01

    As the pile of RNA-Protein complexes sequences mounted, in order to overcome time-consuming problem of the traditional identify RNA-Protein interaction sites (RPIS) method, it is urgent need develop intelligent recognition approach for quickly and reliable recognition of the RNA-Protein interaction sites (RPIS). To settle the question, we developed a new method named iRPIS-PseNNC, in which each sample is a nineteen nucleotides segment that for positive the centre of the segments is RPIS and for negative the segments centre is non-RPIS, and the sample was obtained by sliding window. The RNA sample was formulated by combining the dipeptide position-specific propensity into random forest approach, and by using the random sampling to balance the training dataset. According the voting system, we combine eleven random forest together to construct an ensemble classifier. It is shown that via the rigorous cross validations that the new predictor “iRPIS-PseNNC” achieved very high percentage of accuracy than any other existing algorithms in this field, indicating that the iRPIS-PseNNC predictor will be an effective tool for prediction RNA-Protein interaction sites.

  14. A single site for N-linked glycosylation in the envelope glycoprotein of feline immunodeficiency virus modulates the virus-receptor interaction

    Directory of Open Access Journals (Sweden)

    Samman Ayman

    2008-08-01

    Full Text Available Abstract Feline immunodeficiency virus (FIV targets helper T cells by attachment of the envelope glycoprotein (Env to CD134, a subsequent interaction with CXCR4 then facilitating the process of viral entry. As the CXCR4 binding site is not exposed until CD134-binding has occurred then the virus is protected from neutralising antibodies targeting the CXCR4-binding site on Env. Prototypic FIV vaccines based on the FL4 strain of FIV contain a cell culture-adapted strain of FIV Petaluma, a CD134-independent strain of FIV that interacts directly with CXCR4. In addition to a characteristic increase in charge in the V3 loop homologue of FIVFL4, we identified two mutations in potential sites for N-linked glycosylation in the region of FIV Env analogous to the V1–V2 region of HIV and SIV Env, T271I and N342Y. When these mutations were introduced into the primary GL8 and CPG41 strains of FIV, the T271I mutation was found to alter the nature of the virus-CD134 interaction; primary viruses carrying the T271I mutation no longer required determinants in cysteine-rich domain (CRD 2 of CD134 for viral entry. The T271I mutation did not confer CD134-independent infection upon GL8 or CPG41, nor did it increase the affinity of the CXCR4 interaction, suggesting that the principal effect was targeted at reducing the complexity of the Env-CD134 interaction.

  15. A cation-π interaction at a phenylalanine residue in the glycine receptor binding site is conserved for different agonists

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Hanek, Ariele P; Price, Kerry L

    2011-01-01

    . In the current study, we investigated whether the lower efficacy agonists of the human GlyR β-alanine and taurine also form cation-π interactions with Phe159. By incorporating a series of unnatural amino acids, we found cation-π interactions between Phe159 and the amino groups of β-alanine and taurine....... The strengths of these interactions were significantly weaker than for glycine. Modeling studies suggest that β-alanine and taurine are orientated subtly differently in the binding pocket, with their amino groups further from Phe159 than that of glycine. These data therefore show that similar agonists can have...... similar but not identical orientations and interactions in the binding pocket and provide a possible explanation for the lower potencies of β-alanine and taurine....

  16. Interaction of batrachotoxin with the local anesthetic receptor site in transmembrane segment IVS6 of the voltage-gated sodium channel.

    Science.gov (United States)

    Linford, N J; Cantrell, A R; Qu, Y; Scheuer, T; Catterall, W A

    1998-11-10

    The voltage-gated sodium channel is the site of action of more than six classes of neurotoxins and drugs that alter its function by interaction with distinct, allosterically coupled receptor sites. Batrachotoxin (BTX) is a steroidal alkaloid that binds to neurotoxin receptor site 2 and causes persistent activation. BTX binding is inhibited allosterically by local anesthetics. We have investigated the interaction of BTX with amino acid residues I1760, F1764, and Y1771, which form part of local anesthetic receptor site in transmembrane segment IVS6 of type IIA sodium channels. Alanine substitution for F1764 (mutant F1764A) reduces tritiated BTX-A-20-alpha-benzoate binding affinity, causing a 60-fold increase in Kd. Alanine substitution for I1760, which is adjacent to F1764 in the predicted IVS6 transmembrane alpha helix, causes only a 4-fold increase in Kd. In contrast, mutant Y1771A shows no change in BTX binding affinity. For wild-type and mutant Y1771A, BTX shifted the voltage for half-maximal activation approximately 40 mV in the hyperpolarizing direction and increased the percentage of noninactivating sodium current to approximately 60%. In contrast, these BTX effects were eliminated completely for the F1764A mutant and were reduced substantially for mutant I1760A. Our data suggest that the BTX receptor site shares overlapping but nonidentical molecular determinants with the local anesthetic receptor site in transmembrane segment IVS6 as well as having unique molecular determinants in transmembrane segment IS6, as demonstrated in previous work. Evidently, BTX conforms to a domain-interface allosteric model of ligand binding and action, as previously proposed for calcium agonist and antagonist drugs acting on L-type calcium channels.

  17. Identification of novel Ack1-interacting proteins and Ack1 phosphorylated sites in mouse brain by mass spectrometry

    OpenAIRE

    del Mar Masdeu, Maria; Armendáriz, Beatriz G.; Torre, Anna La; Soriano, Eduardo; Burgaya, Ferran; Ureña, Jesús Mariano

    2017-01-01

    Ack1 (activated Cdc42-associated tyrosine kinase) is a non-receptor tyrosine kinase that is highly expressed in brain. This kinase contains several protein-protein interaction domains and its action is partially regulated by phosphorylation. As a first step to address the neuronal functions of Ack1, here we screened mouse brain samples to identify proteins that interact with this kinase. Using mass spectrometry analysis, we identified new putative partners for Ack1 including cytoskeletal prot...

  18. Palaeoloxodon and Human Interaction: Depositional Setting, Chronology and Archaeology at the Middle Pleistocene Ficoncella Site (Tarquinia, Italy)

    Science.gov (United States)

    Aureli, Daniele; Contardi, Antonio; Giaccio, Biagio; Jicha, Brian; Lemorini, Cristina; Madonna, Sergio; Magri, Donatella; Marano, Federica; Milli, Salvatore; Modesti, Valerio; Palombo, Maria Rita; Rocca, Roxane

    2015-01-01

    The Ficoncella site in northern Latium (Italy) represents a unique opportunity to investigate the modalities of a short occupation in an alluvial setting during the Lower Palaeolithic. The small excavation area yielded a lithic assemblage, a carcass of Palaeoloxodon antiquus, and some other faunal remains. The main objectives of the study are to better characterize the depositional context where the Palaeoloxodon and the lithic assemblage occur, and to evaluate with greater precision the occupation dynamics. A 25 m-long well was drilled just above the top of the terrace of the Ficoncella site and faunal and lithic remains were analyzed with current and innovative techniques. The archaeological site contains floodplain deposits as it is located next to a small incised valley that feeds into a larger valley of the Mignone River. A tephra layer capping the site is 40Ar/39Ar dated to 441± 8 ka. Collectively, the geochronologic, tephrochronologic and geologic data, suggest the site was occupied during MIS 13. The new results should prompt further research at Ficoncella in order to improve our understanding of the dynamics of human settlement in Europe during the Early to Middle Pleistocene. PMID:25898322

  19. Palaeoloxodon and human interaction: depositional setting, chronology and archaeology at the Middle Pleistocene Ficoncella site (Tarquinia, Italy).

    Science.gov (United States)

    Aureli, Daniele; Contardi, Antonio; Giaccio, Biagio; Jicha, Brian; Lemorini, Cristina; Madonna, Sergio; Magri, Donatella; Marano, Federica; Milli, Salvatore; Modesti, Valerio; Palombo, Maria Rita; Rocca, Roxane

    2015-01-01

    The Ficoncella site in northern Latium (Italy) represents a unique opportunity to investigate the modalities of a short occupation in an alluvial setting during the Lower Palaeolithic. The small excavation area yielded a lithic assemblage, a carcass of Palaeoloxodon antiquus, and some other faunal remains. The main objectives of the study are to better characterize the depositional context where the Palaeoloxodon and the lithic assemblage occur, and to evaluate with greater precision the occupation dynamics. A 25 m-long well was drilled just above the top of the terrace of the Ficoncella site and faunal and lithic remains were analyzed with current and innovative techniques. The archaeological site contains floodplain deposits as it is located next to a small incised valley that feeds into a larger valley of the Mignone River. A tephra layer capping the site is 40Ar/39Ar dated to 441± 8 ka. Collectively, the geochronologic, tephrochronologic and geologic data, suggest the site was occupied during MIS 13. The new results should prompt further research at Ficoncella in order to improve our understanding of the dynamics of human settlement in Europe during the Early to Middle Pleistocene.

  20. Diagnostic accuracy of modified kenneth jones scoring criteria (mkjsc) in confirmed cases of tuberculosis in children

    International Nuclear Information System (INIS)

    Farid, A.; Iqbal, S.M.J.; Hanif, A.

    2013-01-01

    Background: Tuberculosis (TB) is a granulomatous disease caused by Mycobacterium tuberculosis. The gold standard for the diagnosis of tuberculosis is detection of Mycobacterium tubercle bacilli. However, clinical scoring systems are most widely used for the diagnosis of TB in children. Objective: To determine the diagnostic accuracy of modified Kenneth Jones scoring criteria (MKJSC) in conformed cases of tuberculosis. Methodology: This cross-sectional comparative study was conducted in the department of Paediatrics, King Edward Medical University / Mayo Hospital, Lahore from January to June 2007. One hundred children below 15 years of age were enrolled. They were diagnosed as suspected cases of TB on the basis of fever and cough for more than 15 days. MKJSC was applied and each child was subjected to confirmatory test for TB. Results: There was an overall male preponderance of 54%. The mean age of study population was 1.8 +- 0.7 years. Out of 100 children, 66% were diagnosed as TB cases (23 with confirmatory tests and 43 with MKJSC of 5 or more). Sensitivity, specificity, positive and negative predictive value of MKJSC was 73.91%, 44.16%, 28.33%, and 85% respectively. Diagnostic accuracy of MKJSC was 51%. Conclusion: Present study does not support the hypothesis that MKJSC is a good alternative to confirmatory tests to diagnose tuberculosis in children. However, MKJSC is a simple tool, which can be applied to improve the case detection rate in the absence of sophisticated tests. (author)

  1. Chemical diversity in the essential oil of Indian valerian (Valeriana jatamansi Jones).

    Science.gov (United States)

    Verma, Ram S; Verma, Rajesh K; Padalia, Rajendra C; Chauhan, Amit; Singh, Anand; Singh, Hemendra P

    2011-10-01

    To explore the diversity in the essential oil yield and composition of Valeriana jatamansi Jones (syn. V. wallichii DC) growing wild in Uttarakhand (Western Himalaya), 17 populations were collected from different locations and grown under similar conditions. Comparative results showed considerable variations in the essential oil yield and composition. The essential oil yield varied from 0.21 to 0.46% in the fresh roots and rhizomes of different populations of V. jatamansi. Analysis of the essential oils by GC (RI) and GC/MS and the subsequent classification by principal component analysis (PCA) resulted in six clusters with significant variations in their terpenoid composition. Major components in the essential oils of the different populations were patchouli alcohol (1; 13.4-66.7%), α-bulnesene (3; <0.05-23.5%), α-guaiene (4; 0.2-13.3%), guaiol (5; <0.05-12.2%), seychellene (6; 0.2-9.9%) viridiflorol (<0.05-7.3%), and β-gurjunene (7; 0.0-7.1%). V. jatamansi populations with contents of 1 higher than 60% may be utilized commercially in perfumery. Copyright © 2011 Verlag Helvetica Chimica Acta AG, Zürich.

  2. Essential Oil Composition of Valeriana Jatamansi Jones from Himalayan Regions of India

    Science.gov (United States)

    Raina, Archana P.; Negi, K. S.

    2015-01-01

    Valeriana jatamansi Jones germplasm collected from sub-temperate Himalayan region of Uttarakhand and North-East state of Meghalaya, India was evaluated under identical conditions at National Bureau of Plant Genetic Resources, Bhowali, India, to study germplasm diversity based on essential oil composition. Twenty one compounds were identified in V. jatamansi root oil by GC and GC-MS. The major compounds identified were patchouli alcohol (0.4-63.7%), maaliol (2.9-53.8%), seychellene (4.1-27.4%), calarene/ß-gurjunene (3.0-20.8%), α-santalene (0.6-12.0%). Other compounds present were bornyl acetate (0.6-1.5%), α-guaiene (0.7-2.3%), α-bulnesene/δ-guaiene (0.7-6.3%), 7-epi-α-selinene (0.4-1.4%), kessane (2.1-3.3%), spathulenol (0.7-3.4%), viridiflorol (0.9-7.1%), α-patchoulene (0.8-6.6%), ß-patchoulene (0.4-0.8%). Two superior chemotypes identified in V. jatamansi oil from Uttarakhand were: patchouli alcohol rich (IC573221, 63.7%) and maaliol rich (IC573222, 53.8%; IC589096, 51.7%), while accession from north-east was patchouli alcohol rich chemotype (IC574522, 57.2%). These superior chemotypes with higher amounts of patchouli alcohol and maaliol could be used for promoting cultivation as well as for meeting need of pharmaceutical industries. PMID:26009656

  3. Monological Drama to Reshape the Northern Irish Identity: A Night in November by Marie Jones

    Directory of Open Access Journals (Sweden)

    Virginie Privas

    2010-03-01

    Full Text Available In this contemporary one-man theatre play, Marie Jones’s character, Kenneth McCallister, is prompted to break free from the prejudices in and against Northern Ireland. Indeed, the playwright aims at finding new ways to deconstruct the preconceived idea that there are two different identities in Northern Ireland closely linked to the division between two religious communities. Instead, she seeks connections, even with the Irish who migrated (the diasporic dimension, though, is not to be discussed within this paper. The author explores this possibility through the psychological evolution of a Northern Irish Protestant who comes to lack references in terms of identity. On stage, he recalls the events that launched him on a quest to redefine his identity, an identity in which his religious denomination is taken into account but is not the only community marker. Marie Jones eventually offers an insight into what being and feeling Irish means for someone who has always lived as a Protestant in Northern Ireland. Monologue and the notion of “frontiers” (be they social, political, geographical, historical or theatrical that emerge only to be destroyed, are some of the theatrical devices she resorts to in order to voice her aim in  this experimental play which ultimately proposes to reshape the contours of Northern Irish drama about the Troubles.

  4. A multifractal detrended fluctuation analysis of financial market efficiency: Comparison using Dow Jones sector ETF indices

    Science.gov (United States)

    Tiwari, Aviral Kumar; Albulescu, Claudiu Tiberiu; Yoon, Seong-Min

    2017-10-01

    This study challenges the efficient market hypothesis, relying on the Dow Jones sector Exchange-Traded Fund (ETF) indices. For this purpose, we use the generalized Hurst exponent and multifractal detrended fluctuation analysis (MF-DFA) methods, using daily data over the timespan from 2000 to 2015. We compare the sector ETF indices in terms of market efficiency between short- and long-run horizons, small and large fluctuations, and before and after the global financial crisis (GFC). Our findings can be summarized as follows. First, there is clear evidence that the sector ETF markets are multifractal in nature. We also find a crossover in the multifractality of sector ETF market dynamics. Second, the utilities and consumer goods sector ETF markets are more efficient compared with the financial and telecommunications sector ETF markets, in terms of price prediction. Third, there are noteworthy discrepancies in terms of market efficiency, between the short- and long-term horizons. Fourth, the ETF market efficiency is considerably diminished after the global financial crisis.

  5. Identification of Insecticidal Constituents from the Essential Oil of Valeriana jatamansi Jones against Liposcelis bostrychophila Badonnel

    Directory of Open Access Journals (Sweden)

    Xin Chao Liu

    2013-01-01

    Full Text Available The aim of this research was to determine chemical composition and insecticidal activities of the essential oil of Valeriana jatamansi Jones roots against booklice, Liposcelis bostrychophila Badonnel, and to isolate insecticidal constituents from the oil. Essential oil of V. jatamansi was obtained by hydrodistillation and analyzed by GC-MS. A total of 27 components in the essential oil were identified. The major compounds were patchoulol (24.3%, α-bulnesene (13.8%, isovaleric acid (12.9%, α-guaiene (8.7%, and 3-methylvaleric acid (8.4%. Based on bioactivity-guided fractionation, isovaleric acid, 3-methylvaleric acid, and patchoulol were isolated and identified as the active constituents. The essential oil exhibited contact toxicity against L. bostrychophila with an LC50 value of 236.4 μg/cm2. Patchoulol (LC50 = 61.35 μg/cm2 exhibited stronger acute toxicity than 3-methylvaleric acid (LC50 = 210.69 μg/cm2 against the booklice. The essential oil also possessed fumigant toxicity against L. bostrychophila with an LC50 value of 6.0 mg/L, while 3-methylvaleric acid and isovaleric acid had LC50 values of 5.53 mg/L and 5.67 mg/L against the booklice, respectively. The results indicated that the essential oil and its constituent compounds have potential to develop into natural insecticides or fumigants for control of insects in stored grains.

  6. Generation and optimization of superpixels as image processing kernels for Jones matrix optical coherence tomography.

    Science.gov (United States)

    Miyazawa, Arata; Hong, Young-Joo; Makita, Shuichi; Kasaragod, Deepa; Yasuno, Yoshiaki

    2017-10-01

    Jones matrix-based polarization sensitive optical coherence tomography (JM-OCT) simultaneously measures optical intensity, birefringence, degree of polarization uniformity, and OCT angiography. The statistics of the optical features in a local region, such as the local mean of the OCT intensity, are frequently used for image processing and the quantitative analysis of JM-OCT. Conventionally, local statistics have been computed with fixed-size rectangular kernels. However, this results in a trade-off between image sharpness and statistical accuracy. We introduce a superpixel method to JM-OCT for generating the flexible kernels of local statistics. A superpixel is a cluster of image pixels that is formed by the pixels' spatial and signal value proximities. An algorithm for superpixel generation specialized for JM-OCT and its optimization methods are presented in this paper. The spatial proximity is in two-dimensional cross-sectional space and the signal values are the four optical features. Hence, the superpixel method is a six-dimensional clustering technique for JM-OCT pixels. The performance of the JM-OCT superpixels and its optimization methods are evaluated in detail using JM-OCT datasets of posterior eyes. The superpixels were found to well preserve tissue structures, such as layer structures, sclera, vessels, and retinal pigment epithelium. And hence, they are more suitable for local statistics kernels than conventional uniform rectangular kernels.

  7. A Closer Look at the Halloween Effect: The Case of the Dow Jones Industrial Average

    Directory of Open Access Journals (Sweden)

    Peter Arendas

    2018-04-01

    Full Text Available The Halloween effect is one of the most famous calendar anomalies. It is based on the observation that stock returns tend to perform much better over the winter half of the year (November–April than over the summer half of the year (May–October. The vast majority of studies that investigated the Halloween effect over the recent decades focused only on stock indices. This means that they evaluated whether a stock index follows the Halloween effect pattern, but they omitted digging a little deeper and analyze the Halloween effect on the individual stocks level. This paper investigates to what extent the blue-chips stocks included in the Dow Jones Industrial Average are affected by the Halloween effect and whether the Halloween effect is widespread or the behavior of the whole index is driven by only a handful of stocks that are strongly affected by the Halloween effect. The results show that, although the strength of the Halloween effect varies quite rapidly from stock to stock, the vast majority of analyzed stocks experienced a notably higher average winter period than summer period returns over the 1980–2017 period. Moreover, in 18 out of 35 cases, the Halloween effect was statistically significant.

  8. A Hybrid Vehicle Detection Method Based on Viola-Jones and HOG + SVM from UAV Images.

    Science.gov (United States)

    Xu, Yongzheng; Yu, Guizhen; Wang, Yunpeng; Wu, Xinkai; Ma, Yalong

    2016-08-19

    A new hybrid vehicle detection scheme which integrates the Viola-Jones (V-J) and linear SVM classifier with HOG feature (HOG + SVM) methods is proposed for vehicle detection from low-altitude unmanned aerial vehicle (UAV) images. As both V-J and HOG + SVM are sensitive to on-road vehicles' in-plane rotation, the proposed scheme first adopts a roadway orientation adjustment method, which rotates each UAV image to align the roads with the horizontal direction so the original V-J or HOG + SVM method can be directly applied to achieve fast detection and high accuracy. To address the issue of descending detection speed for V-J and HOG + SVM, the proposed scheme further develops an adaptive switching strategy which sophistically integrates V-J and HOG + SVM methods based on their different descending trends of detection speed to improve detection efficiency. A comprehensive evaluation shows that the switching strategy, combined with the road orientation adjustment method, can significantly improve the efficiency and effectiveness of the vehicle detection from UAV images. The results also show that the proposed vehicle detection method is competitive compared with other existing vehicle detection methods. Furthermore, since the proposed vehicle detection method can be performed on videos captured from moving UAV platforms without the need of image registration or additional road database, it has great potentials of field applications. Future research will be focusing on expanding the current method for detecting other transportation modes such as buses, trucks, motors, bicycles, and pedestrians.

  9. Smart imaging for power-efficient extraction of Viola-Jones local descriptors

    Science.gov (United States)

    Fernández-Berni, J.; Carmona-Galán, R. A.; del Río, R.; Leñero-Bardallo, Juan A.; Suárez-Cambre, M.; Rodríguez-Vázquez, Á.

    2014-03-01

    In computer vision, local descriptors permit to summarize relevant visual cues through feature vectors. These vectors constitute inputs for trained classifiers which in turn enable different high-level vision tasks. While local descriptors certainly alleviate the computation load of subsequent processing stages by preventing them from handling raw images, they still have to deal with individual pixels. Feature vector extraction can thus become a major limitation for conventional embedded vision hardware. In this paper, we present a power-efficient sensing processing array conceived to provide the computation of integral images at different scales. These images are intermediate representations that speed up feature extraction. In particular, the mixed-signal array operation is tailored for extraction of Haar-like features. These features feed the cascade of classifiers at the core of the Viola-Jones framework. The processing lattice has been designed for the standard UMC 0.18μm 1P6M CMOS process. In addition to integral image computation, the array can be reprogrammed to deliver other early vision tasks: concurrent rectangular area sum, block-wise HDR imaging, Gaussian pyramids and image pre-warping for subsequent reduced kernel filtering.

  10. Vps13-Mcp1 interact at vacuole-mitochondria interfaces and bypass ER-mitochondria contact sites.

    Science.gov (United States)

    John Peter, Arun T; Herrmann, Beatrice; Antunes, Diana; Rapaport, Doron; Dimmer, Kai Stefan; Kornmann, Benoît

    2017-10-02

    Membrane contact sites between endoplasmic reticulum (ER) and mitochondria, mediated by the ER-mitochondria encounter structure (ERMES) complex, are critical for mitochondrial homeostasis and cell growth. Defects in ERMES can, however, be bypassed by point mutations in the endosomal protein Vps13 or by overexpression of the mitochondrial protein Mcp1. How this bypass operates remains unclear. Here we show that the mitochondrial outer membrane protein Mcp1 functions in the same pathway as Vps13 by recruiting it to mitochondria and promoting its association to vacuole-mitochondria contacts. Our findings support a model in which Mcp1 and Vps13 work as functional effectors of vacuole-mitochondria contact sites, while tethering is mediated by other factors, including Vps39. Tethered and functionally active vacuole-mitochondria interfaces then compensate for the loss of ERMES-mediated ER-mitochondria contact sites. © 2017 John Peter et al.

  11. New insights into the dimerization and site-specific cooperative interaction of Azure B with model transport proteins by spectroscopic and computational studies.

    Science.gov (United States)

    Arumugam, Selva Sharma; Subramanian, Nandhitha; Malaichamy, Ilanchelian

    2016-11-01

    In the present study, the interaction of model transport proteins Human serum albumin (HSA) and Bovine serum albumin (BSA) with a photoactive dye, Azure B (AZB) were studied by spectroscopic and in silico methods. The absorption spectral behavior of AZB in the presence of varying concentrations of serum albumins (HSA and BSA) revealed the formation of dye aggregates within the protein cavity. The binding parameters computed from the emission quenching data showed that AZB bind to HSA and BSA with significant affinity and it was revealed that both the serum proteins (HSA and BSA) can bind AZB at more than one binding sites having at least one high-affinity binding site with different affinities (non-independent). The existence of static quenching mechanism was further evidenced from the time-resolved fluorescence spectroscopic analysis. Site-competitive replacement experiments with specific site markers showed that AZB binds to site I of HSA and BSA. AutoDock based blind docking approach and molecular dynamics simulation studies were used to analyze the most probable binding location of AZB in HSA and BSA. The AZB induced unfolding of HSA and BSA was established by using absorption, circular dichroism and FT-IR spectral studies. The influence of AZB complexation on the biological function of HSA and BSA was evaluated by probing the hydrolysis of p-nitrophenyl acetate. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Structure, Dynamics, and Interactions of a C4'-Oxidized Abasic Site in DNA: A Concomitant Strand Scission Reverses Affinities

    Czech Academy of Sciences Publication Activity Database

    Patel, C.; Dršata, Tomáš; Lankaš, Filip; Dumont, E.

    2013-01-01

    Roč. 52, č. 45 (2013), s. 8115-8125 ISSN 0006-2960 Institutional support: RVO:61388963 Keywords : duplex DNA * hydrogen-bonds * AP sites * tandem lesions * oxidation Subject RIV: CE - Biochemistry Impact factor: 3.194, year: 2013

  13. Groundwater contamination from waste management sites: The interaction between risk-based engineering design and regulatory policy: 2. Results

    Science.gov (United States)

    Massmann, Joel; Freeze, R. Allan

    1987-02-01

    The risk-cost-benefit analysis developed in the companion paper (J. Massmann and R. A. Freeze, this issue) is here applied to (1) an assessment of the relative worth of containment-construction activities, site-exploration activities, and monitoring activities as components of a design strategy for the owner/operator of a waste management facility; (2) an assessment of alternative policy options available to a regulatory agency; and (3) a case history. Sensitivity analyses designed to address the first issue show that the allocation of resources by the owner/operator is sensitive to the stochastic parameters used to describe the hydraulic conductivity field at a site. For the cases analyzed, the installation of a dense monitoring network is of less value to the owner/operator than a more conservative containment design. Sensitivity analyses designed to address the second issue suggest that from a regulatory perspective, design standards should be more effective than performance standards in reducing risk, and design specifications on the containment structure should be more effective than those on the monitoring network. Performance bonds posted before construction have a greater potential to influence design than prospective penalties to be imposed at the time of failure. Siting on low-conductivity deposits is a more effective method of risk reduction than any form of regulatory influence. Results of the case history indicate that the methodology can be successfully applied at field sites.

  14. Uptake of heavy metals by Typha capensis from wetland sites polluted by effluent from mineral processing plants: implications of metal-metal interactions.

    Science.gov (United States)

    Zaranyika, M F; Nyati, W

    2017-10-01

    The aim of the present work was to demonstrate the existence of metal-metal interactions in plants and their implications for the absorption of toxic elements like Cr. Typha capensis , a good accumulator of heavy metals, was chosen for the study. Levels of Fe, Cr, Ni, Cd, Pb, Cu and Zn were determined in the soil and roots, rhizomes, stems and leaves of T. capensis from three Sites A, B and C polluted by effluent from a chrome ore processing plant, a gold ore processing plant, and a nickel ore processing plant, respectively. The levels of Cr were extremely high at Site A at 5415 and 786-16,047 μg g -1 dry weight in the soil and the plant, respectively, while the levels of Ni were high at Site C at 176 and 24-891 μg g -1 in the soil and the plant, respectively. The levels of Fe were high at all three sites at 2502-7500 and 906-13,833 μg g -1 in the soil and plant, respectively. For the rest of the metals, levels were modest at 8.5-148 and 2-264 μg g -1 in the soil and plant, respectively. Pearson's correlation analysis confirmed mutual synergistic metal-metal interactions in the uptake of Zn, Cu, Co, Ni, Fe, and Cr, which are attributed to the similarity in the radii and coordination geometry of the cations of these elements. The implications of such metal-metal interactions (or effects of one metal on the behaviour of another) on the uptake of Cr, a toxic element, and possible Cr detoxification mechanism within the plant, are discussed.

  15. The roofs of Wren and Jones: a seventeenth-century migration of technical knowledge from Italy to England

    OpenAIRE

    Simona Valeriani

    2006-01-01

    Seventeenth-century English architecture saw the introduction of a new style, influenced by continental Europe, and driven, to a large extent, by the work of Inigo Jones and Christopher Wren. But along with the aesthetic novelty came novel building techniques; construction methods embedded within the stylistic changes showing that the continental influence was felt as much within the structures of the buildings as it was upon their façades. Focussing here on the methods used to construct wood...

  16. Site-directed mutational analysis of structural interactions of low molecule compounds binding to the N-terminal 8 kDa domain of DNA polymerase β

    International Nuclear Information System (INIS)

    Murakami, Shizuka; Kamisuki, Shinji; Takata, Kei-ichi; Kasai, Nobuyuki; Kimura, Seisuke; Mizushina, Yoshiyuki; Ohta, Keisuke; Sugawara, Fumio; Sakaguchi, Kengo

    2006-01-01

    We previously reported the mode of inhibition of DNA polymerase β (pol. β) by long chain fatty acids and a bile acid, involving binding analyses to the N-terminal 8-kDa DNA binding domain. Here we describe a site-directed mutational analysis in which the key amino acids (L11, K35, H51, K60, L77, and T79), which are direct interaction sites in the domain, were substituted with K, A, A, A, K, and A, respectively. And their pol. β interactions with a C24-long chain fatty acid, nervonic acid (NA), and a bile acid, lithocholic acid (LCA), were investigated by gel mobility shift assay and NMR spectroscopy. In the case of K35A, there was complete loss of DNA binding activity while K60A hardly has any activity. In contrast the other mutations had no appreciable effects. Thus, K35 and K60 are key amino acid sites for binding to template DNA. The DNA binding activities of L11K, H51A, and T79A as well as the wild type were inhibited by NA to the same extent. T79A demonstrated a disturbed interaction with LCA. 1 H- 15 N HSQC NMR analysis indicated that despite their many similarities, the wild-type and the mutant proteins displayed some significant chemical shift differences. Not only were the substituted amino acid residues three-dimensionally shifted, but some amino acids which are positioned far distant from the key amino acids showed a shift. These results suggest that the interaction surface was significantly distorted with the result that LCA could not bind to the domain. These findings confirm our previous biochemical and 3D structural proposals concerning inhibition by NA and LCA

  17. Effect of mutations in the A site of 16 S rRNA on aminoglycoside antibiotic-ribosome interaction

    DEFF Research Database (Denmark)

    Recht, M I; Douthwaite, S; Dahlquist, K D

    1999-01-01

    antibiotics, which also interact with this region of rRNA. Mutations of certain nucleotides in rRNA reduce aminoglycoside binding affinity, as previously demonstrated using a model RNA oligonucleotide system. Here, predictions from the oligonucleotide system were tested in the ribosome by mutation...... for the aminoglycoside paromomycin, whereas no discernible reduction in affinity was observed with 1406 mutant ribosomes. These data are consistent with prior NMR structural determination of aminoglycoside interaction with the decoding region, and further our understanding of how aminoglycoside resistance can...

  18. Comparative cephalometric study of Class II malocclusion treatment with Pendulum and Jones jig appliances followed by fixed corrective orthodontics.

    Science.gov (United States)

    Patel, Mayara Paim; Henriques, José Fernando Castanha; de Almeida, Renato Rodrigues; Pinzan, Arnaldo; Janson, Guilherme; de Freitas, Marcos Roberto

    2013-01-01

    The purpose of this study was to cephalometrically compare the skeletal and dentoalveolar effects in the treatment of Class II malocclusion with Pendulum and Jones jig appliances, followed by fixed corrective orthodontics, and to compare such effects to a control group. The sample was divided into three groups. Group 1: 18 patients treated with Pendulum, Group 2: 25 patients treated with Jones jig, and Group 3: 19 young subjects with untreated Class II malocclusions and initial mean age of 12.88 years. The chi-square test was applied to assess severity and gender distribution. Groups 1 and 2 were compared to the control group by means of the one-way ANOVA and Tukey tests in order to differentiate treatment changes from those occurred by craniofacial growth. There were no significant changes among the three groups with regard to the components of the maxilla and the mandible, maxillomandibular relationship, cephalometric and tegumental pattern. Buccal tipping of mandibular incisors was significantly greater in the experimental groups and increased mesial angulation of the maxillary second molars was found in the Jones jig group. In the experimental groups, dental relationship, overbite and overjet were corrected. It can be stated that the distalization achieved its purpose of correcting the Class II.

  19. Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions.

    Science.gov (United States)

    Levitsky, Victor G; Ignatieva, Elena V; Ananko, Elena A; Turnaev, Igor I; Merkulova, Tatyana I; Kolchanov, Nikolay A; Hodgman, T C

    2007-12-19

    Reliable transcription factor binding site (TFBS) prediction methods are essential for computer annotation of large amount of genome sequence data. However, current methods to predict TFBSs are hampered by the high false-positive rates that occur when only sequence conservation at the core binding-sites is considered. To improve this situation, we have quantified the performance of several Position Weight Matrix (PWM) algorithms, using exhaustive approaches to find their optimal length and position. We applied these approaches to bio-medically important TFBSs involved in the regulation of cell growth and proliferation as well as in inflammatory, immune, and antiviral responses (NF-kappaB, ISGF3, IRF1, STAT1), obesity and lipid metabolism (PPAR, SREBP, HNF4), regulation of the steroidogenic (SF-1) and cell cycle (E2F) genes expression. We have also gained extra specificity using a method, entitled SiteGA, which takes into account structural interactions within TFBS core and flanking regions, using a genetic algorithm (GA) with a discriminant function of locally positioned dinucleotide (LPD) frequencies. To ensure a higher confidence in our approach, we applied resampling-jackknife and bootstrap tests for the comparison, it appears that, optimized PWM and SiteGA have shown similar recognition performances. Then we applied SiteGA and optimized PWMs (both separately and together) to sequences in the Eukaryotic Promoter Database (EPD). The resulting SiteGA recognition models can now be used to search sequences for BSs using the web tool, SiteGA. Analysis of dependencies between close and distant LPDs revealed by SiteGA models has shown that the most significant correlations are between close LPDs, and are generally located in the core (footprint) region. A greater number of less significant correlations are mainly between distant LPDs, which spanned both core and flanking regions. When SiteGA and optimized PWM models were applied together, this substantially reduced

  20. "Not the Romantic, All Happy, Coochy Coo Experience": A Qualitative Analysis of Interactions on an Irish Parenting Web Site

    Science.gov (United States)

    Brady, Ellen; Guerin, Suzanne

    2010-01-01

    Support groups in online communities provide an anonymous place to exchange information and advice. Previous research has suggested that these groups offer a safe, nonjudgmental forum for new parents to share experiences and interact anonymously. This study investigated how participants in online parenting groups experience support via the…

  1. CD91 interacts with mannan-binding lectin (MBL) through the MBL-associated serine protease-binding site

    DEFF Research Database (Denmark)

    Duus, Karen; Thielens, Nicole M; Lacroix, Monique

    2010-01-01

    CD91 plays an important role in the scavenging of apoptotic material, possibly through binding to soluble pattern-recognition molecules. In this study, we investigated the interaction of CD91 with mannan-binding lectin (MBL), ficolins and lung surfactant proteins. Both MBL and L-ficolin were foun...

  2. Interaction of D-LSD with binding sites in brain: a study in vivo and in vitro

    International Nuclear Information System (INIS)

    Ebersole, B.L.J.

    1985-01-01

    The localization of [ 3 H]-d-lysergic acid diethylamide ([ 3 H]LSD) binding sites in the mouse brain was compared in vivo and in vitro. Radioautography of brain sections incubated with [ 3 H]LSD in vitro revealed substantial specific [ 3 H]LSD binding in cortical layers III-IV and areas CA1 and dentate gyrus in hippocampus. In contrast, in brain sections from animals that received [ 3 H]LSD in vivo, binding in hippocampus was scant and diffuse, although the pattern of labeling in cortex was similar to that seen in vitro. The low specific binding in hippocampus relative to cortex was confirmed by homogenate filtration studies of brain areas from mice that received injections of [ 3 H]LSD. Time-course studies established that peak specific binding at ten minutes was the same in cortex and hippocampus. At all times, binding in hippocampus was about one-third of that in cortex; in contrast, the concentration of free [ 3 H]LSD did not vary between regions. This finding was unexpected, because binding studies in vitro in membrane preparations indicated that the density and affinity of [ 3 H]LSD binding sites were similar in both brain regions. Saturation binding studies in vivo showed that the lower amount of [ 3 H]LSD binding in hippocampus was attributable to a lower density of sites labeled by [ 3 H]LSD. The pharmacological identify of [ 3 H]LSD binding sites in vivo may be relevant to the hallucinogenic properties of LSD and of other related hallucinogens

  3. Interaction of bispyridinium compounds with the orthosteric binding site of human α7 and Torpedo californica nicotinic acetylcholine receptors (nAChRs).

    Science.gov (United States)

    Niessen, K V; Tattersall, J E H; Timperley, C M; Bird, M; Green, C; Seeger, T; Thiermann, H; Worek, F

    2011-09-25

    Standard treatment of poisoning by organophosphorus (OP) nerve agents with atropine and oximes lacks efficacy with different nerve agents. A direct pharmacologic intervention at the nicotinic acetylcholine receptor (nAChR) was proposed as an alternative therapeutic approach and promising in vitro and in vivo results were obtained with the bispyridinium compound SAD-128. In addition, a number of SAD-128 analogues improved neuromuscular transmission of soman-poisoned diaphragms in vitro. We investigated the interaction of six of these SAD-128 analogues with the orthosteric binding site of the human α7 nAChR and Torpedo californica nAChR with a high-throughput assay using radioactive ligands. The determined affinity constants indicate a weak interaction of three test compounds (K(i) in the micromolar range) with both receptors, but no interaction could be recorded with the other three test compounds. The six SAD-128 analogues showed a low intrinsic inhibitory potency with human acetylcholinesterase (IC₅₀ > 400 μM). In conclusion, the results of the present study do not indicate a correlation between the affinity to the orthosteric binding site and the functional improvement of neuromuscular transmission and it is assumed that other mechanisms contribute to the therapeutic effect of the tested compounds. Crown Copyright © 2011. Published by Elsevier Ireland Ltd. All rights reserved.

  4. The influence of soil organic carbon on interactions between microbial parameters and metal concentrations at a long-term contaminated site

    Energy Technology Data Exchange (ETDEWEB)

    Muhlbachova, G. [Crop Research Institute, Drnovska 507, 161 06 Prague 6, Ruzyne (Czech Republic); Sagova-Mareckova, M., E-mail: sagova@vurv.cz [Crop Research Institute, Drnovska 507, 161 06 Prague 6, Ruzyne (Czech Republic); Omelka, M. [Charles University, Faculty of Mathematics and Physics, Dept. of Probability and Mathematical Statistics, Prague 8, Karlin (Czech Republic); Szakova, J.; Tlustos, P. [Czech University of Life Sciences, Department of Agroenvironmental Chemistry and Plant Nutrition, Prague 6, Suchdol (Czech Republic)

    2015-01-01

    The effects of lead, zinc, cadmium, arsenic and copper deposits on soil microbial parameters were investigated at a site exposed to contamination for over 200 years. Soil samples were collected in triplicates at 121 sites differing in contamination and soil organic carbon (SOC). Microbial biomass, respiration, dehydrogenase activity and metabolic quotient were determined and correlated with total and extractable metal concentrations in soil. The goal was to analyze complex interactions between toxic metals and microbial parameters by assessing the effect of soil organic carbon in the relationships. The effect of SOC was significant in all interactions and changed the correlations between microbial parameters and metal fractions from negative to positive. In some cases, the effect of SOC was combined with that of clay and soil pH. In the final analysis, dehydrogenase activity was negatively correlated to total metal concentrations and acetic acid extractable metals, respiration and metabolic quotient were to ammonium nitrate extractable metals. Dehydrogenase activity was the most sensitive microbial parameter correlating most frequently with contamination. Total and extractable zinc was most often correlated with microbial parameters. The large data set enabled robust explanation of discrepancies in organic matter functioning occurring frequently in analyzing of contaminated soil processes. - Highlights: • Soil organic carbon affected all interactions between metals and microorganisms. • Soil organic carbon adjustment changed correlations from positive to negative. • Ammonium nitrate extractable metals were the most influencing fraction. • Dehydrogenase activity was the most affected soil parameter. • Zinc was the most toxic metal among studied metals.

  5. Comparison of the Pendulum appliance and the Jones Jig: A prospective comparative study.

    Science.gov (United States)

    Shetty, Sushruth; Maurya, Rajkumar; Raj, H V Pruthvi; Patil, Anand

    2017-01-01

    To compare two molar distalization devices, the Pendulum appliance (PA) and the Jones Jig (JJ) in dental Class II patients. Pretreatment and postdistalization lateral cephalograms and study models of 20 subjects (6 males, 14 females) Class II malocclusion subjects were examined. PA and JJ group both consisted of 10 patients each with a mean pretreatment age of 12 years 1 month for females and 12 years 5 months for males. The PA and the JJ appliance were activated once in a month until Class II molar relationship was corrected to a super Class I molar relationship in both groups. Initial and final measurements and treatment changes were compared by means of Paired t -test. Maxillary first molar distalized an average of 3.85 mm in the PA and 2.75 mm in the JJ between T1 and T2; rate of molar distalization was 1.59 mm/month for PA, and the JJ appliance averaged 0.88 mm/month, distal molar tipping was greater in PA (6.2°) than in the JJ (3.9°). Average mesial movement of the premolars was 2.2 mm with PA and JJ both. JJ showed a greater rotation of first molars after distalization as compared to PA. The increase in vertical facial height was also greater for JJ as compared to PA. Both the appliances were effective in molar distalization with PA requiring less distalization time (16 days less than JJ). Some adverse effects were noted with both which one should strive to control.

  6. EPR of Cu(II) in sarcosine cadmium chloride: probe into dopant site - symmetry and copper-sarcosine interaction

    CERN Document Server

    Pathinettam-Padiyan, D; Murugesan, R

    2000-01-01

    The electron paramagnetic resonance spectra of Cu(II) doped sarcosine cadmium chloride single crystals have been investigated at room temperature. Experimental results reveal that the Cu(II) ion enters the lattice interstitially. The observed superhyperfine lines indicate the superposition of two sets of quintet structure with interaction of nitrogen atoms and the two isotopes of copper. The spin Hamiltonian parameters are evaluated by Schonland method and the electric field symmetry around the copper ion is rhombic. An admixture of d sub z sup 2 orbital with the d sub x sub sup 2 sub - sub y sub sup 2 ground state is observed. Evaluation of MO coefficients reveals that the in-plane interaction between copper and nitrogen is strong in this lattice.

  7. Mapping of protein-protein interaction sites in the plant-type [2Fe-2S] ferredoxin.

    Directory of Open Access Journals (Sweden)

    Haruka Kameda

    Full Text Available Knowing the manner of protein-protein interactions is vital for understanding biological events. The plant-type [2Fe-2S] ferredoxin (Fd, a well-known small iron-sulfur protein with low redox potential, partitions electrons to a variety of Fd-dependent enzymes via specific protein-protein interactions. Here we have refined the crystal structure of a recombinant plant-type Fd I from the blue green alga Aphanothece sacrum (AsFd-I at 1.46 Å resolution on the basis of the synchrotron radiation data. Incorporating the revised amino-acid sequence, our analysis corrects the 3D structure previously reported; we identified the short α-helix (67-71 near the active center, which is conserved in other plant-type [2Fe-2S] Fds. Although the 3D structures of the four molecules in the asymmetric unit are similar to each other, detailed comparison of the four structures revealed the segments whose conformations are variable. Structural comparison between the Fds from different sources showed that the distribution of the variable segments in AsFd-I is highly conserved in other Fds, suggesting the presence of intrinsically flexible regions in the plant-type [2Fe-2S] Fd. A few structures of the complexes with Fd-dependent enzymes clearly demonstrate that the protein-protein interactions are achieved through these variable regions in Fd. The results described here will provide a guide for interpreting the biochemical and mutational studies that aim at the manner of interactions with Fd-dependent enzymes.

  8. Site-Directed Mutagenesis of Myoglobin for Studies of Their Interaction with Iron(III by Multi-Spectroscopic Techniques

    Directory of Open Access Journals (Sweden)

    Qian Tang

    2013-01-01

    Full Text Available In order to investigate how the amino acids on the surface of myoglobin molecule influence myoglobin's structure and function, a variety of spectroscopy techniques were applied in the study of the interaction between Fe(III and myoglobin (wild type and its mutants, D44K, D60K, and K56D. The results demonstrate that Fe(III can quench the fluorescence of wild type and mutants of myoglobin, and the quenching mechanisms are static quenching. It is found that the binding distance between Fe(III and myoglobin mutants gets smaller, the binding capacity increases by the values of binding constant and the bimolecular quenching constant as well as the binding distance. Those data also indicate that the metal ion Fe(III can interact strongly with myoglobin mutants. The three-dimensional conformation change after surface amino acids are replaced is detected by the UV absorption spectroscopy and fluorescence spectroscopy, which make mutants become more dynamic and change its function and interaction with Fe(III strongly.

  9. Interaction of the D-isomer of 4-methylene glutamate (4-MG) with an active site thiol group of γ-glutamylcysteine synthetase (γ-GCS)

    International Nuclear Information System (INIS)

    Simondsen, R.P.; Meister, A.

    1986-01-01

    γ-GCS has an SH-group at or close to the glutamate binding site. During efforts to find a covalently bound inhibitor, the authors examined interaction of the enzyme with 4-MG with the thought that a glutamate analog with an α,β-unsaturated moiety might bind to the glutamate site and react with the active site thiol. 4-MG is not a significant substrate, but inhibits in the usual assay. Preincubation of the enzyme with DL-4-MG inactivated markedly and to about the same extent as found after preincubation with half the concentration of D-4-MG (prepared by action of glutamate decarboxylase on DL-4-MG); L-4-MG did not inactivate. Inactivation by 4-MG was decreased in the presence of L-glutamate. Inactivation by 4-MG was prevented by prior treatment of the enzyme with cystamine, which forms a disulfide with the active site thiol. After inactivation of the enzyme with 4-[2- 14 C]MG followed by separation of the enzyme by gel filtration, 0.9 mole of label was found per mole of enzyme, amino acid analysis after acid hydrolysis of the labeled enzyme gave labeled products that include the expected adduct formed by reaction of cysteine with 4-MG

  10. Use of Multiple Methods to Estimate Walrus (Odobenus rosmarus rosmarus Abundance in the Penny Strait-Lancaster Sound and West Jones Sound Stocks, Canada

    Directory of Open Access Journals (Sweden)

    Robert EA Stewart

    2014-12-01

    Full Text Available Surveys to estimate walrus abundance at terrestrial haulout sites in the Penny Strait-Lancaster Sound (PS-LS and West Jones Sound (WJS stocks were conducted in 1977 and 1998-2009. The Minimum Counted Population (MCP was similar in 1977 (565 to recent years (557 for the PS-LS stock. The MCP for the WJS stock was higher in recent surveys (404 than in 1977 (290. Regression analysis of MCP and density (number of walrus divided by number of haulouts surveyed showed no significant trends over time. We also calculated bounded count estimates for comparison. Finally, we used broad-scale behavioural data to estimate the proportion of the total stock that could be considered countable, to produce two adjusted estimates. We selected recent surveys with good coverage and ignored adjusted estimates that were lower than MCP. For the PS-LS stock, the adjusted MCP (with 95% CL was 672 (575-768 and 727 (623-831 walrus in 2007 and 2009, respectively. For WJS, the best estimates were the adjusted MCP of 503 (473-534 in 2008 and the adjusted bounded count of 470 (297-1732 in 2009. While both stocks appear to have remained stable over three decades, differences in survey coverage and possible differences in walrus distribution make precise population estimation difficult.

  11. Interaction of Zn(II)bleomycin-A2 and Zn(II)peplomycin with a DNA hairpin containing the 5'-GT-3' binding site in comparison with the 5'-GC-3' binding site studied by NMR spectroscopy.

    Science.gov (United States)

    Follett, Shelby E; Ingersoll, Azure D; Murray, Sally A; Reilly, Teresa M; Lehmann, Teresa E

    2017-10-01

    Bleomycins are a group of glycopeptide antibiotics synthesized by Streptomyces verticillus that are widely used for the treatment of various neoplastic diseases. These antibiotics have the ability to chelate a metal center, mainly Fe(II), and cause site-specific DNA cleavage. Bleomycins are differentiated by their C-terminal regions. Although this antibiotic family is a successful course of treatment for some types of cancers, it is known to cause pulmonary fibrosis. Previous studies have identified that bleomycin-related pulmonary toxicity is linked to the C-terminal region of these drugs. This region has been shown to closely interact with DNA. We examined the binding of Zn(II)peplomycin and Zn(II)bleomycin-A 2 to a DNA hairpin of sequence 5'-CCAGTATTTTTACTGG-3', containing the binding site 5'-GT-3', and compared the results with those obtained from our studies of the same MBLMs bound to a DNA hairpin containing the binding site 5'-GC-3'. We provide evidence that the DNA base sequence has a strong impact in the final structure of the drug-target complex.

  12. Strategies for the decision process of siting radioactive waste repositories concerning communication and interaction with the society

    International Nuclear Information System (INIS)

    Almeida, Ivan Pedro Salati de

    2009-01-01

    The objective of this paper is to discuss the strategies to be followed in the siting and construction process of radioactive waste repositories considering the communication and relationship with the society. The paper analyzes the prospective advantages and disadvantages of each type of strategy. The strategies can be classified under three different types: 'define, announce and defend' strategy (also called DAD), participative strategy and spontaneous candidacy of host community. Up to the 90s the most common way of construct repositories was the DAD strategy. This type of strategy, despite of some cases of success, is gradually facing opposition in democratic regimes. Examples of failure are the first attempt to construct the Hungarian repository from 1982 to 1990; the French attempt of the construction of high and intermediate waste repository from 1987 to 1989 (both cancelled and substituted by the participative approach) and even the recent discussion to freeze the implantation of the Yucca Mountain repository in United States. The participative strategy has been preferred currently by most of the new repositories projects. Examples are the second attempt in Hungary, the construction of a repository in Slovenia and in the United Kingdom. The participative strategy has the disadvantage of greater expenses at the beginning of the process until the site of the repository is defined. This occurs because the body responsible for the construction has to deal with several potential candidates and spend time and money in the communication and participation process until the definition of the site by technical, economical and social criteria. On the other hand, this process decreases the risk of rejection by the local population. The spontaneous candidacy strategy was also analyzed and it is shown it has some similarities with the participative strategy but hides new risks in the process. (author)

  13. Structure/functional aspects of the human riboflavin transporter-3 (SLC52A3): role of the predicted glycosylation and substrate-interacting sites.

    Science.gov (United States)

    Subramanian, Veedamali S; Sabui, Subrata; Teafatiller, Trevor; Bohl, Jennifer A; Said, Hamid M

    2017-08-01

    The human riboflavin (RF) transporter-3 (hRFVT-3; product of the SLC52A3 gene) plays an essential role in the intestinal RF absorption process and is expressed exclusively at the apical membrane domain of polarized enterocytes. Previous studies have characterized different physiological/biological aspects of this transporter, but nothing is known about the glycosylation status of the hRFVT-3 protein and role of this modification in its physiology/biology. Additionally, little is known about the residues in the hRFVT-3 protein that interact with the ligand, RF. We addressed these issues using appropriate biochemical/molecular approaches, a protein-docking model, and established intestinal/renal epithelial cells. Our results showed that the hRFVT-3 protein is glycosylated and that glycosylation is important for its function. Mutating the predicted N -glycosylation sites at Asn 94 and Asn 168 led to a significant decrease in RF uptake; it also led to a marked intracellular (in the endoplasmic reticulum, ER) retention of the mutated proteins as shown by live-cell confocal imaging studies. The protein-docking model used in this study has identified a number of putative substrate-interacting sites: Ser 16 , Ile 20 , Trp 24 , Phe 142 , Thr 314 , and Asn 315 Mutating these potential interacting sites was indeed found to lead to a significant inhibition in RF uptake and to intracellular (ER) retention of the mutated proteins (except for the Phe 142 mutant). These results demonstrate that the hRFVT-3 protein is glycosylated and this glycosylation is important for its function and cell surface expression. This study also identified a number of residues in the hRFVT-3 polypeptide that are important for its function/cell surface expression.

  14. Multi-criteria site selection for fire services: the interaction with analytic hierarchy process and geographic information systems

    Directory of Open Access Journals (Sweden)

    T. Erden

    2010-10-01

    Full Text Available This study combines AHP and GIS to provide decision makers with a model to ensure optimal site location(s for fire stations selected. The roles of AHP and GIS in determining optimal locations are explained, criteria for site selection are outlined, and case study results for finding the optimal fire station locations in Istanbul, Turkey are included. The city of Istanbul has about 13 million residents and is the largest and most populated city in Turkey. The rapid and constant growth of Istanbul has resulted in the increased number of fire related cases. Fire incidents tend to increase year by year in parallel with city expansion, population and hazardous material facilities. Istanbul has seen a rise in reported fire incidents from 12 769 in 1994 to 30 089 in 2009 according to the interim report of Istanbul Metropolitan Municipality Department of Fire Brigade. The average response time was approximately 7 min 3 s in 2009. The goal of this study is to propose optimal sites for new fire station creation to allow the Fire Brigade in Istanbul to reduce the average response time to 5 min or less. After determining the necessity of suggesting additional fire stations, the following steps are taken into account: six criteria are considered in this analysis. They are: High Population Density (HPD; Proximity to Main Roads (PMR; Distance from Existing Fire Stations (DEF; Distance from Hazardous Material Facilities (DHM; Wooden Building Density (WBD; and Distance from the Areas Subjected to Earthquake Risk (DER. DHM criterion, with the weight of 40%, is the most important criterion in this analysis. The remaining criteria have a weight range from 9% to 16%. Moreover, the following steps are performed: representation of criterion map layers in GIS environment; classification of raster datasets; calculating the result raster map (suitability map for potential fire stations; and offering a model that supports decision makers in selecting fire station sites

  15. Novel Kv7.1-phosphatidylinositol 4,5-bisphosphate interaction sites uncovered by charge neutralization scanning

    DEFF Research Database (Denmark)

    Eckey, Karina; Wrobel, Eva; Strutz-Seebohm, Nathalie

    2014-01-01

    Kv7.1 to Kv7.5 α-subunits belong to the family of voltage-gated potassium channels (Kv). Assembled with the β-subunit KCNE1, Kv7.1 conducts the slowly activating potassium current IKs, which is one of the major currents underlying repolarization of the cardiac action potential. A known regulator...... of corresponding long QT syndrome mutants suggested impaired PIP2 regulation as the cause for channel dysfunction. To clarify the underlying structural mechanism of PIP2 binding, molecular dynamics simulations of Kv7.1/KCNE1 complexes containing two PIP2 molecules in each subunit at specific sites were performed...

  16. Heavy Metal Behavior in Lichen-Mine Waste Interactions at an Abandoned Mine Site in Southwest Japan

    Directory of Open Access Journals (Sweden)

    Yuri Sueoka

    2015-09-01

    Full Text Available The lichen, Stereocaulon exutum Nylander, occurring in a contaminated abandoned mine site was investigated to clarify (1 the behavior of heavy metals and As during the slag weathering processes mediated by the lichen; and (2 the distribution of these elements in the lichen thallus on slag. The heavy metals and As in the slag are dissolved from their original phases during the weathering process by lichen substances (organic acids and hypha penetration, in addition to non-biological weathering. The dissolved elements are absorbed into the lichen thallus. Some of these dissolved elements are distributed in the cells of the hyphae. The others are distributed on the surface of the hyphae as formless particles and show lateral distribution inside the cortex of the thallus. The Cu and Zn concentrations in the thalli are positively correlated with the concentrations in the corresponding substrata and a positive intercept in the regression curve obtained using a linear function. These chemical characteristics make this lichen a good biomarker for Cu and Zn contamination of the substrata of the lichen. Therefore, the present study supposes that Stereocaulon exutum has a possible practical application in biomonitoring or risk assessment of heavy metal pollution at abandoned mine sites.

  17. [Phosphate sites of RNA-ligands interacting with ribosome at different stages of translation. Thiophosphate method of analysis].

    Science.gov (United States)

    Dabrowski, M; Junemann, R; Schafer, M A; Spahn, C M; Nierhaus, K H; Alekseeva, E V; Dontsova, O A; Shpanchenko, O V; Bogdanov, A A

    1996-11-01

    A novel footprinting method was recently developed which identifies phosphate groups of RNA involved in strong RNA-RNA and RNA-protein interactions. The method is based on iodine-dependent RNA cleavage at phosphothioate groups as long as these groups are not protected from iodine. Our recent studies of mRNA and tRNA regions protected in active ribosomes are summarized; initiation state of ribosomes as well as two elongation states in pre- and post-translocational states were analyzed. Only one phosphate group of mRNA, which was two positions upstream of the decoding codons, was weakly protected in longation complexes, whereas this group and the phosphate groups in the Shine-Dalgarno sequence were protected in the initiation complex. No protection was observed downstream of the decoding codons. On the contrary, numerous phosphate residues of tRNA were protected by the ribosome. The tRNA protection patterns significantly varied between two tRNAs simultaneously bound to the ribosome. The protection pattern of an individual tRNA was not significantly affected by translocation. The data indicate that both tRNA molecules are tightly bound to the ribosome, whereas mRNA is fixed predominantly by two tRNAs via codon-anticodon interaction. A possible translocation mechanism is suggested.

  18. In Silico Structure Prediction of Human Fatty Acid Synthase-Dehydratase: A Plausible Model for Understanding Active Site Interactions.

    Science.gov (United States)

    John, Arun; Umashankar, Vetrivel; Samdani, A; Sangeetha, Manoharan; Krishnakumar, Subramanian; Deepa, Perinkulam Ravi

    2016-01-01

    Fatty acid synthase (FASN, UniProt ID: P49327) is a multienzyme dimer complex that plays a critical role in lipogenesis. Consequently, this lipogenic enzyme has gained tremendous biomedical importance. The role of FASN and its inhibition is being extensively researched in several clinical conditions, such as cancers, obesity, and diabetes. X-ray crystallographic structures of some of its domains, such as β-ketoacyl synthase, acetyl transacylase, malonyl transacylase, enoyl reductase, β-ketoacyl reductase, and thioesterase, (TE) are already reported. Here, we have attempted an in silico elucidation of the uncrystallized dehydratase (DH) catalytic domain of human FASN. This theoretical model for DH domain was predicted using comparative modeling methods. Different stand-alone tools and servers were used to validate and check the reliability of the predicted models, which suggested it to be a highly plausible model. The stereochemical analysis showed 92.0% residues in favorable region of Ramachandran plot. The initial physiological substrate β-hydroxybutyryl group was docked into active site of DH domain using Glide. The molecular dynamics simulations carried out for 20 ns in apo and holo states indicated the stability and accuracy of the predicted structure in solvated condition. The predicted model provided useful biochemical insights into the substrate-active site binding mechanisms. This model was then used for identifying potential FASN inhibitors using high-throughput virtual screening of the National Cancer Institute database of chemical ligands. The inhibitory efficacy of the top hit ligands was validated by performing molecular dynamics simulation for 20 ns, where in the ligand NSC71039 exhibited good enzyme inhibition characteristics and exhibited dose-dependent anticancer cytotoxicity in retinoblastoma cancer cells in vitro.

  19. Selective intra-dinucleotide interactions and periodicities of bases separated by K sites: a new vision and tool for phylogeny analyses

    Directory of Open Access Journals (Sweden)

    Carlos Y. Valenzuela

    Full Text Available Abstract Direct tests of the random or non-random distribution of nucleotides on genomes have been devised to test the hypothesis of neutral, nearly-neutral or selective evolution. These tests are based on the direct base distribution and are independent of the functional (coding or non-coding or structural (repeated or unique sequences properties of the DNA. The first approach described the longitudinal distribution of bases in tandem repeats under the Bose–Einstein statistics. A huge deviation from randomness was found. A second approach was the study of the base distribution within dinucleotides whose bases were separated by 0, 1, 2… K nucleotides. Again an enormous difference from the random distribution was found with significances out of tables and programs. These test values were periodical and included the 16 dinucleotides. For example a high “positive” (more observed than expected dinucleotides value, found in dinucleotides whose bases were separated by (3K + 2 sites, was preceded by two smaller “negative” (less observed than expected dinucleotides values, whose bases were separated by (3K or (3K + 1 sites. We examined mtDNAs, prokaryote genomes and some eukaryote chromosomes and found that the significant non-random interactions and periodicities were present up to 1000 or more sites of base separation and in human chromosome 21 until separations of more than 10 millions sites. Each nucleotide has its own significant value of its distance to neutrality; this yields 16 hierarchical significances. A three dimensional table with the number of sites of separation between the bases and the 16 significances (the third dimension is the dinucleotide, individual or taxon involved gives directly an evolutionary state of the analyzed genome that can be used to obtain phylogenies. An example is provided.

  20. Using the k-d Tree Data Structure to Accelerate Monte Carlo Simulations.

    Science.gov (United States)

    Chen, Qile P; Xue, Bai; Siepmann, J Ilja

    2017-04-11

    The k-d tree data structure is implemented in a Monte Carlo (MC) molecular simulation program to accelerate the range search for particles or interaction sites within the cutoff distance when Lennard-Jones and Coulomb interactions are computed. MC simulations are performed for different molecules in various ensembles to assess the efficiency enhancements due to the k-d tree data structure. It is found that the use of k-d trees accelerates significantly simulations for Lennard-Jones particles in the NVT and NVT-Gibbs ensembles and for n-butane and 2,4,6,8,10,12,14,16,18,20,22-undecamethylpentacosane represented by the TraPPE-UA force field in the NpT ensemble. Simulations for TraPPE-UA ethanol in the NpT ensemble and for the rigid TIP4P water model in the Gibbs ensemble gain slightly in efficiency with the k-d tree, whereas simulations for TIP4P water in the NpT ensemble do not benefit from the use of the k-d tree. The speed-up can be attributed to the reduction in the number of distance calculations in the range search from scaling as [Formula: see text] to [Formula: see text]. In addition, these tests suggest that the efficiency gain from the use of the k-d tree data structure depends on the flexibility of the molecular model (requiring configurational-bias MC moves to sample changes in conformation), on the ensemble (with open ensembles requiring special MC moves to aid particle transfers), and on the number of interaction sites per molecule (with compact multisite models not seeing an efficiency gain). Overall, the use of the k-d tree data structure can substantially enhance MC simulation efficiency for a variety of systems, and it will enable simulations for larger system sizes in the future.

  1. Interactions between the R2R3-MYB transcription factor, AtMYB61, and target DNA binding sites.

    Directory of Open Access Journals (Sweden)

    Michael B Prouse

    Full Text Available Despite the prominent roles played by R2R3-MYB transcription factors in the regulation of plant gene expression, little is known about the details of how these proteins interact with their DNA targets. For example, while Arabidopsis thaliana R2R3-MYB protein AtMYB61 is known to alter transcript abundance of a specific set of target genes, little is known about the specific DNA sequences to which AtMYB61 binds. To address this gap in knowledge, DNA sequences bound by AtMYB61 were identified using cyclic amplification and selection of targets (CASTing. The DNA targets identified using this approach corresponded to AC elements, sequences enriched in adenosine and cytosine nucleotides. The preferred target sequence that bound with the greatest affinity to AtMYB61 recombinant protein was ACCTAC, the AC-I element. Mutational analyses based on the AC-I element showed that ACC nucleotides in the AC-I element served as the core recognition motif, critical for AtMYB61 binding. Molecular modelling predicted interactions between AtMYB61 amino acid residues and corresponding nucleotides in the DNA targets. The affinity between AtMYB61 and specific target DNA sequences did not correlate with AtMYB61-driven transcriptional activation with each of the target sequences. CASTing-selected motifs were found in the regulatory regions of genes previously shown to be regulated by AtMYB61. Taken together, these findings are consistent with the hypothesis that AtMYB61 regulates transcription from specific cis-acting AC elements in vivo. The results shed light on the specifics of DNA binding by an important family of plant-specific transcriptional regulators.

  2. Reference interaction site model with hydrophobicity induced density inhomogeneity: An analytical theory to compute solvation properties of large hydrophobic solutes in the mixture of polyatomic solvent molecules.

    Science.gov (United States)

    Cao, Siqin; Sheong, Fu Kit; Huang, Xuhui

    2015-08-07

    Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achieve this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute.

  3. Studies of the Interaction between Isoimperatorin and Human Serum Albumin by Multispectroscopic Method: Identification of Possible Binding Site of the Compound Using Esterase Activity of the Protein

    Directory of Open Access Journals (Sweden)

    Samira Ranjbar

    2013-01-01

    Full Text Available Isoimperatorin is one of the main components of Prangos ferulacea as a linear furanocoumarin and used as anti-inflammatory, analgesic, antispasmodic, and anticancer drug. Human serum albumin (HSA is a principal extracellular protein with a high concentration in blood plasma and carrier for many drugs to different molecular targets. Since the carrying of drug by HSA may affect on its structure and action, we decided to investigate the interaction between HSA and isoimperatorin using fluorescence and UV spectroscopy. Fluorescence data indicated that isoimperatorin quenches the intrinsic fluorescence of the HSA via a static mechanism and hydrophobic interaction play the major role in the drug binding. The binding average distance between isoimperatorin and Trp 214 of HSA was estimated on the basis of the theory of Förster energy transfer. Decrease of protein surface hydrophobicity (PSH was also documented upon isoimperatorin binding. Furthermore, the synchronous fluorescence spectra show that the microenvironment of the tryptophan residues does not have obvious changes. Site marker compettive and fluorescence experiments revealed that the binding of isoimperatorin to HSA occurred at or near site I. Finally, the binding details between isoimperatorin and HSA were further confirmed by molecular docking and esterase activity inhibition studies which revealed that drug was bound at subdomain IIA.

  4. Molecular screening of compounds to the predicted Protein-Protein Interaction site of Rb1-E7 with p53- E6 in HPV.

    Science.gov (United States)

    Shaikh, Faraz; Sanehi, Parvish; Rawal, Rakesh

    2012-01-01

    Cervical cancer is malignant neoplasm of the cervix uteri or cervical area. Human Papillomaviruses (HPVs) which are heterogeneous groups of small double stranded DNA viruses are considered as the primary cause of cervical cancer, involved in 90% of all Cervical Cancers. Two early HPV genes, E6 and E7, are known to play crucial role in tumor formation. E6 binds with p53 and prevents its translocation and thereby inhibit the ability of p53 to activate or repress target genes. E7 binds to hypophosphorylated Rb and thereby induces cells to enter into premature S-phase by disrupting Rb-E2F complexes. The strategy of the research work was to target the site of interaction of Rb1 -E7 & p53-E6. A total of 88 compounds were selected for molecular screening, based on comprehensive literature survey for natural compounds with anti-cancer activity. Molecular docking analysis was carried out with Molegro Virtual Docker, to screen the 88 chosen compounds and rank them according to their binding affinity towards the site of interaction of the viral oncoproteins and human tumor suppressor proteins. The docking result revealed that Nicandrenone a member of Withanolides family of chemical compounds as the most likely molecule that can be used as a candidate drug against HPV induced cervical cancer. HPV - Human Papiloma Virus, HTSP - Human Tumor Suppressor Proteins, VOP - Viral oncoproteins.

  5. Interaction of on-site and near real time measured turbidity and enzyme activity in stream water.

    Science.gov (United States)

    Stadler, Philipp; Farnleitner, Andreas H.; Zessner, Matthias

    2013-04-01

    On-site and on-line systems that provide an integrated surveillance of physicochemical and microbiological parameters gain significance in water quality monitoring. Particular relating to diffuse pollution from agricultural areas and use-orientated protection of waters the detection of faecal pollution is a fundamental part. For the near real time and on-site detection of microbiological faecal pollution of water, the beta-D- Glucuronidase (GLUC) enzymatic activity has been suggested as a surrogate parameter. Due to possible short measure intervals of three hours, this method has high potential as a water quality monitoring tool. While cultivation based standard determination takes more than one working day (Cabral 2010) the potential advantage of detecting the GLUC activity is the high temporal measuring resolution. Yet, there is still a big gap of knowledge on the sensitivity and specificity concerning the faecal indication capacity of GLUC in relation to standard assays (Cabral 2010). Interference effects of physicochemical parameters on the enzymatic activity respectively fluorescence have been discussed (Molina-Munoz et al. 2007; Tryland and Fiksdal 1998, Biswal et al. 2003). Results from a monitoring of a rivulet in an agricultural catchment in Lower Austria (HOAL - Hydrological Open Air Laboratory) are presented here. The HOAL offers technical resources that allow measurements at high temporal and spatial resolution and to apply various hydrological methods in one catchment. Two automated enzymatic measuring devices (Coliguard, mbOnline, Austria) and physicochemical in-stream measurements are used, as well as in-stream spectroscopy (spectrolyser, s::can, Austria). Accuracy of both enzymatic measuring devices is compared through diverse hydrological and seasonal conditions. Reference analyses by cultivation based determination were performed. Data from Coliguard devices is combined with physicochemical and spectroscopy data to gain information about the

  6. Influenza human monoclonal antibody 1F1 interacts with three major antigenic sites and residues mediating human receptor specificity in H1N1 viruses.

    Directory of Open Access Journals (Sweden)

    Tshidi Tsibane

    Full Text Available Most monoclonal antibodies (mAbs to the influenza A virus hemagglutinin (HA head domain exhibit very limited breadth of inhibitory activity due to antigenic drift in field strains. However, mAb 1F1, isolated from a 1918 influenza pandemic survivor, inhibits select human H1 viruses (1918, 1943, 1947, and 1977 isolates. The crystal structure of 1F1 in complex with the 1918 HA shows that 1F1 contacts residues that are classically defined as belonging to three distinct antigenic sites, Sa, Sb and Ca(2. The 1F1 heavy chain also reaches into the receptor binding site (RBS and interacts with residues that contact sialoglycan receptors and determine HA receptor specificity. The 1F1 epitope is remarkably similar to the previously described murine HC63 H3 epitope, despite significant sequence differences between H1 and H3 HAs. Both antibodies potently inhibit receptor binding, but only HC63 can block the pH-induced conformational changes in HA that drive membrane fusion. Contacts within the RBS suggested that 1F1 may be sensitive to changes that alter HA receptor binding activity. Affinity assays confirmed that sequence changes that switch the HA to avian receptor specificity affect binding of 1F1 and a mAb possessing a closely related heavy chain, 1I20. To characterize 1F1 cross-reactivity, additional escape mutant selection and site-directed mutagenesis were performed. Residues 190 and 227 in the 1F1 epitope were found to be critical for 1F1 reactivity towards 1918, 1943 and 1977 HAs, as well as for 1I20 reactivity towards the 1918 HA. Therefore, 1F1 heavy-chain interactions with conserved RBS residues likely contribute to its ability to inhibit divergent HAs.

  7. Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation.

    Directory of Open Access Journals (Sweden)

    Dan Su

    2015-01-01

    Full Text Available Cellular stresses activate the tumor suppressor p53 protein leading to selective binding to DNA response elements (REs and gene transactivation from a large pool of potential p53 REs (p53REs. To elucidate how p53RE sequences and local chromatin context interact to affect p53 binding and gene transactivation, we mapped genome-wide binding localizations of p53 and H3K4me3 in untreated and doxorubicin (DXR-treated human lymphoblastoid cells. We examined the relationships among p53 occupancy, gene expression, H3K4me3, chromatin accessibility (DNase 1 hypersensitivity, DHS, ENCODE chromatin states, p53RE sequence, and evolutionary conservation. We observed that the inducible expression of p53-regulated genes was associated with the steady-state chromatin status of the cell. Most highly inducible p53-regulated genes were suppressed at baseline and marked by repressive histone modifications or displayed CTCF binding. Comparison of p53RE sequences residing in different chromatin contexts demonstrated that weaker p53REs resided in open promoters, while stronger p53REs were located within enhancers and repressed chromatin. p53 occupancy was strongly correlated with similarity of the target DNA sequences to the p53RE consensus, but surprisingly, inversely correlated with pre-existing nucleosome accessibility (DHS and evolutionary conservation at the p53RE. Occupancy by p53 of REs that overlapped transposable element (TE repeats was significantly higher (p<10-7 and correlated with stronger p53RE sequences (p<10-110 relative to nonTE-associated p53REs, particularly for MLT1H, LTR10B, and Mer61 TEs. However, binding at these elements was generally not associated with transactivation of adjacent genes. Occupied p53REs located in L2-like TEs were unique in displaying highly negative PhyloP scores (predicted fast-evolving and being associated with altered H3K4me3 and DHS levels. These results underscore the systematic interaction between chromatin status and p53

  8. Inhibition of protein 4.1 R and NuMA interaction by mutagenization of their binding-sites abrogates nuclear localization of 4.1 R.

    Science.gov (United States)

    Mattagajasingh, Subhendra N; Huang, Shu-Ching; Benz, Edward J

    2009-04-01

    Protein 4.1R(4.1R) is a multifunctional structural protein recently implicated in nuclear assembly and cell division. We earlier demonstrated that 4.1R forms a multiprotein complex with mitotic spindle and spindle pole organizing proteins, such as NuMA, dynein, and dynactin, by binding to residues 1788-1810 of NuMA through amino acids encoded by exons 20 and 21 in 24 kD domain. Employing random-and site-directed mutagenesis combined with glycine- and alanine-scanning, we have identified amino acids of 4.1 R and NuMA that sustain their interaction, and have analyzed the effect of mutating the binding sites on their intracellular colocalization. We found that V762, V765, and V767 of 4.1 R, and 11800, 11801,11803, Tl 804, and M1805 of NuMA are necessary for their interaction. GST-fusion peptides of the 4.1R24 kD domain bound to residues 1785-2115 of NuMA in in vitro binding assays, but the binding was inhibited by alanine substitutions of V762, V765, and V767 of 4.1 R, or residues 1800-1805 of NuMA. Additionally, expression of variants of 4.1 R or NuMA that inhibit their in vitro binding also abrogated nuclear localization of 4.1 Rand colocalization with NuMA. Our findings suggest a crucial role of 4.1 R/NuMA interaction in localization and function of 4.1 R in the nucleus.

  9. EPRI's on-site soil-structure interaction research and its application to design/analysis verification

    International Nuclear Information System (INIS)

    Stepp, J.C.; Tang, H.T.

    1988-01-01

    Soil structure, interaction (SSI) research at the Electric Power Research Institute (EPRI) is focused on validating modeling and computational procedures. A data base has been obtained with instrumented scale models of stiff structures founded both on unsaturated alluvial soils and on rock. Explosives were used to induce strong ground-motion for two experiments, one on rock and the other on alluvium. A third experiment, a one-fourth scale containment structure on saturated alluvium, relies on earthquakes as the energy source. Analysis of the explosion-induced SSI data shows a marked shift in the fundamental frequency of the soil-structure system to a lower frequency. The magnitude of the shift is a function of foundation conditions and level of excitation. Analytical simulation was found to require more sophisticated soil constitutive models and computer codes than are used in current practice. The current phase of the program concentrates on evaluating SSI models used in current design practice by comparing predicted with recorded data at points in the soil-structure system. (author)

  10. Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server.

    KAUST Repository

    Olimpieri, Pier Paolo

    2013-06-26

    MOTIVATION: Antibodies or immunoglobulins are proteins of paramount importance in the immune system. They are extremely relevant as diagnostic, biotechnological and therapeutic tools. Their modular structure makes it easy to re-engineer them for specific purposes. Short of undergoing a trial and error process, these experiments, as well as others, need to rely on an understanding of the specific determinants of the antibody binding mode. RESULTS: In this article, we present a method to identify, on the basis of the antibody sequence alone, which residues of an antibody directly interact with its cognate antigen. The method, based on the random forest automatic learning techniques, reaches a recall and specificity as high as 80% and is implemented as a free and easy-to-use server, named prediction of Antibody Contacts. We believe that it can be of great help in re-design experiments as well as a guide for molecular docking experiments. The results that we obtained also allowed us to dissect which features of the antibody sequence contribute most to the involvement of specific residues in binding to the antigen. AVAILABILITY: http://www.biocomputing.it/proABC. CONTACT: anna.tramontano@uniroma1.it or paolo.marcatili@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

  11. Gene interactions and genetics of blast resistance and yield ...

    Indian Academy of Sciences (India)

    2014-08-11

    Aug 11, 2014 ... and environmental variance is estimated from mean variance of the nonsegregating generations (P1, P2, and F1) ( ... tive variance, assuming absence of linkage and environment interaction (Warner 1952). The information is ...... Pesticide Outlook 14, 150–152. Jinks J. L. and Jones R. M 1958 Estimation of ...

  12. Percutaneous internal fixation of proximal fifth metatarsal jones fractures (Zones II and III) with Charlotte Carolina screw and bone marrow aspirate concentrate: an outcome study in athletes.

    Science.gov (United States)

    Murawski, Christopher D; Kennedy, John G

    2011-06-01

    Internal fixation is a popular first-line treatment method for proximal fifth metatarsal Jones fractures in athletes; however, nonunions and screw breakage can occur, in part because of nonspecific fixation hardware and poor blood supply. To report the results from 26 patients who underwent percutaneous internal fixation with a specialized screw system of a proximal fifth metatarsal Jones fracture (zones II and III) and bone marrow aspirate concentrate. Case series; Level of evidence, 4. Percutaneous internal fixation for a proximal fifth metatarsal Jones fracture (zones II and III) was performed on 26 athletic patients (mean age, 27.47 years; range, 18-47). All patients were competing at some level of sport and were assessed preoperatively and postoperatively using the Foot and Ankle Outcome Score and SF-12 outcome scores. The mean follow-up time was 20.62 months (range, 12-28). Of the 26 fractures, 17 were traditional zone II Jones fractures, and the remaining 9 were zone III proximal diaphyseal fractures. The mean Foot and Ankle Outcome Score significantly increased, from 51.15 points preoperatively (range, 14-69) to 90.91 at final follow-up (range, 71-100; P fixation of proximal fifth metatarsal Jones fractures, with a Charlotte Carolina screw and bone marrow aspirate concentrate, provides more predictable results while permitting athletes a return to sport at their previous levels of competition, with few complications.

  13. Volatility Transmission Between Dow Jones Stock Index And Emerging Islamic Stock Index: Case Of Subprime Financial Crises

    Directory of Open Access Journals (Sweden)

    Amir Saadaoui

    2015-02-01

    Full Text Available In the course of the recent global crisis, the stock shocks are distributed and transmitted from their homes in the developed stock market to emerging stock markets. By supporting the development of emerging stock markets, this study aims to see the transmission of volatility between the Dow Jones stock index and the Dow Jones emerging Islamic stock indiex. In this study we have divided the period into three, periods, before, during and after this crisis to demonstrate the resilience of the Islamic market index in response to the global financial crisis. Another aim of this study is to provide a new guide line for investors in emerging stock market before making investment decisions. The data are daily, going from 02/01/2005 until 31/12/2012. To measure the transmission we used bivariate BEKK-GARCH and DCC-GARCH model. The result shows that there is a transmission mainly during the crisis period which means that the crisis affects all the financial assets whether Islamic or not. The same result also shows the preference to invest in both Islamic and classical stock indexes since they are less risky.

  14. Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction.

    Science.gov (United States)

    Palmer, David S; Frolov, Andrey I; Ratkova, Ekaterina L; Fedorov, Maxim V

    2010-12-15

    We report a simple universal method to systematically improve the accuracy of hydration free energies calculated using an integral equation theory of molecular liquids, the 3D reference interaction site model. A strong linear correlation is observed between the difference of the experimental and (uncorrected) calculated hydration free energies and the calculated partial molar volume for a data set of 185 neutral organic molecules from different chemical classes. By using the partial molar volume as a linear empirical correction to the calculated hydration free energy, we obtain predictions of hydration free energies in excellent agreement with experiment (R = 0.94, σ = 0.99 kcal mol (- 1) for a test set of 120 organic molecules).

  15. Myosin heavy chain-like localizes at cell contact sites during Drosophila myoblast fusion and interacts in vitro with Rolling pebbles 7

    Energy Technology Data Exchange (ETDEWEB)

    Bonn, Bettina R.; Rudolf, Anja; Hornbruch-Freitag, Christina; Daum, Gabor; Kuckwa, Jessica; Kastl, Lena; Buttgereit, Detlev [Developmental Biology, Department of Biology, Philipps-Universität Marburg, Karl-von-Frisch-Strasse 8, 35037 Marburg (Germany); Renkawitz-Pohl, Renate, E-mail: renkawit@biologie.uni-marburg.de [Developmental Biology, Department of Biology, Philipps-Universität Marburg, Karl-von-Frisch-Strasse 8, 35037 Marburg (Germany)

    2013-02-15

    Besides representing the sarcomeric thick filaments, myosins are involved in many cellular transport and motility processes. Myosin heavy chains are grouped into 18 classes. Here we show that in Drosophila, the unconventional group XVIII myosin heavy chain-like (Mhcl) is transcribed in the mesoderm of embryos, most prominently in founder cells (FCs). An ectopically expressed GFP-tagged Mhcl localizes in the growing muscle at cell–cell contacts towards the attached fusion competent myoblast (FCM). We further show that Mhcl interacts in vitro with the essential fusion protein Rolling pebbles 7 (Rols7), which is part of a protein complex established at cell contact sites (Fusion-restricted Myogenic-Adhesive Structure or FuRMAS). Here, branched F-actin is likely needed to widen the fusion pore and to integrate the myoblast into the growing muscle. We show that the localization of Mhcl is dependent on the presence of Rols7, and we postulate that Mhcl acts at the FuRMAS as an actin motor protein. We further show that Mhcl deficient embryos develop a wild-type musculature. We thus propose that Mhcl functions redundantly to other myosin heavy chains in myoblasts. Lastly, we found that the protein is detectable adjacent to the sarcomeric Z-discs, suggesting an additional function in mature muscles. - Highlights: ► The class XVIII myosin encoding gene Mhcl is transcribed in the mesoderm. ► Mhcl localization at contact sites of fusing myoblasts depends on Rols7. ► Mhcl interacts in vitro with Rols7 which is essential for myogenesis. ► Functional redundancy with other myosins is likely as mutants show no muscle defects. ► Mhcl localizes adjacent to Z-discs of sarcomeres and might support muscle integrity.

  16. The rapid-onset dystonia parkinsonism mutation D923N of the Na+, K+-ATPase alpha3 isoform disrupts Na+ interaction at the third Na+ site.

    Science.gov (United States)

    Einholm, Anja Pernille; Toustrup-Jensen, Mads S; Holm, Rikke; Andersen, Jens Peter; Vilsen, Bente

    2010-08-20

    Rapid-onset dystonia parkinsonism (RDP), a rare neurological disorder, is caused by mutation of the neuron-specific alpha3-isoform of Na(+), K(+)-ATPase. Here, we present the functional consequences of RDP mutation D923N. Relative to the wild type, the mutant exhibits a remarkable approximately 200-fold reduction of Na(+) affinity for activation of phosphorylation from ATP, reflecting a defective interaction of the E(1) form with intracellular Na(+). This is the largest effect on Na(+) affinity reported so far for any Na(+), K(+)-ATPase mutant. D923N also affects the interaction with extracellular Na(+) normally driving the E(1)P to E(2)P conformational transition backward. However, no impairment of K(+) binding was observed for D923N, leading to the conclusion that Asp(923) is specifically associated with the third Na(+) site that is selective toward Na(+). The crystal structure of the Na(+), K(+)-ATPase in E(2) form shows that Asp(923) is located in the cytoplasmic half of transmembrane helix M8 inside a putative transport channel, which is lined by residues from the transmembrane helices M5, M7, M8, and M10 and capped by the C terminus, recently found involved in recognition of the third Na(+) ion. Structural modeling of the E(1) form of Na(+), K(+)-ATPase based on the Ca(2+)-ATPase crystal structure is consistent with the hypothesis that Asp(923) contributes to a site binding the third Na(+) ion. These results in conjunction with our previous findings with other RDP mutants suggest that a selective defect in the handling of Na(+) may be a general feature of the RDP disorder.

  17. Growth rate variation among passerine species in tropical and temperate sites: an antagonistic interaction between parental food provisioning and nest predation risk

    Science.gov (United States)

    Martin, Thomas E.; Llyod, Penn; Bosque, Carlos; Barton, Daniel C.; Biancucci, Atilio L.; Cheng, Yi-Ru; Ton, Riccardo

    2011-01-01

    Causes of interspecific variation in growth rates within and among geographic regions remain poorly understood. Passerine birds represent an intriguing case because differing theories yield the possibility of an antagonistic interaction between nest predation risk and food delivery rates on evolution of growth rates. We test this possibility among 64 Passerine species studied on three continents, including tropical and north and south temperate latitudes. Growth rates increased strongly with nestling predation rates within, but not between, sites. The importance of nest predation was further emphasized by revealing hidden allometric scaling effects. Nestling predation risk also was associated with reduced total feeding rates and per-nestling feeding rates within each site. Consequently, faster growth rates were associated with decreased per-nestling food delivery rates across species, both within and among regions. These relationships suggest that Passerines can evolve growth strategies in response to predation risk whereby food resources are not the primary limit on growth rate differences among species. In contrast, reaction norms of growth rate relative to brood size suggest that food may limit growth rates within species in temperate, but not tropical, regions. Results here provide new insight into evolution of growth strategies relative to predation risk and food within and among species.

  18. Multiple RNA interactions position Mrd1 at the site of the small subunit pseudoknot within the 90S pre-ribosome.

    Science.gov (United States)

    Segerstolpe, Åsa; Granneman, Sander; Björk, Petra; de Lima Alves, Flavia; Rappsilber, Juri; Andersson, Charlotta; Högbom, Martin; Tollervey, David; Wieslander, Lars

    2013-01-01

    Ribosomal subunit biogenesis in eukaryotes is a complex multistep process. Mrd1 is an essential and conserved small (40S) ribosomal subunit synthesis factor that is required for early cleavages in the 35S pre-ribosomal RNA (rRNA). Yeast Mrd1 contains five RNA-binding domains (RBDs), all of which are necessary for optimal function of the protein. Proteomic data showed that Mrd1 is part of the early pre-ribosomal complexes, and deletion of individual RBDs perturbs the pre-ribosomal structure. In vivo ultraviolet cross-linking showed that Mrd1 binds to the pre-rRNA at two sites within the 18S region, in helix 27 (h27) and helix 28. The major binding site lies in h27, and mutational analyses shows that this interaction requires the RBD1-3 region of Mrd1. RBD2 plays the dominant role in h27 binding, but other RBDs also contribute directly. h27 and helix 28 are located close to the sequences that form the central pseudoknot, a key structural feature of the mature 40S subunit. We speculate that the modular structure of Mrd1 coordinates pseudoknot formation with pre-rRNA processing and subunit assembly.

  19. Addictive use of social networking sites can be explained by the interaction of Internet use expectancies, Internet literacy, and psychopathological symptoms.

    Science.gov (United States)

    Wegmann, Elisa; Stodt, Benjamin; Brand, Matthias

    2015-09-01

    Most people use the Internet in a functional way to achieve certain goals and needs. However, there is an increasing number of people who experience negative consequences like loss of control and distress based on an excessive use of the Internet and its specific online applications. Some approaches postulate similarities with behavioral addictions as well as substance dependencies. They differentiate between a generalized and a specific Internet addiction, such as the pathological use of social networking sites (SIA-SNS). Prior studies particularly identified the use of applications, personal characteristics, and psychopathological symptoms as significant predictors for the development and maintenance of this phenomenon. So far, it remains unclear how psychopathological symptoms like depression and social anxiety interact with individual expectancies of Internet use and capabilities of handling the Internet, summarized as Internet literacy. The current study (N = 334) investigated the interaction of these components in a structural equation model. The results indicate that the effects of depression and social anxiety on SIA-SNS were mediated by Internet use expectancies and self-regulation. Thus, Internet use expectancies seem to be crucial for SIA-SNS, which is in line with prior models. SNS use may be reinforced by experienced gratification and relief from negative feelings. Individual competences in handling the Internet may be preventive for the development of SIA-SNS.

  20. TERRA mimicking ssRNAs prevail over the DNA substrate for telomerase in vitro due to interactions with the alternative binding site.

    Science.gov (United States)

    Azhibek, Dulat; Skvortsov, Dmitry; Andreeva, Anna; Zatsepin, Timofei; Arutyunyan, Alexandr; Zvereva, Maria; Dontsova, Olga

    2016-06-01

    Telomerase is a key component of the telomere length maintenance system in the majority of eukaryotes. Telomerase displays maximal activity in stem and cancer cells with high proliferative potential. In humans, telomerase activity is regulated by various mechanisms, including the interaction with telomere ssDNA overhangs that contain a repetitive G-rich sequence, and with noncoding RNA, Telomeric repeat-containing RNA (TERRA), that contains the same sequence. So these nucleic acids can compete for telomerase RNA templates in the cell. In this study, we have investigated the ability of different model substrates mimicking telomere DNA overhangs and TERRA RNA to compete for telomerase in vitro through a previously developed telomerase inhibitor assay. We have shown in this study that RNA oligonucleotides are better competitors for telomerase that DNA ones as RNA also use an alternative binding site on telomerase, and the presence of 2'-OH groups is significant in these interactions. In contrast to DNA, the possibility of forming intramolecular G-quadruplex structures has a minor effect for RNA binding to telomerase. Taking together our data, we propose that TERRA RNA binds better to telomerase compared with its native substrate - the 3'-end of telomere DNA overhang. As a result, some specific factor may exist that participates in switching telomerase from TERRA to the 3'-end of DNA for telomere elongation at the distinct period of a cell cycle in vivo. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  1. GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site*

    Science.gov (United States)

    Lu, Shaoyong; Banerjee, Avik; Jang, Hyunbum; Zhang, Jian; Gaponenko, Vadim; Nussinov, Ruth

    2015-01-01

    K-Ras4B, a frequently mutated oncogene in cancer, plays an essential role in cell growth, differentiation, and survival. Its C-terminal membrane-associated hypervariable region (HVR) is required for full biological activity. In the active GTP-bound state, the HVR interacts with acidic plasma membrane (PM) headgroups, whereas the farnesyl anchors in the membrane; in the inactive GDP-bound state, the HVR may interact with both the PM and the catalytic domain at the effector binding region, obstructing signaling and nucleotide exchange. Here, using molecular dynamics simulations and NMR, we aim to figure out the effects of nucleotides (GTP and GDP) and frequent (G12C, G12D, G12V, G13D, and Q61H) and infrequent (E37K and R164Q) oncogenic mutations on full-length K-Ras4B. The mutations are away from or directly at the HVR switch I/effector binding site. Our results suggest that full-length wild-type GDP-bound K-Ras4B (K-Ras4BWT-GDP) is in an intrinsically autoinhibited state via tight HVR-catalytic domain interactions. The looser association in K-Ras4BWT-GTP may release the HVR. Some of the oncogenic mutations weaken the HVR-catalytic domain association in the K-Ras4B-GDP/-GTP bound states, which may facilitate the HVR disassociation in a nucleotide-independent manner, thereby up-regulating oncogenic Ras signaling. Thus, our results suggest that mutations can exert their effects in more than one way, abolishing GTP hydrolysis and facilitating effector binding. PMID:26453300

  2. GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site.

    Science.gov (United States)

    Lu, Shaoyong; Banerjee, Avik; Jang, Hyunbum; Zhang, Jian; Gaponenko, Vadim; Nussinov, Ruth

    2015-11-27

    K-Ras4B, a frequently mutated oncogene in cancer, plays an essential role in cell growth, differentiation, and survival. Its C-terminal membrane-associated hypervariable region (HVR) is required for full biological activity. In the active GTP-bound state, the HVR interacts with acidic plasma membrane (PM) headgroups, whereas the farnesyl anchors in the membrane; in the inactive GDP-bound state, the HVR may interact with both the PM and the catalytic domain at the effector binding region, obstructing signaling and nucleotide exchange. Here, using molecular dynamics simulations and NMR, we aim to figure out the effects of nucleotides (GTP and GDP) and frequent (G12C, G12D, G12V, G13D, and Q61H) and infrequent (E37K and R164Q) oncogenic mutations on full-length K-Ras4B. The mutations are away from or directly at the HVR switch I/effector binding site. Our results suggest that full-length wild-type GDP-bound K-Ras4B (K-Ras4B(WT)-GDP) is in an intrinsically autoinhibited state via tight HVR-catalytic domain interactions. The looser association in K-Ras4B(WT)-GTP may release the HVR. Some of the oncogenic mutations weaken the HVR-catalytic domain association in the K-Ras4B-GDP/-GTP bound states, which may facilitate the HVR disassociation in a nucleotide-independent manner, thereby up-regulating oncogenic Ras signaling. Thus, our results suggest that mutations can exert their effects in more than one way, abolishing GTP hydrolysis and facilitating effector binding. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Exploring the interactions and binding sites between Cd and functional groups in soil using two-dimensional correlation spectroscopy and synchrotron radiation based spectromicroscopies

    International Nuclear Information System (INIS)

    Sun, Fusheng; Polizzotto, Matthew L.; Guan, Dongxing; Wu, Jun; Shen, Qirong; Ran, Wei; Wang, Boren; Yu, Guanghui

    2017-01-01

    Highlights: • The interactions and binding between Cd and functional groups are essential for their fates. • Two-dimensional correlation spectroscopy can identify Cd binding to functional groups in soils. • Synchrotron radiation based spectromicroscopy shows the micro-scale distribution of Cd in soils. • Soil functional groups controlling Cd binding can be modified by fertilization treatments. - Abstract: Understanding how heavy metals bind and interact in soils is essential for predicting their distributions, reactions and fates in the environment. Here we propose a novel strategy, i.e., combining two-dimensional correlation spectroscopy (2D COS) and synchrotron radiation based spectromicroscopies, for identifying heavy metal binding to functional groups in soils. The results showed that although long-term (23 yrs) organic fertilization treatment caused the accumulation of Cd (over 3 times) in soils when compared to no fertilization and chemical fertilization treatments, it significantly (p < 0.05) reduced the Cd concentration in wheat grain. The 2D COS analyses demonstrated that soil functional groups controlling Cd binding were modified by fertilization treatments, providing implications for the reduced bioavailability of heavy metals in organic fertilized soils. Furthermore, correlative micro X-ray fluorescence spectromicroscopy, electron probe micro-analyzer mapping, and synchrotron-radiation-based FTIR spectromicroscopy analysis showed that Cd, minerals, and organic functional groups were heterogeneously distributed at the micro-scale in soil colloids. Only minerals, rather than organic groups, had a similar distribution pattern with Cd. Together, this strategy has a potential to explore the interactions and binding sites among heavy metals, minerals and organic components in soil.

  4. Exploring the interactions and binding sites between Cd and functional groups in soil using two-dimensional correlation spectroscopy and synchrotron radiation based spectromicroscopies

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Fusheng [Jiangsu Provincial Key Lab for Organic Solid Waste Utilization and National Engineering Research Center for Organic-Based Fertilizers, College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095 (China); Department of Soil Science, North Carolina State University, Raleigh, NC 27695 (United States); Polizzotto, Matthew L. [Department of Soil Science, North Carolina State University, Raleigh, NC 27695 (United States); Guan, Dongxing [Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210026 (China); Wu, Jun [College of Environment, Zhejiang University of Technology, Hangzhou 310014 (China); Shen, Qirong; Ran, Wei [Jiangsu Provincial Key Lab for Organic Solid Waste Utilization and National Engineering Research Center for Organic-Based Fertilizers, College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095 (China); Wang, Boren [Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081 (China); Yu, Guanghui, E-mail: yuguanghui@njau.edu.cn [Jiangsu Provincial Key Lab for Organic Solid Waste Utilization and National Engineering Research Center for Organic-Based Fertilizers, College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095 (China)

    2017-03-15

    Highlights: • The interactions and binding between Cd and functional groups are essential for their fates. • Two-dimensional correlation spectroscopy can identify Cd binding to functional groups in soils. • Synchrotron radiation based spectromicroscopy shows the micro-scale distribution of Cd in soils. • Soil functional groups controlling Cd binding can be modified by fertilization treatments. - Abstract: Understanding how heavy metals bind and interact in soils is essential for predicting their distributions, reactions and fates in the environment. Here we propose a novel strategy, i.e., combining two-dimensional correlation spectroscopy (2D COS) and synchrotron radiation based spectromicroscopies, for identifying heavy metal binding to functional groups in soils. The results showed that although long-term (23 yrs) organic fertilization treatment caused the accumulation of Cd (over 3 times) in soils when compared to no fertilization and chemical fertilization treatments, it significantly (p < 0.05) reduced the Cd concentration in wheat grain. The 2D COS analyses demonstrated that soil functional groups controlling Cd binding were modified by fertilization treatments, providing implications for the reduced bioavailability of heavy metals in organic fertilized soils. Furthermore, correlative micro X-ray fluorescence spectromicroscopy, electron probe micro-analyzer mapping, and synchrotron-radiation-based FTIR spectromicroscopy analysis showed that Cd, minerals, and organic functional groups were heterogeneously distributed at the micro-scale in soil colloids. Only minerals, rather than organic groups, had a similar distribution pattern with Cd. Together, this strategy has a potential to explore the interactions and binding sites among heavy metals, minerals and organic components in soil.

  5. Cell adhesion molecules in the development of inflammatory infiltrates in giant cell arteritis: inflammation-induced angiogenesis as the preferential site of leukocyte-endothelial cell interactions.

    Science.gov (United States)

    Cid, M C; Cebrián, M; Font, C; Coll-Vinent, B; Hernández-Rodríguez, J; Esparza, J; Urbano-Márquez, A; Grau, J M

    2000-01-01

    To investigate the expression pattern of adhesion molecules involved in leukocyte-endothelial cell interactions in giant cell arteritis (GCA). Immunohistochemical analysis was performed on frozen temporal artery sections from 32 patients with biopsy-proven GCA and from 12 control patients with other diseases. Adhesion molecules identified were intercellular adhesion molecule 1 (ICAM-1), ICAM-2, ICAM-3, vascular cell adhesion molecule 1 (VCAM-1), platelet endothelial cell adhesion molecule 1 (PECAM-1), E-selectin, P-selectin, L-selectin, lymphocyte function-associated antigen 1 (LFA-1), very late activation antigen 4 (VLA-4), Mac-1 (CD18/CD11b), and gp 150,95 (CD18/CD11c). Clinical and biochemical parameters of inflammation in the patients, as well as the duration of previous corticosteroid treatment, were prospectively recorded. Constitutive (PECAM-1, ICAM-1, ICAM-2, and P-selectin) and inducible (E-selectin and VCAM-1) endothelial adhesion molecules for leukocytes were mainly expressed by adventitial microvessels and neovessels within inflammatory infiltrates. Concurrent analysis of leukocyte receptors indicated a preferential use of VLA-4/VCAM-1 and LFA-1/ICAM-1 at the adventitia and Mac-1/ICAM-1 at the intima-media junction. The intensity of inducible endothelial adhesion molecule expression (E-selectin and VCAM-1) correlated with the intensity of the systemic inflammatory response. Previous corticosteroid treatment reduced, but did not completely abrogate, the expression of the inducible endothelial adhesion molecules E-selectin and VCAM-1. Inflammation-induced angiogenesis is the main site of leukocyte-endothelial cell interactions leading to the development of inflammatory infiltrates in GCA. The distribution of leukocyte-endothelial cell ligand pairs suggests a heterogeneity in leukocyte-endothelial cell interactions used by different functional cell subsets at distinct areas of the temporal artery.

  6. Biomechanical warfare in ecology; negative interactions between species by habitat modification

    NARCIS (Netherlands)

    Van Wesenbeeck, B.K.; Van de Koppel, J.; Herman, P.M.J.; Bakker, J.P.; Bouma, T.J.

    2007-01-01

    Since the introduction of the term ecosystem engineering by Jones et al. many studies have focused on positive, facilitative interactions caused by ecosystem engineering. Much less emphasis has been placed on the role of ecosystem engineering in causing negative interactions between species. Here,

  7. Biomechanical warfare in ecology; negative interactions between species by habitat modification

    NARCIS (Netherlands)

    van Wesenbeeck, B. K.; van de Koppel, J.; Herman, P. M. J.; Bakker, J. P.; Bouma, T. J.

    Since the introduction of the term ecosystem engineering by Jones et al. many studies have focused on positive, facilitative interactions caused by ecosystem engineering. Much less emphasis has been placed on the role of ecosystem engineering in causing negative interactions between species. Here,

  8. Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer

    Directory of Open Access Journals (Sweden)

    Casuyac Miqueas

    2016-01-01

    Full Text Available This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNRusing the classical molecular dynamic (MD simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator. The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO potential for hydrogen – hydrogen interaction and the LennardJones potential for the physisorbed H2 on SiNR. By varying the temperatures (60 K Δ 130 K, we observed that the Δxdisplacement of H2 on the surface SiNR shows a Brownian motion on a Lennard-Jones potential and a Gaussian probability distribution can be plotted describing the diffusion of H2. The calculated mean square displacement (MSD was approximately increasing in time and the activation energy barrier for diffusion has been found to be 43.23meV.

  9. Modeling of Hydraulic Fracturing on the Basis of the Particle Method

    Science.gov (United States)

    Berezhnoi, D. V.; Gabsalikova, N. F.; Izotov, V. G.; Miheev, V. V.

    2018-01-01

    A technique of calculating the deformation of the soil environment when it interacts with a liquid on the basis of the particle method a is realized. To describe the behavior of the solid and liquid phases of the soil, a classical two-parameter Lennard-Jones interaction potential and its modified version proposed by the authors were chosen. The model problem of deformation and partial destruction of a soil massif under strong pressure from the liquid pumped into it is solved. Analysis of the results shows that the use of the modified Lennard-Jones potential for describing the solid phase of the soil environment makes it possible to describe the process of formation of cracks in the soil during hydraulic fracturing of the formation.

  10. Interaction of alpha-conotoxin ImII and its analogs with nicotinic receptors and acetylcholine-binding proteins: additional binding sites on Torpedo receptor.

    Science.gov (United States)

    Kasheverov, Igor E; Zhmak, Maxim N; Fish, Alexander; Rucktooa, Prakash; Khruschov, Alexey Yu; Osipov, Alexey V; Ziganshin, Rustam H; D'hoedt, Dieter; Bertrand, Daniel; Sixma, Titia K; Smit, August B; Tsetlin, Victor I

    2009-11-01

    alpha-Conotoxins interact with nicotinic acetylcholine receptors (nAChRs) and acetylcholine-binding proteins (AChBPs) at the sites for agonists/competitive antagonists. alpha-Conotoxins blocking muscle-type or alpha7 nAChRs compete with alpha-bungarotoxin. However, alpha-conotoxin ImII, a close homolog of the alpha7 nAChR-targeting alpha-conotoxin ImI, blocked alpha7 and muscle nAChRs without displacing alpha-bungarotoxin (Ellison et al. 2003, 2004), suggesting binding at a different site. We synthesized alpha-conotoxin ImII, its ribbon isomer (ImIIiso), 'mutant' ImII(W10Y) and found similar potencies in blocking human alpha7 and muscle nAChRs in Xenopus oocytes. Both isomers displaced [(125)I]-alpha-bungarotoxin from human alpha7 nAChRs in the cell line GH(4)C(1) (IC(50) 17 and 23 microM, respectively) and from Lymnaea stagnalis and Aplysia californica AChBPs (IC(50) 2.0-9.0 microM). According to SPR measurements, both isomers bound to immobilized AChBPs and competed with AChBP for immobilized alpha-bungarotoxin (K(d) and IC(50) 2.5-8.2 microM). On Torpedo nAChR, alpha-conotoxin [(125)I]-ImII(W10Y) revealed specific binding (K(d) 1.5-6.1 microM) and could be displaced by alpha-conotoxin ImII, ImIIiso and ImII(W10Y) with IC(50) 2.7, 2.2 and 3.1 microM, respectively. As alpha-cobratoxin and alpha-conotoxin ImI displaced [(125)I]-ImII(W10Y) only at higher concentrations (IC(50)> or = 90 microM), our results indicate that alpha-conotoxin ImII and its congeners have an additional binding site on Torpedo nAChR distinct from the site for agonists/competitive antagonists.

  11. The Emperor Jones de Louis Gruenberg : le long voyage au cœur/corps de l’Autre race Louis Gruenberg’s Emperor Jones: The Long Journey into the Heart of the Other Race

    Directory of Open Access Journals (Sweden)

    Benoît Depardieu

    2009-11-01

    Full Text Available On January 7, 1933, two years before Gershwin’s Porgy and Bess, The Emperor Jones, composed by Louis Gruenberg in 1931, had its world premiere at the Metropolitan Opera of New York. Although Gruenberg’s opera looks like a mere musical adaptation of O’Neill’s acclaimed play, first performed in 1920, some alterations made by the composer allow to question its ambivalent reception by the audience and the critics. Apart from the singular choice of O’Neill’s play and Gruenberg’s special interest in African American music and vocal traditions, this paper analyses the influence of the Harlem Renaissance period and the fantasmatics of race, present in both the play and the opera, albeit exacerbated in the latter through the scopic enjoyment of the body of the black Other.

  12. MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease.

    Science.gov (United States)

    Gunner, M R; Zhu, Xuyu; Klein, Max C

    2011-12-01

    The pK(a)s of 96 acids and bases introduced into buried sites in the staphylococcal nuclease protein (SNase) were calculated using the multiconformation continuum electrostatics (MCCE) program and the results compared with experimental values. The pK(a)s are obtained by Monte Carlo sampling of coupled side chain protonation and position as a function of pH. The dependence of the results on the protein dielectric constant (ε(prot)) in the continuum electrostatics analysis and on the Lennard-Jones non-electrostatics parameters was evaluated. The pK(a)s of the introduced residues have a clear dependence on ε(prot,) whereas native ionizable residues do not. The native residues have electrostatic interactions with other residues in the protein favoring ionization, which are larger than the desolvation penalty favoring the neutral state. Increasing ε(prot) scales both terms, which for these residues leads to small changes in pK(a). The introduced residues have a larger desolvation penalty and negligible interactions with residues in the protein. For these residues, changing ε(prot) has a large influence on the calculated pK(a). An ε(prot) of 8-10 and a Lennard-Jones scaling of 0.25 is best here. The X-ray crystal structures of the mutated proteins are found to provide somewhat better results than calculations carried out on mutations made in silico. Initial relaxation of the in silico mutations by Gromacs and extensive side chain rotamer sampling within MCCE can significantly improve the match with experiment. Copyright © 2011 Wiley-Liss, Inc.

  13. Effective diameters and corresponding states of fluids

    Science.gov (United States)

    Del Río, Fernando

    Effective hard-sphere diameters of fluids with purely repulsive interactions are derived from a generalized corresponding-states principle of Leland, Rowlinson and coworkers. Various alternative definitions are discussed and related. Virial expansions of the effective diameters and their corresponding volumes are obtained and compared with results of perturbation theory. Applications are made to inverse-power potentials, the repulsive part of the Lennard-Jones potential and hard spherocylinders and dumbells.

  14. Molecular dynamics simulation of a chemical reaction

    International Nuclear Information System (INIS)

    Gorecki, J.; Gryko, J.

    1988-06-01

    Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs

  15. Generalized Lyapunov exponents of the random harmonic oscillator: Cumulant expansion approach

    Science.gov (United States)

    Vallejos, Raúl O.; Anteneodo, Celia

    2012-02-01

    The cumulant expansion is used to estimate generalized Lyapunov exponents of the random-frequency harmonic oscillator. Three stochastic processes are considered: Gaussian white noise, Ornstein-Uhlenbeck, and Poisson shot noise. In some cases, nontrivial numerical difficulties arise. These are mostly solved by implementing an appropriate importance-sampling Monte Carlo scheme. We analyze the relation between random-frequency oscillators and many-particle systems with pairwise interactions like the Lennard-Jones gas.

  16. Noise-immune complex correlation for optical coherence angiography based on standard and Jones matrix optical coherence tomography.

    Science.gov (United States)

    Makita, Shuichi; Kurokawa, Kazuhiro; Hong, Young-Joo; Miura, Masahiro; Yasuno, Yoshiaki

    2016-04-01

    This paper describes a complex correlation mapping algorithm for optical coherence angiography (cmOCA). The proposed algorithm avoids the signal-to-noise ratio dependence and exhibits low noise in vasculature imaging. The complex correlation coefficient of the signals, rather than that of the measured data are estimated, and two-step averaging is introduced. Algorithms of motion artifact removal based on non perfusing tissue detection using correlation are developed. The algorithms are implemented with Jones-matrix OCT. Simultaneous imaging of pigmented tissue and vasculature is also achieved using degree of polarization uniformity imaging with cmOCA. An application of cmOCA to in vivo posterior human eyes is presented to demonstrate that high-contrast images of patients' eyes can be obtained.

  17. Geochemical modelling of water-rock interactions at the Osamu Utsumi mine and Morro do Ferro analogue study sites, Pocos de Caldas, Brazil

    International Nuclear Information System (INIS)

    Nordstrom, D.K.; Puigdomenech, I.; McNutt, R.H.

    1990-01-01

    Geochemical processes involving water-rock interactions have been modelled using groundwater composition, mineralogical data, ion plots and computations of speciation, non-thermodynamic mass balance and thermodynamic mass transfer for two natural analogue sites near Pocos de Caldas, Brazil: the Osamu Utsumi mine and Morro do Ferro. The main rock type is an alkaline igneous complex composed of volcanic and sub-volcanic phonolites that have been hydrothermally altered and highly weathered. This altered rock mass grades from a laterite at the surface to a saprolite and finally to unweathered, hydrothermally altered bedrock at depth. The mine site contains high concentrations of uranium and Morro do Ferro contains high concentrations of thorium and rare-earths. The reaction models can reproduce the water chemistry and mineral occurences and they were validated by predicting the masses of minerals precipitated and the pH of the final water. The model computations can also reproduce the pH and iron concentrations of the water samples during CO 2 degassing and iron(II) oxidation from exposure to air. The results from the geochemical reaction models reveal that the dominant processes are production of CO 2 in the soil zone through aerobic decay of organic matter, dissolution of fluorite, calcite, K-feldspar, albite and manganese oxides, oxidation of pyrite and sphalerite and precipitation of ferric oxides, silica and kaolinite. Recharge waters are undersaturated with respect to barite and discharging waters and deeper groundwaters are saturated to supersaturated with respect to barite, demonstrating a strong equilibrium solubility control. Strontium isotope data demonstrate that sources other than calcium-bearing minerals are required to account for the dissolved strontium in the ground. These may include K-feldspar, smectite-chlorite mixed-layer clays and goyazite. (author) 24 figs., 4 tabs., 18 refs

  18. Ouincy Jones / Quincy Jones ; intervjueerinud Emil Wilbekin

    Index Scriptorium Estoniae

    Jones, Quincy, 1933-

    2009-01-01

    Endise jazzartisti ja preaguse muusikaärimehe, produtsendi Quincy Jonesi mõtteid tööst viieosalise dokumentaalfilmiga "Say it Loud: Black Music in America" , tööst Michael Jacksoniga ja muusikast

  19. Pramana – Journal of Physics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    We have carried out Monte Carlo simulations in Gibbs ensemble for two-and three-dimensional double Yukawa fluid. We have compared liquid–vapour equilibrium curve with that of Lennard-Jones, when parameters occurring in double Yukawa potential are chosen to fit Lennard-Jones potential. The results are in good ...

  20. Equation of state of matter irradiated by short laser pulse and geometry of spalled cupola

    Science.gov (United States)

    Petrov, Yu. V.; Zhakhovskii, V. V.; Inogamov, N. A.; Ashitkov, S. I.; Khokhlov, V. A.; Upadhyay, A. K.; Agranat, M. B.; Anisimov, S. I.; Nishihara, K.; Rethfeld, B.; Urbassek, H. M.

    2008-05-01

    The motion of both Lennard-Jones solids and metals induced by ultrashort laser irradiation near the ablation threshold is investigated by molecular dynamics simulation. The universality of the ablation threshold fluence with respect to the cohesion energy of solids irradiated by femtosecond laser pulses is demonstrated for Lennard-Jones solid and metals simulated by many-body EAM potentials.

  1. Vapour–liquid equilibria of the two-and three-dimensional ...

    Indian Academy of Sciences (India)

    We have carried out Monte Carlo simulations in Gibbs ensemble for two-and three-dimensional double Yukawa fluid. We have compared liquid–vapour equilibrium curve with that of Lennard-Jones, when parameters occurring in double Yukawa potential are chosen to fit Lennard-Jones potential. The results are in good ...

  2. Characterization of iron and manganese minerals and their associated microbiota in different mine sites to reveal the potential interactions of microbiota with mineral formation.

    Science.gov (United States)

    Park, Jin Hee; Kim, Bong-Soo; Chon, Chul-Min

    2018-01-01

    Different environmental conditions such as pH and dissolved elements of mine stream induce precipitation of different minerals and their associated microbial community may vary. Therefore, mine precipitates from various environmental conditions were collected and their associated microbiota were analyzed through metagenomic DNA sequencing. Various Fe and Mn minerals including ferrihydrite, schwertmannite, goethite, birnessite, and Mn-substituted δ-FeOOH (δ-(Fe 1-x , Mn x )OOH) were found in the different environmental conditions. The Fe and Mn minerals were enriched with toxic metal(loid)s including As, Cd, Ni and Zn, indicating they can act as scavengers of toxic metal(loid)s in mine streams. Under acidic conditions, Acidobacteria was dominant phylum and Gallionella (Fe oxidizing bacteria) was the predominant genus in these Fe rich environments. Manganese oxidizing bacteria, Hyphomicrobium, was found in birnessite forming environments. Leptolyngbya within Cyanobacteria was found in Fe and Mn oxidizing environments, and might contribute to Fe and Mn oxidation through the production of molecular oxygen. The potential interaction of microbial community with minerals in mine sites can be traced by analysis of microbial community in different Fe and Mn mineral forming environments. Iron and Mn minerals contribute to the removal of toxic metal(loid)s from mine water. Therefore, the understanding characteristics of mine precipitates and their associated microbes helps to develop strategies for the management of contaminated mine water. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. In situ determination of the dynamic properties of thinly-layered rock to evaluate rock-structure interaction at a nuclear power plant site

    International Nuclear Information System (INIS)

    Johnson, William J.; Rizzo, Paul C.

    1988-01-01

    The presence of layers of weak sedimentary rock in a column of otherwise competent rock can significantly affect the seismic response of nuclear power plant structures due to rock-structure interaction effects. The determination of the dynamic properties of thinly-layered rock is, however, difficult. When borings are placed close enough to allow for a characterization of refracted waves, other potential problems such as the identification of clear P- and S-wave arrivals, extremely short duration of records, near-field waves, instrumental stability, and overall record resolution become magnified. Other problems such as cultural noise and signal amplitude can become critical when high resolution is required. Conventional storage oscilloscopes and seismographs are inadequate under these conditions, but modern digital recording systems with the application of stringent calibration and recording procedures can yield successful results. A case history of a high-precision cross-hole survey to a depth of 150 meters in thinly-bedded sedimentary rock at a nuclear power plant site is presented in order to illustrate the systems and procedures necessary to obtain successful results under adverse conditions. (author)

  4. A QM/MM and QM/QM/MM study of Kerr, Cotton-Mouton and Jones linear birefringences in liquid acetonitrile

    DEFF Research Database (Denmark)

    Fahleson, Tobias; Olsen, Jógvan Magnus Haugaard; Norman, Patrick

    2018-01-01

    QM/MM and QM/QM/MM protocols are applied to the ab initio study of the three linear birefringences Kerr, Cotton-Mouton, and Jones, as shown by acetonitrile in the gas and pure liquid phases. The relevant first-order properties as well as linear, quadratic, and cubic frequency-dependent response...

  5. The white-margined penstemon (Penstemon albomarginatus Jones), a rare Mohave Desert species, and the Hualapai Mountains land exchange in Mohave County, Arizona

    Science.gov (United States)

    John L. Anderson

    2001-01-01

    The white-margined penstemon (Penstemon albomarginatus Jones) is a rare Mohave Desert species with an unusual tripartite distribution with disjunct localities in Arizona, California, and Nevada. The Arizona population is the largest single population occurring with a range of 15 miles by 5 miles in Dutch Flat near Yucca, Arizona in Mohave County. The land ownership...

  6. Sex Differences in Left-Handedness Are Also Evident in Scandinavia and in Twins: Comment on Papadatou-Pastou, Martin, Munafo, and Jones (2008)

    Science.gov (United States)

    Vuoksimaa, Eero; Kaprio, Jaakko

    2010-01-01

    The lack of sex difference in left-handedness in Scandinavian countries reported by Papadatou-Pastou, Martin, Munafo, and Jones (2008) is questioned. We investigated the sex difference in left-handedness in two Finnish, one Norwegian, and one Swedish population-based sample not included in the Papadatou-Pastou et al. (2008) meta-analysis. The…

  7. Scaling of viscous dynamics in simple liquids

    DEFF Research Database (Denmark)

    Bøhling, Lasse; Ingebrigtsen, Trond; Grzybowski, A.

    2012-01-01

    Supercooled liquids are characterized by relaxation times that increase dramatically by cooling or compression. From a single assumption follows a scaling law according to which the relaxation time is a function of h(ρ) over temperature, where ρ is the density and the function h(ρ) depends...... on the liquid in question. This scaling is demonstrated to work well for simulations of the Kob–Andersen binary Lennard-Jones mixture and two molecular models, as well as for the experimental results for two van der Waals liquids, dibutyl phthalate and decahydroisoquinoline. The often used power-law density...... scaling, h(ρ)∝ργ, is an approximation to the more general form of scaling discussed here. A thermodynamic derivation was previously given for an explicit expression for h(ρ) for liquids of particles interacting via the generalized Lennard-Jones potential. Here a statistical mechanics derivation is given...

  8. Phononless soliton waves as early forerunners of crystalline material fracture

    International Nuclear Information System (INIS)

    Dubovskij, O.A.; Orlov, A.V.

    2007-01-01

    Phononless soliton waves of compression are shown to generate at a critical tension of crystals featuring real Lennard-Jones potential of interatomic interaction just before their fracture. A new method of nonlinear micro dynamics was applied to define the initial atomic displacements at high excitation energies. A solution is found that corresponds to a soliton wave running before the front of fracture. In a bounded crystal, the soliton being reflected from the crystal boundary passes the front of fracture and deforms while moving in the opposite direction. The amplitude and spectral characteristics of that type of soliton waves in crystals with a modified Lennard-Jones potential have been investigated. An approximate analytical solution was found for the soliton waves [ru

  9. Isomorph invariance of the structure and dynamics of classical crystals

    DEFF Research Database (Denmark)

    Albrechtsen, Dan; Olsen, Andreas Elmerdahl; Pedersen, Ulf Rørbæk

    2014-01-01

    This paper shows by computer simulations that some crystalline systems have curves in their thermodynamic phase diagrams, so-called isomorphs, along which structure and dynamics in reduced units are invariant to a good approximation. The crystals are studied in a classical-mechanical framework......, which is generally a good description except significantly below melting. The existence of isomorphs for crystals is validated by simulations of particles interacting via the Lennard-Jones pair potential arranged into a face-centered cubic (fcc) crystalline structure; the slow vacancy-jump dynamics...... of a defective fcc crystal is also shown to be isomorph invariant. In contrast, a NaCl crystal model does not exhibit isomorph invariances. Other systems simulated, though in less detail, are the Wahnström binary Lennard-Jones crystal with the MgZn2 Laves crystal structure, monatomic fcc crystals of particles...

  10. Graphene on Cu(111) at the nonzero temperatures: Molecular dynamic simulation

    Science.gov (United States)

    Sidorenkov, A. V.; Kolesnikov, S. V.; Saletsky, A. M.

    2017-11-01

    We present results of molecular dynamic simulation of continuous graphene monolayer on Cu(111). In this paper, we investigate the dependencies of the average binding energy and the average binding distance on the temperature. The interaction between carbon and copper atoms was described by Lennard-Jones potential. It is shown that the binding energy practically remains constant in a wide range of temperatures 0-800 K. However, in the same temperature range, the binding distance of graphene on Cu(111) surface has a linear dependence on temperature. The dependence of the linear thermal expansion coefficient of the binding distance on Lennard-Jones parameters has been calculated. We suggest a simple theoretical model to explain this dependence qualitatively.

  11. Revision of the Jones Criteria for the diagnosis of acute rheumatic fever in the era of Doppler echocardiography: a scientific statement from the American Heart Association.

    Science.gov (United States)

    Gewitz, Michael H; Baltimore, Robert S; Tani, Lloyd Y; Sable, Craig A; Shulman, Stanford T; Carapetis, Jonathan; Remenyi, Bo; Taubert, Kathryn A; Bolger, Ann F; Beerman, Lee; Mayosi, Bongani M; Beaton, Andrea; Pandian, Natesa G; Kaplan, Edward L

    2015-05-19

    Acute rheumatic fever remains a serious healthcare concern for the majority of the world's population despite its decline in incidence in Europe and North America. The goal of this statement was to review the historic Jones criteria used to diagnose acute rheumatic fever in the context of the current epidemiology of the disease and to update those criteria to also take into account recent evidence supporting the use of Doppler echocardiography in the diagnosis of carditis as a major manifestation of acute rheumatic fever. To achieve this goal, the American Heart Association's Council on Cardiovascular Disease in the Young and its Rheumatic Fever, Endocarditis, and Kawasaki Disease Committee organized a writing group to comprehensively review and evaluate the impact of population-specific differences in acute rheumatic fever presentation and changes in presentation that can result from the now worldwide availability of nonsteroidal anti-inflammatory drugs. In addition, a methodological assessment of the numerous published studies that support the use of Doppler echocardiography as a means to diagnose cardiac involvement in acute rheumatic fever, even when overt clinical findings are not apparent, was undertaken to determine the evidence basis for defining subclinical carditis and including it as a major criterion of the Jones criteria. This effort has resulted in the first substantial revision to the Jones criteria by the American Heart Association since 1992 and the first application of the Classification of Recommendations and Levels of Evidence categories developed by the American College of Cardiology/American Heart Association to the Jones criteria. This revision of the Jones criteria now brings them into closer alignment with other international guidelines for the diagnosis of acute rheumatic fever by defining high-risk populations, recognizing variability in clinical presentation in these high-risk populations, and including Doppler echocardiography as a tool

  12. Analysis of compression forces between varying sizes of cannulated screws versus rail external fixation for treatment of Jones type fifth metatarsal fracture.

    Science.gov (United States)

    Freschi, Scot A; Vardaxis, Vassilios; Dodson, Nic

    2008-01-01

    This study compared peak compression load in Newtons and stiffness in Newtons/millimeter for varying interfragmental screw sizes versus mini rail external fixation for the surgical treatment of Jones fifth metatarsal fractures. Four groups were included into this study: (1) Jones fracture with external fixation (Orthofix, Inc., McKinney, TX); (2) Jones fracture with 4.5-mm interfragmental cannulated screw; (3) Jones fracture with 5.5-mm interfragmental cannulated screw; and (4) Jones fracture with 6.5-mm interfragmental cannulated screw. There was no statistically significant difference between the peak compression achieved with the different groups of interfragmental cannulated screws: 4.5-mm interfragmental cannulated screw = 30.56 (+/- 9.40) N; 5.5-mm interfragmental cannulated screw = 30.69 (+/- 10.75) N; and 6.5-mm interfragmental cannulated screw = 32.84 (+/- 9.65) N. When comparing the compression achieved with the different groups of interfragmental cannulated screws to that achieved with the small rail external fixator (69.70 [+/- 14.69] N), a statistically significant difference was noted. There was no statistically significant difference in regard to stiffness (Newtons/millimeter) noted between the intramedullary cannulated screw groups: 4.5 cannulated screw 5.25 (+/- 1.96), 5.5 cannulated screw 5.50 (+/- 2.01), and 6.5 cannulated screw 6.75 (+/- 2.60). A statistically significant difference was noted when the stiffness (Newtons/millimeter) of the rail external fixator (12.69 (+/- 4.52) was compared to the stiffness achieved with the different interfragmental screws. The results indicated that the small rail external fixation device provided increased compression and an increased ability to resist bending when compared to the different intramedullary cannulated screws.

  13. 78 FR 42804 - Whirlpool Corporation, Including On-Site Leased Workers From Aerotek/Tek Systems (Subcontractor...

    Science.gov (United States)

    2013-07-17

    ... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-82,346] Whirlpool Corporation, Including On-Site Leased Workers From Aerotek/Tek Systems (Subcontractor of IBM Corporation) and Jones Lang... firm. The workers were engaged in production of refrigerators and trash compactors as well as...

  14. Effect of river excavation on a bank filtration site - assessing transient surface water - groundwater interaction by 3D heat and solute transport modelling

    Science.gov (United States)

    Wang, W.; Oswald, S. E.; Munz, M.; Strasser, D.

    2017-12-01

    Bank filtration is widely used either as main- or pre-treatment process for water supply. The colmation of the river bottom as interface to groundwater plays a key role for hydraulic control of flow paths and location of several beneficial attenuation processes, such as pathogen filtration, mixing, biodegradation and sorption. Along the flow path, mixing happens between the `young' infiltrated water and ambient `old' groundwater. To clarify the mechanisms and their interaction, modelling is often used for analysing spatial and temporal distribution of the travelling time, quantifying mixing ratios, and estimating the biochemical reaction rates. As the most comprehensive tool, 2-D or 3-D spatially-explicit modelling is used in several studies, and for area with geological heterogeneity, the adaptation of different natural tracers could constrain the model in respect to model non-uniqueness and improve the interpretation of the flow field. In our study, we have evaluated the influence of a river excavation and bank reconstruction project on the groundwater-surface water exchange at a bank filtration site. With data from years of field site monitoring, we could include besides heads and temperature also the analysis of stable isotope data and ions to differentiate between infiltrated water and groundwater. Thus, we have set up a 3-D transient heat and mass transport groundwater model, taking the strong local geological heterogeneity into consideration, especially between river and water work wells. By transferring the effect of the river excavation into a changing hydraulic conductivity of the riverbed, model could be calibrated against both water head and temperature time-series observed. Finally, electrical conductivity dominated by river input was included as quasi-conservative tracer. The `triple' calibrated, transient model was then used to i) understand the flow field and quantify the long term changes in infiltration rate and distribution brought by the

  15. Exploring the Relationship Between Online Social Network Site Usage and the Impact on Quality of Life for Older and Younger Users: An Interaction Analysis.

    Science.gov (United States)

    Quinn, Darren; Chen, Liming; Mulvenna, Maurice D; Bond, Raymond

    2016-09-29

    Analyzing content generated by users of social network sites has been shown to be beneficial across a number of disciplines. Such analysis has revealed the precise behavior of users that details their distinct patterns of engagement. An issue is evident whereby without direct engagement with end users, the reasoning for anomalies can only be the subject of conjecture. Furthermore, the impact of engaging in social network sites on quality of life is an area which has received little attention. Of particular interest is the impact of online social networking on older users, which is a demographic that is specifically vulnerable to social isolation. A review of the literature reveals a lack of knowledge concerning the impact of these technologies on such users and even less is known regarding how this impact varies across different demographics. The objective of our study was to analyze user interactions and to survey the attitudes of social network users directly, capturing data in four key areas: (1) functional usage, (2) behavioral patterns, (3) technology, and (4) quality of life. An online survey was constructed, comprising 32 questions. Each question directly related to a research question. Respondents were recruited through a variety of methods including email campaigns, Facebook advertisements, and promotion from related organizations. In total, data was collected from 919 users containing 446 younger and 473 older users. In comparison to younger users, a greater proportion of older users (289/473, 61.1% older vs 218/446, 48.9% younger) (PFacebook had either a positive or huge impact on their quality of life. Furthermore, a greater percentage of older users strongly agreed that Facebook strengthened their relationship with other people (64/473, 13.5% older vs 40/446, 9.0%younger) (P=.02). In comparison to younger users, a greater proportion of older users had more positive emotions-classified as slightly better or very good-during their engagement with

  16. Shoot water relations of mature black spruce families displaying a genotype x environment interaction in growth rate. I. Family and site effects over three growing seasons

    Science.gov (United States)

    Kurt H. Johnsen; John E Major

    1999-01-01

    Pressure-volume curves were determined for black spruce (Picea mariana (Mill.) BSP) trees from four full-sib families. During the first two years, trees were measured from a plantation on a dry site. In the third year, trees were sampled from the dry site and a wet site. Diurnal measurements of shoot water potential allowed in situ ...

  17. Resolving dispersion and induction components for polarisable molecular simulations of ionic liquids

    Science.gov (United States)

    Pádua, Agílio A. H.

    2017-05-01

    One important development in interaction potential models, or atomistic force fields, for molecular simulation is the inclusion of explicit polarisation, which represents the induction effects of charged or polar molecules on polarisable electron clouds. Polarisation can be included through fluctuating charges, induced multipoles, or Drude dipoles. This work uses Drude dipoles and is focused on room-temperature ionic liquids, for which fixed-charge models predict too slow dynamics. The aim of this study is to devise a strategy to adapt existing non-polarisable force fields upon addition of polarisation, because induction was already contained to an extent, implicitly, due to parametrisation against empirical data. Therefore, a fraction of the van der Waals interaction energy should be subtracted so that the Lennard-Jones terms only account for dispersion and the Drude dipoles for induction. Symmetry-adapted perturbation theory is used to resolve the dispersion and induction terms in dimers and to calculate scaling factors to reduce the Lennard-Jones terms from the non-polarisable model. Simply adding Drude dipoles to an existing fixed-charge model already improves the prediction of transport properties, increasing diffusion coefficients, and lowering the viscosity. Scaling down the Lennard-Jones terms leads to still faster dynamics and densities that match experiment extremely well. The concept developed here improves the overall prediction of density and transport properties and can be adapted to other models and systems. In terms of microscopic structure of the ionic liquids, the inclusion of polarisation and the down-scaling of Lennard-Jones terms affect only slightly the ordering of the first shell of counterions, leading to small decreases in coordination numbers. Remarkably, the effect of polarisation is major beyond first neighbours, significantly weakening spatial correlations, a structural effect that is certainly related to the faster dynamics of

  18. Thermal interactions of the AD79 Vesuvius pyroclastic density currents and their deposits at Villa dei Papiri (Herculaneum archaeological site, Italy)

    Science.gov (United States)

    Giordano, G.; Zanella, E.; Trolese, M.; Baffioni, C.; Vona, A.; Caricchi, C.; De Benedetti, A. A.; Corrado, S.; Romano, C.; Sulpizio, R.; Geshi, N.

    2018-05-01

    Pyroclastic density currents (PDCs) can have devastating impacts on urban settlements, due to their dynamic pressure and high temperatures. Our degree of understanding of the interplay between these hot currents and the affected infrastructures is thus fundamental not only to implement our strategies for risk reduction, but also to better understand PDC dynamics. We studied the temperature of emplacement of PDC deposits that destroyed and buried the Villa dei Papiri, an aristocratic Roman edifice located just outside the Herculaneum city, during the AD79 plinian eruption of Mt Vesuvius (Italy) by using the thermal remanent magnetization of embedded lithic clasts. The PDC deposits around and inside the Villa show substantial internal thermal disequilibrium. In areas affected by convective mixing with surface water or with collapsed walls, temperatures average at around 270 °C (min 190 °C, max 300 °C). Where the deposits show no evidence of mixing with external material, the temperature is much higher, averaging at 350 °C (min 300 °C; max 440 °C). Numerical simulations and comparison with temperatures retrieved at the very same sites from the reflectance of charcoal fragments indicate that such thermal disequilibrium can be maintained inside the PDC deposit for time-scales well over 24 hours, i.e. the acquisition time of deposit temperatures for common proxies. We reconstructed in detail the history of the progressive destruction and burial of Villa dei Papiri and infer that the rather homogeneous highest deposit temperatures (average 350 °C) were carried by the ash-sized fraction in thermal equilibrium with the fluid phase of the incoming PDCs. These temperatures can be lowered on short time- (less than hours) and length-scales (meters to tens of meters) only where convective mixing with external materials or fluids occurs. By contrast, where the Villa walls remained standing the thermal exchange was only conductive and very slow, i.e. negligible at 50 cm

  19. Molecular simulation of adsorption and transport diffusion of model fluids in carbon nanotubes

    Science.gov (United States)

    Düren, Tina; Keil, Frerich J.; Seaton, Nigel A.

    Grand canonical Monte Carlo (GCMC) and dual-control-volume grand canonical molecular dynamics (DCV-GCMD) simulations were carried out with Lennard-Jones model fluids in carbon nanotubes, with the objective of investigating the effect of varying molecular properties on adsorption and diffusion. The influence of the molecular weight, and the Lennard Jones parameters σ (a measure of the molecule size) and ɛ (a measure of the interaction strength) on adsorption isotherms, fluxes, and transport diffusivities was studied. For these simulations, the properties of component 1 in the mixture were held constant and one of the properties of component 2 was changed systematically. Furthermore, the validity of Graham's law, which relates the fluxes of two counter diffusing species to their molecular weight, was investigated on a molecular level. Graham's law is fulfilled for the whole range of molecular weights and Lennard-Jones parameters σ investigated. However, large deviations were observed for large values of ɛ2. Here, the interaction of the two components in the mixture becomes so strong that component 1 is dragged along by component 2.

  20. Parsing partial molar volumes of small molecules: a molecular dynamics study.

    Science.gov (United States)

    Patel, Nisha; Dubins, David N; Pomès, Régis; Chalikian, Tigran V

    2011-04-28

    We used molecular dynamics (MD) simulations in conjunction with the Kirkwood-Buff theory to compute the partial molar volumes for a number of small solutes of various chemical natures. We repeated our computations using modified pair potentials, first, in the absence of the Coulombic term and, second, in the absence of the Coulombic and the attractive Lennard-Jones terms. Comparison of our results with experimental data and the volumetric results of Monte Carlo simulation with hard sphere potentials and scaled particle theory-based computations led us to conclude that, for small solutes, the partial molar volume computed with the Lennard-Jones potential in the absence of the Coulombic term nearly coincides with the cavity volume. On the other hand, MD simulations carried out with the pair interaction potentials containing only the repulsive Lennard-Jones term produce unrealistically large partial molar volumes of solutes that are close to their excluded volumes. Our simulation results are in good agreement with the reported schemes for parsing partial molar volume data on small solutes. In particular, our determined interaction volumes() and the thickness of the thermal volume for individual compounds are in good agreement with empirical estimates. This work is the first computational study that supports and lends credence to the practical algorithms of parsing partial molar volume data that are currently in use for molecular interpretations of volumetric data.

  1. Role of Interactions between Autographa californica Multiple Nucleopolyhedrovirus Procathepsin and Chitinase Chitin-Binding or Active-Site Domains in Viral Cathepsin Processing

    Science.gov (United States)

    Hodgson, Jeffrey J.; Arif, Basil M.

    2013-01-01

    The binding of Autographa californica multiple nucleopolyhedrovirus chitinase (CHIA) to viral cathepsin protease progenitor (proV-CATH) governs cellular/endoplasmic reticulum (ER) coretention of CHIA and proV-CATH, thus coordinating simultaneous cellular release of both host tissue-degrading enzymes upon host cell death. CHIA is a proposed proV-CATH folding chaperone because insertional inactivation of chiA causes production of proV-CATH aggregates that are incompetent for proteolytic maturation into active V-CATH enzyme. We wanted to determine whether the N-terminal chitin-binding domain (CBD, 149 residues) and C-terminal CHIA active-site domain (ASD, 402 residues) of CHIA bind to proV-CATH independently of one another and whether either domain is dispensable for CHIA's putative proV-CATH folding chaperone activity. We demonstrate that N-terminally green fluorescent protein (GFP)-fused CHIA, ASD, and CBD each colocalize with proV-CATH-RFP in ER-like patterns and that both ASD and CBD independently associate with proV-CATH in vivo using bimolecular fluorescence complementation (BiFC) and in vitro using reciprocal nickel-histidine pulldown assays. Altogether, the data from colocalization, BiFC, and reciprocal copurification analyses suggest specific and independent interactions between proV-CATH and both domains of CHIA. These data also demonstrate that either CHIA domain is dispensable for normal proV-CATH processing. Furthermore, in contrast to prior evidence suggesting that a lack of chiA expression causes proV-CATH to become aggregated, insoluble, and unable to mature into V-CATH, a chiA deletion bacmid virus we engineered to express just v-cath produced soluble proV-CATH that was prematurely secreted from cells and proteolytically matured into active V-CATH enzyme. PMID:23302896

  2. TECHNICAL EVALUATION OF THE INTERACTION OF GROUNDWATER WITH THE COLUMBIA RIVER AT THE DEPARTMENT OF ENERGY HANFORD SITE 100-D AREA

    Energy Technology Data Exchange (ETDEWEB)

    PETERSEN SW

    2008-11-05

    river water and site groundwater in this zone has been estimated to be equal parts of groundwater and river water, a wide range of mixing ratios likely occurs at various times of the day and year. The degree of mixing and dilution appears to be greatly influenced by the river stage and other groundwater/surface water interaction. The extent of mixing, thus, has implications for the design and operation of the groundwater remediation systems. Improved understanding of this 'dilution' mechanism is needed to design an optimum 'systems approach' to accelerate remediation of the near-shore contaminant plumes. More information on the pathway from near-river mapped plumes to riverbed receptor locations is also needed to develop a defensible proposed plan for a future ROD for final remedial action of contaminated groundwater. In April 2008, an expert panel of scientists was convened to review existing information and provide observations and suggestions to improve the current understanding of groundwater surface water interactions in the 100 Areas (primarily focusing on 100-D Area), and to identify what additional analyses or approaches may provide critical information needed to design and implement remediation systems that will minimize impacts to river aquatic systems. Specific objectives provided to the panel included: (1) comment on approaches and methods to improve the current understanding of groundwater-surface water interactions, specifically how contaminated groundwater enters the riverbed and how this relates to remediation of chromate in the groundwater in the 100 Areas; (2) evaluate past and current data collection methods, data analysis techniques, assumptions, and groundwater transport and mixing mechanisms; (3) evaluate the current monitoring network (monitoring wells, aquifer tubes, and shoreline/river monitoring); (4) evaluate the role played by modeling; and (5) suggest additional research to fill data gaps and perform modeling.

  3. Phenotypic variation and fitness in a metapopulation of tubeworms (Ridgeia piscesae Jones at hydrothermal vents.

    Directory of Open Access Journals (Sweden)

    Verena Tunnicliffe

    Full Text Available We examine the nature of variation in a hot vent tubeworm, Ridgeia piscesae, to determine how phenotypes are maintained and how reproductive potential is dictated by habitat. This foundation species at northeast Pacific hydrothermal sites occupies a wide habitat range in a highly heterogeneous environment. Where fluids supply high levels of dissolved sulphide for symbionts, the worm grows rapidly in a "short-fat" phenotype characterized by lush gill plumes; when plumes are healthy, sperm package capture is higher. This form can mature within months and has a high fecundity with continuous gamete output and a lifespan of about three years in unstable conditions. Other phenotypes occupy low fluid flux habitats that are more stable and individuals grow very slowly; however, they have low reproductive readiness that is hampered further by small, predator cropped branchiae, thus reducing fertilization and metabolite uptake. Although only the largest worms were measured, only 17% of low flux worms were reproductively competent compared to 91% of high flux worms. A model of reproductive readiness illustrates that tube diameter is a good predictor of reproductive output and that few low flux worms reached critical reproductive size. We postulate that most of the propagules for the vent fields originate from the larger tubeworms that live in small, unstable habitat patches. The large expanses of worms in more stable low flux habitat sustain a small, but long-term, reproductive output. Phenotypic variation is an adaptation that fosters both morphological and physiological responses to differences in chemical milieu and predator pressure. This foundation species forms a metapopulation with variable growth characteristics in a heterogeneous environment where a strategy of phenotypic variation bestows an advantage over specialization.

  4. Optimization of long range potential interaction parameters in ion mobility spectrometry

    Science.gov (United States)

    Wu, Tianyang; Derrick, Joseph; Nahin, Minal; Chen, Xi; Larriba-Andaluz, Carlos

    2018-02-01

    The problem of optimizing Lennard-Jones (L-J) potential parameters to perform collision cross section (CCS) calculations in ion mobility spectrometry has been undertaken. The experimental CCS of 16 small organic molecules containing carbon, hydrogen, oxygen, nitrogen, and fluoride in N2 was compared to numerical calculations using Density Functional Theory (DFT). CCS calculations were performed using the momentum transfer algorithm IMoS and a 4-6-12 potential without incorporating the ion-quadrupole potential. A ceteris paribus optimization method was used to optimize the intercept σ and potential well-depth ɛ for the given atoms. This method yields important information that otherwise would remain concealed. Results show that the optimized L-J parameters are not necessarily unique with intercept and well-depth following an exponential relation at an existing line of minimums. Similarly, the method shows that some molecules containing atoms of interest may be ill-conditioned candidates to perform optimizations of the L-J parameters. The final calculated CCSs for the chosen parameters differ 1% on average from their experimental counterparts. This result conveys the notion that DFT calculations can indeed be used as potential candidates for CCS calculations and that effects, such as the ion-quadrupole potential or diffuse scattering, can be embedded into the L-J parameters without loss of accuracy but with a large increase in computational efficiency.

  5. Bence Jones proteinuria in smoldering multiple myeloma as a predictor marker of progression to symptomatic multiple myeloma.

    Science.gov (United States)

    González-Calle, V; Dávila, J; Escalante, F; de Coca, A G; Aguilera, C; López, R; Bárez, A; Alonso, J M; Hernández, R; Hernández, J M; de la Fuente, P; Puig, N; Ocio, E M; Gutiérrez, N C; García-Sanz, R; Mateos, M V

    2016-10-01

    The diagnosis of smoldering multiple myeloma (SMM) includes patients with a heterogeneous risk of progression to active multiple myeloma (MM): some patients will never progress, whereas others will have a high risk of progression within the first 2 years. Therefore, it is important to improve risk assessment at diagnosis. We conducted a retrospective study in a large cohort of SMM patients, in order to investigate the role of Bence Jones (BJ) proteinuria at diagnosis in the progression to active MM. We found that SMM patients presenting with BJ proteinuria had a significantly shorter median time to progression (TTP) to MM compared with patients without BJ proteinuria (22 vs 88 months, respectively; hazard ratio=2.3, 95% confidence interval=1.4-3.9, P=0.002). We also identified risk subgroups based on the amount of BJ proteinuria: ⩾500 mg/24 h, <500 mg/24 h and without it, with a significantly different median TTP (13, 37 and 88 months, P<0.001). Thus, BJ proteinuria at diagnosis is an independent variable of progression to MM that identifies a subgroup of high-risk SMM patients (51% risk of progression at 2 years) and ⩾500 mg of BJ proteinuria may allow, if validated in another series, to reclassify these patients to MM requiring therapy before the end-organ damage development.

  6. Phenotypic and Genetic Characterization of Erwiniua carotovora spp. carotovora (JOnes Bergey et al. Isolates from Grafted Tomato in Sardinia, Italy

    Directory of Open Access Journals (Sweden)

    M. Fiori

    2005-04-01

    Full Text Available A disease symptomatically similar to that caused by Erwinia carotovora occurred on “Cuore di Bue” and “Cencara” tomato plants grafted on “Beaufort” and “He-Man”, or ungrafted, in greenhouses in Sardinia (Italy. Symptoms were: dark brown/black longitudinal stem lesions, soft stem rot, pith breakdown of the stems, hollow stems, vascular tissue discoloration, wilting and collapse of the plants. Numerous bacterial colonies from stem tissues were isolated on yeast extract salts (YS medium. Seven isolates (DPP As-1, DPP As-2, DPP As-3, DPP As-14, DPP Pu6, DPP Pu7 e DPP Pu8 were selected on the basis of their ability to cause rot on potato pieces and a hypersensitivity reaction in “White burley” tobacco leaves. Pathogenicity tests revealed that five of these isolates infected artichoke, basil, dwarf bean, fennel, marrow, melon, pepper, eggplant, grafted and ungrafted tomato, and white cabbage. Of the remaining two isolates, one (DPP As-1 did not infect white cabbage, and the other (DPP Pu8 did not infect basil, marrow or white cabbage. Phenotypic properties and ELISA, also performed on naturally infected tissues, revealed that all the isolates were E. c. ssp. carotovora (Jones Bergey et al. PCR-RFLP analysis placed two (DPP As-2 and DPP As-3 of the seven isolates in RFLP group 8. Five isolates belonged to a hitherto unknown RFLP group. Prevention and control measures for this disease are suggested.

  7. Novel method for localization of common carotid artery transverse section in ultrasound images using modified Viola-Jones detector.

    Science.gov (United States)

    Ríha, Kamil; Mašek, Jan; Burget, Radim; Beneš, Radek; Závodná, Eva

    2013-10-01

    This article describes a novel method for highly accurate and effective localization of the transverse section of the carotis comunis artery in ultrasound images. The method has a high success rate, approximately 97%. Unlike analytical methods based on geometric descriptions of the object sought, the method proposed here can cover a large area of shape variation of the artery under study, which normally occurs during examinations as a result of the pressure on the examined tissue, tilt of the probe, setup of the sonographic device, and other factors. This method shows great promise in automating the process of determining circulatory system parameters in the non-invasive clinical diagnostics of cardiovascular diseases. The method employs a Viola-Jones detector that has been specially adapted for efficient detection of transverse sections of the carotid artery. This algorithm is trained on a set of labeled images using the AdaBoost algorithm, Haar-like features and the Matthews coefficient. The training algorithm of the artery detector was modified using evolutionary algorithms. The method for training a cascade of classifiers achieves on a small number of positive and negative training data samples (about 500 images) a high success rate in a computational time that allows implementation of the detector in real time. Testing was performed on images of different patients for whom different ultrasonic instruments were used under different conditions (settings) so that the algorithm developed is applicable in general radiologic practice. 2013 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved

  8. The domain II loops of Bacillus thuringiensis Cry1Aa form an overlapping interaction site for two Bombyx mori larvae functional receptors, ABC transporter C2 and cadherin-like receptor.

    Science.gov (United States)

    Adegawa, Satomi; Nakama, Yui; Endo, Haruka; Shinkawa, Naoki; Kikuta, Shingo; Sato, Ryoichi

    2017-02-01

    Information about the receptor-interaction region of Cry toxins, insecticidal proteins produced by Bacillus thuringiensis, is needed to elucidate the mode of action of Cry toxins and improve their toxicity through protein engineering. We analyzed the interaction sites on Cry1Aa with ABC transporter C2 (ABCC2), one of the most important Cry1A toxin receptors. A competitive binding assay revealed that the Bombyx mori ABCC2 (BmABCC2) Cry1A binding site was the same as the BtR175 binding site, suggesting that the loop region of Cry1Aa domain II is a binding site. Next, we constructed several domain II loop mutant toxins and tested their binding affinity in an SPR analysis, and also performed a cell swelling assay to evaluate receptor-mediated cytotoxicity. Our results indicate that the loop regions required for BtR175 and BmABCC2 binding and the regions important for cytotoxicity partially overlap. Our results also suggest that receptor binding is necessary but not sufficient for cytotoxicity. This is the first report showing the region of interaction between ABCC2 and Cry1Aa and the cytotoxicity-relevant properties of the Cry1Aa domain II loop region. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Modeling dynamics of {sup 137}Cs in forest surface environments: Application to a contaminated forest site near Fukushima and assessment of potential impacts of soil organic matter interactions

    Energy Technology Data Exchange (ETDEWEB)

    Ota, Masakazu, E-mail: ohta.masakazu@jaea.go.jp; Nagai, Haruyasu; Koarashi, Jun

    2016-05-01

    A process-based model for {sup 137}Cs transfer in forest surface environments was developed to assess the dynamic behavior of Fukushima-derived {sup 137}Cs in a Japanese forest. The model simulation successfully reproduced the observed data from 3 year migration of {sup 137}Cs in the organic and mineral soil layers at a contaminated forest near Fukushima. The migration of {sup 137}Cs from the organic layer to the mineral soil was explained by the direct deposition pattern on the forest floor and the turnover of litter materials in the organic layer under certain ecological conditions. Long-term predictions indicated that more than 90% of the deposited {sup 137}Cs would remain within the top 5 cm of the soil for up to 30 years after the accident, suggesting that the forest acts as an effective long-term reservoir of {sup 137}Cs with limited transfer via the groundwater pathway. The model was also used to explore the potential impacts of soil organic matter (SOM) interactions on the mobility and bioavailability of {sup 137}Cs in the soil–plant system. The simulation results for hypothetical organic soils with modified parameters of {sup 137}Cs turnover revealed that the SOM-induced reduction of {sup 137}Cs adsorption elevates the fraction of dissolved {sup 137}Cs in the soil solution, thereby increasing the soil-to-plant transfer of {sup 137}Cs without substantially altering the fractional distribution of {sup 137}Cs in the soil. Slower fixation of {sup 137}Cs on the flayed edge site of clay minerals and enhanced mobilization of the clay-fixed {sup 137}Cs in organic-rich soils also appeared to elevate the soil-to-plant transfer of {sup 137}Cs by increasing the fraction of the soil-adsorbed (exchangeable) {sup 137}Cs. A substantial proportion (approximate 30%–60%) of {sup 137}Cs in these organic-rich soils was transferred to layers deeper than 5 cm decades later. These results suggested that SOM influences the behavior of {sup 137}Cs in forests over a prolonged

  10. Functional role of fumarate site Glu59 involved in allosteric regulation and subunit-subunit interaction of human mitochondrial NAD(P)+-dependent malic enzyme.

    Science.gov (United States)

    Hsieh, Ju-Yi; Chiang, Yu-Hsiu; Chang, Kuan-Yu; Hung, Hui-Chih

    2009-02-01

    Here we report on the role of Glu59 in the fumarate-mediated allosteric regulation of the human mitochondrial NAD(P)+-dependent malic enzyme (m-NAD-ME). In the present study, Glu59 was substituted by Asp, Gln or Leu. Our kinetic data strongly indicated that the charge properties of this residue significantly affect the allosteric activation of the enzyme. The E59L enzyme shows nonallosteric kinetics and the E59Q enzyme displays a much higher threshold in enzyme activation with elevated activation constants, K(A,Fum) and alphaK(A,Fum). The E59D enzyme, although retaining the allosteric property, is quite different from the wild-type in enzyme activation. The K(A,Fum) and alphaK(A,Fum) of E59D are also much greater than those of the wild-type, indicating that not only the negative charge of this residue but also the group specificity and side chain interactions are important for fumarate binding. Analytical ultracentrifugation analysis shows that both the wild-type and E59Q enzymes exist as a dimer-tetramer equilibrium. In contrast to the E59Q mutant, the E59D mutant displays predominantly a dimer form, indicating that the quaternary stability in the dimer interface is changed by shortening one carbon side chain of Glu59 to Asp59. The E59L enzyme also shows a dimer-tetramer model similar to that of the wild-type, but it displays more dimers as well as monomers and polymers. Malate cooperativity is not significantly notable in the E59 mutant enzymes, suggesting that the cooperativity might be related to the molecular geometry of the fumarate-binding site. Glu59 can precisely maintain the geometric specificity for the substrate cooperativity. According to the sequence alignment analysis and our experimental data, we suggest that charge effect and geometric specificity are both critical factors in enzyme regulation. Glu59 discriminates human m-NAD-ME from mitochondrial NADP+-dependent malic enzyme and cytosolic NADP+-dependent malic enzyme in fumarate activation and

  11. An Analytical Model for Adsorption and Diffusion of Atoms/Ions on Graphene Surface

    Directory of Open Access Journals (Sweden)

    Yan-Zi Yu

    2015-01-01

    Full Text Available Theoretical investigations are made on adsorption and diffusion of atoms/ions on graphene surface based on an analytical continuous model. An atom/ion interacts with every carbon atom of graphene through a pairwise potential which can be approximated by the Lennard-Jones (L-J potential. Using the Fourier expansion of the interaction potential, the total interaction energy between the adsorption atom/ion and a monolayer graphene is derived. The energy-distance relationships in the normal and lateral directions for varied atoms/ions, including gold atom (Au, platinum atom (Pt, manganese ion (Mn2+, sodium ion (Na1+, and lithium-ion (Li1+, on monolayer graphene surface are analyzed. The equilibrium position and binding energy of the atoms/ions at three particular adsorption sites (hollow, bridge, and top are calculated, and the adsorption stability is discussed. The results show that H-site is the most stable adsorption site, which is in agreement with the results of other literatures. What is more, the periodic interaction energy and interaction forces of lithium-ion diffusing along specific paths on graphene surface are also obtained and analyzed. The minimum energy barrier for diffusion is calculated. The possible applications of present study include drug delivery system (DDS, atomic scale friction, rechargeable lithium-ion graphene battery, and energy storage in carbon materials.

  12. Method and system of Jones-matrix mapping of blood plasma films with "fuzzy" analysis in differentiation of breast pathology changes

    Science.gov (United States)

    Zabolotna, Natalia I.; Radchenko, Kostiantyn O.; Karas, Oleksandr V.

    2018-01-01

    A fibroadenoma diagnosing of breast using statistical analysis (determination and analysis of statistical moments of the 1st-4th order) of the obtained polarization images of Jones matrix imaginary elements of the optically thin (attenuation coefficient τ fibroadenoma" of breast was 82.7% by the method of linear discriminant analysis, and by the "fuzzy" logic method is 95.3%. The obtained results allow to confirm the potentially high level of reliability of the method of differentiation by "fuzzy" analysis.

  13. The renal and hepatic distribution of Bence Jones proteins depends on glycosylation: a scintigraphic study in rats

    Directory of Open Access Journals (Sweden)

    M.J.B.A. Prado

    1997-07-01

    Full Text Available The aim of the present study was to evaluate renal and liver distribution of two monoclonal immunoglobulin light chains. The chains were purified individually from the urine of patients with multiple myeloma and characterized as lambda light chains with a molecular mass of 28 kDa. They were named BJg (high amount of galactose residues exposed and BJs (sialic acid residues exposed on the basis of carbohydrate content. A scintigraphic study was performed on male Wistar rats weighing 250 g for 60 min after iv administration of 1 mg of each protein (7.4 MBq, as the intact proteins and also after carbohydrate oxidation. Images were obtained with a Siemens gamma camera with a high-resolution collimator and processed with a MicroDelta system. Hepatic and renal distribution were established and are reported as percent of injected dose. Liver uptake of BJg was significantly higher than liver uptake of BJs (94.3 vs 81.4% (P<0.05. This contributed to its greater removal from the intravascular compartment, and consequently lower kidney accumulation of BJg in comparison to BJs (5.7 vs 18.6% (P<0.05. After carbohydrate oxidation, there was a decrease in hepatic accumulation of both proteins and consequently a higher renal overload. The tissue distribution of periodate-treated BJg was similar to that of native BJs: 82.7 vs 81.4% in the liver and 17.3 vs 18.6% in the kidneys. These observations indicate the important role of sugar residues of Bence Jones proteins for their recognition by specific membrane receptors, which leads to differential tissue accumulation and possible toxicity

  14. Olkiluoto site description 2011

    International Nuclear Information System (INIS)

    2012-12-01

    This fourth version of the Olkiluoto Site Report, produced by the OMTF (Olkiluoto Modelling Task Force), updates the Olkiluoto Site Report 2008 with the data and knowledge obtained up to December 2010. A descriptive model of the site (the Site Descriptive Model, SDM), i.e. a model describing the geological and hydrogeological structure of the site, properties of the bedrock and the groundwater and its flow, and the associated interacting processes and mechanisms. The SDM is divided into six parts: surface system, geology, rock mechanics, hydrogeology, hydrogeochemistry and transport properties

  15. Olkiluoto site description 2011

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-12-15

    This fourth version of the Olkiluoto Site Report, produced by the OMTF (Olkiluoto Modelling Task Force), updates the Olkiluoto Site Report 2008 with the data and knowledge obtained up to December 2010. A descriptive model of the site (the Site Descriptive Model, SDM), i.e. a model describing the geological and hydrogeological structure of the site, properties of the bedrock and the groundwater and its flow, and the associated interacting processes and mechanisms. The SDM is divided into six parts: surface system, geology, rock mechanics, hydrogeology, hydrogeochemistry and transport properties.

  16. A Global Survey and Interactive Map Suite of Deep Underground Facilities; Examples of Geotechnical and Engineering Capabilities, Achievements, Challenges: (Mines, Shafts, Tunnels, Boreholes, Sites and Underground Facilities for Nuclear Waste and Physics R&D)

    Science.gov (United States)

    Tynan, M. C.; Russell, G. P.; Perry, F.; Kelley, R.; Champenois, S. T.

    2017-12-01

    This global survey presents a synthesis of some notable geotechnical and engineering information reflected in four interactive layer maps for selected: 1) deep mines and shafts; 2) existing, considered or planned radioactive waste management deep underground studies, sites, or disposal facilities; 3) deep large diameter boreholes, and 4) physics underground laboratories and facilities from around the world. These data are intended to facilitate user access to basic information and references regarding deep underground "facilities", history, activities, and plans. In general, the interactive maps and database [http://gis.inl.gov/globalsites/] provide each facility's approximate site location, geology, and engineered features (e.g.: access, geometry, depth, diameter, year of operations, groundwater, lithology, host unit name and age, basin; operator, management organization, geographic data, nearby cultural features, other). Although the survey is not all encompassing, it is a comprehensive review of many of the significant existing and historical underground facilities discussed in the literature addressing radioactive waste management and deep mined geologic disposal safety systems. The global survey is intended to support and to inform: 1) interested parties and decision makers; 2) radioactive waste disposal and siting option evaluations, and 3) safety case development as a communication tool applicable to any mined geologic disposal facility as a demonstration of historical and current engineering and geotechnical capabilities available for use in deep underground facility siting, planning, construction, operations and monitoring.

  17. Model of OSBP-Mediated Cholesterol Supply to Aichi Virus RNA Replication Sites Involving Protein-Protein Interactions among Viral Proteins, ACBD3, OSBP, VAP-A/B, and SAC1.

    Science.gov (United States)

    Ishikawa-Sasaki, Kumiko; Nagashima, Shigeo; Taniguchi, Koki; Sasaki, Jun

    2018-04-15

    Positive-strand RNA viruses, including picornaviruses, utilize cellular machinery for genome replication. Previously, we reported that each of the 2B, 2BC, 2C, 3A, and 3AB proteins of Aichi virus (AiV), a picornavirus, forms a complex with the Golgi apparatus protein ACBD3 and phosphatidylinositol 4-kinase IIIβ (PI4KB) at viral RNA replication sites (replication organelles [ROs]), enhancing PI4KB-dependent phosphatidylinositol 4-phosphate (PI4P) production. Here, we demonstrate AiV hijacking of the cellular cholesterol transport system involving oxysterol-binding protein (OSBP), a PI4P-binding cholesterol transfer protein. AiV RNA replication was inhibited by silencing cellular proteins known to be components of this pathway, OSBP, the ER membrane proteins VAPA and VAPB (VAP-A/B), the PI4P-phosphatase SAC1, and PI-transfer protein β. OSBP, VAP-A/B, and SAC1 were present at RNA replication sites. We also found various previously unknown interactions among the AiV proteins (2B, 2BC, 2C, 3A, and 3AB), ACBD3, OSBP, VAP-A/B, and SAC1, and the interactions were suggested to be involved in recruiting the component proteins to AiV ROs. Importantly, the OSBP-2B interaction enabled PI4P-independent recruitment of OSBP to AiV ROs, indicating preferential recruitment of OSBP among PI4P-binding proteins. Protein-protein interaction-based OSBP recruitment has not been reported for other picornaviruses. Cholesterol was accumulated at AiV ROs, and inhibition of OSBP-mediated cholesterol transfer impaired cholesterol accumulation and AiV RNA replication. Electron microscopy showed that AiV-induced vesicle-like structures were close to ER membranes. Altogether, we conclude that AiV directly recruits the cholesterol transport machinery through protein-protein interactions, resulting in formation of membrane contact sites between the ER and AiV ROs and cholesterol supply to the ROs. IMPORTANCE Positive-strand RNA viruses utilize host pathways to modulate the lipid composition of

  18. Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites.

    OpenAIRE

    Smalla, M.; Schmieder, P.; Kelly, M.; Ter Laak, A.; Krause, G.; Ball, L.; Wahl, M.; Bork, P.; Oschkinat, H.

    1999-01-01

    The sterile alpha motif (SAM) is a protein interaction domain of around 70 amino acids present predominantly in the N- and C-termini of more than 60 diverse proteins that participate in signal transduction and transcriptional repression. SAM domains have been shown to homo- and hetero-oligomerize and to mediate specific protein-protein interactions. A highly conserved subclass of SAM domains is present at the intracellular C-terminus of more than 40 Eph receptor tyrosine kinases that are invo...

  19. Interaction of α-cyperone with human serum albumin: Determination of the binding site by using Discovery Studio and via spectroscopic methods

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qing; He, Jiawei; Wu, Di; Wang, Jing; Yan, Jin; Li, Hui, E-mail: lihuilab@sina.com

    2015-08-15

    α-Cyperone, as the main constituent of Cyperus rotundus, is a sesquiterpene ketone. In this work, LigandFit and CDOCKER docking programs of Discovery Studio 3.1 were used to preliminarily estimate and further confirm the binding sites of α-cyperone. LigandFit results showed that α-cyperone is mainly bound in subdomain IIA. This finding was further confirmed by CDOCKER results. Site marker competitive experimental results also suggested that α-cyperone contains the same binding site as warfarin. Software simulation results further revealed that α-cyperone is mainly bound in subdomain IIA. Site marker competitive experiment results are consistent with simulation results. 3D fluorescence and CD spectroscopy results indicated that the native conformation of HSA molecule is affected by the presence of α-cyperone. - Highlights: • This work carried out by adopting molecular docking and spectroscopic studies. • Discovery studio 3.1 was used for estimating the binding sites. • The insertion of α-cyperone molecule caused the microenvironment of HSA changed. • The native conformation of HSA was changed during binding with α-cyperone.

  20. Interaction of α-cyperone with human serum albumin: Determination of the binding site by using Discovery Studio and via spectroscopic methods

    International Nuclear Information System (INIS)

    Wang, Qing; He, Jiawei; Wu, Di; Wang, Jing; Yan, Jin; Li, Hui

    2015-01-01

    α-Cyperone, as the main constituent of Cyperus rotundus, is a sesquiterpene ketone. In this work, LigandFit and CDOCKER docking programs of Discovery Studio 3.1 were used to preliminarily estimate and further confirm the binding sites of α-cyperone. LigandFit results showed that α-cyperone is mainly bound in subdomain IIA. This finding was further confirmed by CDOCKER results. Site marker competitive experimental results also suggested that α-cyperone contains the same binding site as warfarin. Software simulation results further revealed that α-cyperone is mainly bound in subdomain IIA. Site marker competitive experiment results are consistent with simulation results. 3D fluorescence and CD spectroscopy results indicated that the native conformation of HSA molecule is affected by the presence of α-cyperone. - Highlights: • This work carried out by adopting molecular docking and spectroscopic studies. • Discovery studio 3.1 was used for estimating the binding sites. • The insertion of α-cyperone molecule caused the microenvironment of HSA changed. • The native conformation of HSA was changed during binding with α-cyperone