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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. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.)

  10. 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.

  11. 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...

  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. 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.

  14. 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 ...

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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...

  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. 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. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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...

  11. 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

  12. 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

  13. 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

  14. 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

  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. 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.

  5. 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....

  6. 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.

  7. 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.

  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. 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...

  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. 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.

  19. 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.

  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

    2017-07-28

    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.

  1. 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.

  2. 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.

  3. 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....

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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.

  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...

  19. 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....

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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...

  11. 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

  12. 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...

  13. 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...

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  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. 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

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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,…

  14. 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...

  15. 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

  16. 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...

  17. 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

  18. 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.

  19. 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

  20. 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!

  1. 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.

  2. 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

  3. 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.

  4. 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…

  5. 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

  6. 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…

  7. 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 ...

  8. 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

  9. 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...

  10. 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…

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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....

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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...

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  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. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  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. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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...

  20. 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.

  1. 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

  2. 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.

  3. 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...

  4. 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

  5. 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...

  6. 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.

  7. 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

  8. 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...

  9. 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...

  10. 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.

  11. 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…

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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.

  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. 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.

  2. 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)

  3. 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/.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. Solvent density inhomogeneities and solvation free energies in supercritical diatomic fluids: a density functional approach.

    Science.gov (United States)

    Husowitz, B; Talanquer, V

    2007-02-07

    Density functional theory is used to explore the solvation properties of a spherical solute immersed in a supercritical diatomic fluid. The solute is modeled as a hard core Yukawa particle surrounded by a diatomic Lennard-Jones fluid represented by two fused tangent spheres using an interaction site approximation. The authors' approach is particularly suitable for thoroughly exploring the effect of different interaction parameters, such as solute-solvent interaction strength and range, solvent-solvent long-range interactions, and particle size, on the local solvent structure and the solvation free energy under supercritical conditions. Their results indicate that the behavior of the local coordination number in homonuclear diatomic fluids follows trends similar to those reported in previous studies for monatomic fluids. The local density augmentation is particularly sensitive to changes in solute size and is affected to a lesser degree by variations in the solute-solvent interaction strength and range. The associated solvation free energies exhibit a nonmonotonous behavior as a function of density for systems with weak solute-solvent interactions. The authors' results suggest that solute-solvent interaction anisotropies have a major influence on the nature and extent of local solvent density inhomogeneities and on the value of the solvation free energies in supercritical solutions of heteronuclear molecules.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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...

  6. 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.

  7. 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

  8. 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

  9. Prediction of vapor-liquid equilibrium and PVTx properties of geological fluid system with SAFT-LJ EOS including multi-polar contribution. Part I: Application to H 2O-CO 2 system

    Science.gov (United States)

    Sun, Rui; Dubessy, Jean

    2010-04-01

    Molecular based equations of state (EOS) are attractive because they can take into account the energetic contribution of the main types of molecular interactions. This study models vapor-liquid equilibrium (VLE) and PVTx properties of the H 2O-CO 2 binary system using a Lennard-Jones (LJ) referenced SAFT (Statistical Associating Fluid Theory) EOS. The improved SAFT-LJ EOS is defined in terms of the residual molar Helmholtz energy, which is a sum of four terms representing the contributions from LJ segment-segment interactions, chain-forming among the LJ segments, short-range associations and long-range multi-polar interactions. CO 2 is modeled as a linear chain molecule with a constant quadrupole moment, and H 2O is modeled as a spherical molecule with four association sites and a dipole moment. The multi-polar contribution to Helmholtz energy, including the dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole contribution for H 2O-CO 2 system, is calculated using the theory of Gubbins and Twu (1978). Six parameters for pure H 2O and four parameters for pure CO 2 are needed in our model. The Van der Waals one-fluid mixing rule is used to calculate the Lennard-Jones energy parameter and volume parameter for the mixture. Two or three binary parameters are needed for CO 2-H 2O mixtures, which are evaluated from phase equilibrium data of the binary system. Comparison with the experimental data shows that our model represents the PVT properties of CO 2 better than other SAFT EOS without a quadrupole contribution. For the CO 2-H 2O system, our model agrees well with the vapor-liquid equilibrium data from 323-623 K. The average relative deviation for CO 2 solubility (expressed in mole fraction) in water is within 6%. Our model can also predict the PVTx properties of CO 2-H 2O mixtures up to 1073 K and 3000 bar. The good performance of this model indicates that: (1) taking account of the multi-polar contribution explicitly improves the agreement of calculated

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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....

  1. 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

  2. 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

  3. 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).

  4. 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.

  5. 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

  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. 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

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. Non-chiral, auxetic system of noncentrosymmetric molecules in two dimensions

    International Nuclear Information System (INIS)

    Wojciechowski, K.W.

    2002-12-01

    A two-dimensional model of tri-atomic molecules (which 'atoms' are distributed on vertices of equilateral triangles, and which are further referred to as cyclic trimers) is solved exactly in the static (zero-temperature) limit for the nearest-neighbor site-site interactions. It is shown that the cyclic trimers (noncentrosymmetric by the definition) can form a mechanically stable and elastically isotropic non-chiral phase of negative Poisson ratio. The properties of the system are illustrated by three examples of the atom-atom interaction potentials: (i) the purely repulsive (n-inverse-power) potential, (ii) the purely attractive (n-power) potential and (iii) the Lennard-Jones-like potential which shows both the repulsive and the attractive part. The analytic form of the dependence of the Poisson ratio on the interatomic potential is obtained. It is shown that the Poisson ratio depends, in a universal way, only on the trimer anisotropy parameter both (1) in the limit of n → ∞ for the cases (i) and (ii), as well as (2) at the zero external pressure for any potential with a doubly differentiable minimum, the case (iii) is an example. (author)

  13. 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.

  14. 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.

  15. [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.

  16. Virial expansion of the second layer in physical adsorption - An ab initio calculation for helium on argon crystal

    Science.gov (United States)

    Oh, B. K.; Kim, S. K.

    1974-01-01

    A model of helium adsorption on an argon crystal is built up from the premise that local adsorption predominates in the first layer and nonlocal adsorption in the second. Application of the virial expansion theorem to the second layer gives a series in which the first term represents the motion of a single molecule in the external potential field and the second a two-body interaction under this field. The thermodynamic functions of the adsorbed phase are calculated ab initio, the gas-solid interaction potential being derived from lattice summation and the partition function from an appropriate choice of a site-spacing polynomial to describe the periodic potential. The mutual interaction of adsorbed molecules is calculated with a two-dimensional Lennard-Jones potential. The second virial coefficient is calculated and its dependence on temperature and choice of potential is studied. It is found that the second virial coefficient is very well approximated by a two-dimensional gas in free space. The adsorption isotherm, isosteric heat, and specific heat are obtained and compared with the results of Ross and Steele, giving excellent agreement.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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

  2. Molecular docking using the molecular lipophilicity potential as hydrophobic descriptor: impact on GOLD docking performance.

    Science.gov (United States)

    Nurisso, Alessandra; Bravo, Juan; Carrupt, Pierre-Alain; Daina, Antoine

    2012-05-25

    GOLD is a molecular docking software widely used in drug design. In the initial steps of docking, it creates a list of hydrophobic fitting points inside protein cavities that steer the positioning of ligand hydrophobic moieties. These points are generated based on the Lennard-Jones potential between a carbon probe and each atom of the residues delimitating the binding site. To thoroughly describe hydrophobic regions in protein pockets and properly guide ligand hydrophobic moieties toward favorable areas, an in-house tool, the MLP filter, was developed and herein applied. This strategy only retains GOLD hydrophobic fitting points that match the rigorous definition of hydrophobicity given by the molecular lipophilicity potential (MLP), a molecular interaction field that relies on an atomic fragmental system based on 1-octanol/water experimental partition coefficients (log P(oct)). MLP computations in the binding sites of crystallographic protein structures revealed that a significant number of points considered hydrophobic by GOLD were actually polar according to the MLP definition of hydrophobicity. To examine the impact of this new tool, ligand-protein complexes from the Astex Diverse Set and the PDB bind core database were redocked with and without the use of the MLP filter. Reliable docking results were obtained by using the MLP filter that increased the quality of docking in nonpolar cavities and outperformed the standard GOLD docking approach.

  3. 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.

  4. Set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data.

    Science.gov (United States)

    Eckl, Bernhard; Vrabec, Jadran; Hasse, Hans

    2008-10-09

    A parametrization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e., vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl ether, sulfur dioxide, dimethyl sulfide, thiophene, hydrogen cyanide, acetonitrile, and nitromethane. Most of the models are able to describe the experimental VLE data with deviations of a few percent.

  5. Molecular dynamics studies of superionic conductors

    International Nuclear Information System (INIS)

    Rahman, A.

    1979-01-01

    Over the last fifteen years computer modeling of liquids and solids has become a useful method of understanding the structural and dynamical correlations in these systems. Some characteristics of the method are presented with an example from work on homogeneous nucleation in monoatomic liquids; the interaction potential determines the structure: a Lennard--Jones system nucleates a close packed structure while an alkali metal potential nucleates a bcc packing. In the study of ionic systems like CaF 2 the Coulomb interaction together with the short range repulsion is enough to produce a satisfactory model for the motion of F - ions in CaF 2 at approx. 1600 0 K. Analysis of this motion shows that F - ions reside at their fluorite sites for about 6 x 10 -12 s and that the diffusion is mainly due to F - jumps in the 100 direction. The motion can be analyzed in terms of the generation and annihilation of anti-Frenkel pairs. The temperature dependence of the F - diffusion constant at two different densities has also been calculated. The computer model does not correspond with experiment in this regard

  6. 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.

  7. 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.

  8. Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations.

    Science.gov (United States)

    Pavlova, Anna; Parks, Jerry M; Gumbart, James C

    2018-02-13

    Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co 3+ , Co 2+ , and Co 1+ , and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.

  9. A study of τ , the critical exponent of nuclear fragmentation

    International Nuclear Information System (INIS)

    Cardenas, R.; Lopez, J.A.; Barranon, A.; Dorso, C.O.

    2001-01-01

    Full text: When nuclei break into pieces, fragments with different sizes mass and charge numbers, are generated. Using the Fisher droplet model this fragmentation process can be characterized as a second order phase transitions of the excited nuclear matter. For breakups occurring near the critical point, the mass distribution should obeys a power law of the form ∼ A - τ , with τ being a critical exponent, apparently universal to processes at different scales with values within 2 ≤ τ ≤3. In this work we study the behavior of this exponent considering four different models. In summary the findings are as follows. Using percolation theory for a cubic system with 216 sites, a value of τ = 2.3 was obtained. A spherical system, also yielded a value of τ = 2.3. The third model, consisting of two 74-particle colliding nuclei interacting via a Lennard-Jones potential, also produced fragments with a power law distribution of τ = 2.3. Finally, studying a series of collisions of 147-particle nuclei using a more realistic potential (Pandharipande), a τ = 1.92 was obtained. This last result, however, can be expected for breakups not occurring near the critical point. Further refinements of this last study are in progress. JAL acknowledges support from the National Science Foundation, through grant PHY-96-00038. (Author)

  10. Assessing the accuracy of integral equation theories for nano-sized hydrophobic solutes in water

    Science.gov (United States)

    Fujita, Takatoshi; Yamamoto, Takeshi

    2017-07-01

    Integral equation theories provide an efficient route for computing the solvation free energy (SFE) of molecular systems in water. The accuracy of those theories is usually tested against small molecules via comparison of SFE with reference data. However, tests against larger molecules in the nanometer regime are scarce in literature despite recent applications to such systems. Here, we thus study the accuracy and validity of a commonly used integral equation theory, namely, a three-dimensional reference interaction site model (3D-RISM), by considering the following problems: (1) solvation of a small to large Lennard-Jones particle, (2) binding of planar hydrophobic systems with varying size and hydrophobicity, and (3) self-assembly of amphiphilic molecules into a nanocapsule. The energy representation method is also utilized for comparison. The results show that the 3D-RISM method works successfully for small molecules, while the accuracy degrades systematically with system size and hydrophobicity. The size-dependent error in SFE does not cancel adequately between two solute configurations, resulting in a substantial error in the free energy difference. It is also shown that the free energy profiles for hydrophobic association exhibit a fictitious high-energy barrier, suggesting that care must be taken for studying such systems. The numerical difficulties observed above are discussed based on the relation between hypernetted-chain approximation, classical density functional theory with quadratic expansion, and the size-dependent error arising from the cavity region of the system.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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...

  16. 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

  17. 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.

  18. Modeling New Adsorbents for Ethylene/Ethane Separations by Adsorption via {Pi}-Complexation

    Energy Technology Data Exchange (ETDEWEB)

    Blas, F. J.; Vega, L. F.; Gubbins, K. E.

    1998-01-01

    The adsorption of olefins and paraffins in a novel model porous adsorbent is studied by means of molecular simulations. The adsorbents are synthesized by effective dispersion of CuCI on substrates with hydrocarbon-phobic surfaces, such as {gamma}-A1{sub 2}O{sub 3}. The Cu(I) cations are able to undergo {pi}-complexation with olefin molecules. Ethane and ethylene are studied as adsorbents, and the molecules are modeled as having two Lennard-Jones sites. Ethylene molecules have two additional associating square-well sites placed in the line perpendicular to the symmetry axis of the molecules in order to reproduce the {pi}-complexation.

  19. 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.

  20. Computer simulation of the thermal pressure in solids and the equation of state

    International Nuclear Information System (INIS)

    Welch, D.O.; Dienes, G.J.; Paskin, A.

    1976-01-01

    The equation of state of solids was investigated with molecular dynamics techniques by obtaining the pressure as a function of temperature over a wide range of compressions. Data were obtained for fcc crystals with Lennard--Jones interactions and for bcc crystals with Morse interactions. The results were analyzed in terms of the Mie--Gruneisen equation of state. The Gruneisen constant at zero temperature is found to be essentially that obtained from the volume dependence of the mean-squared lattice vibration frequency, and its temperature dependence can be approximated well with a self-consistent cell model. Calculated results are compared with experimental data for argon along the melting line

  1. 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...

  2. 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....

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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-...

  10. 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.

  11. 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...

  12. 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.

  13. Isomorphs in the phase diagram of a model liquid without inverse power law repulsion

    DEFF Research Database (Denmark)

    Veldhorst, Arnold Adriaan; Bøhling, Lasse; Dyre, J. C.

    2012-01-01

    scattering function are calculated. The results are shown to reflect a hidden scale invariance; despite its exponential repulsion the Buckingham potential is well approximated by an inverse power-law plus a linear term in the region of the first peak of the radial distribution function. As a consequence...... the dynamics of the viscous Buckingham liquid is mimicked by a corresponding model with purely repulsive inverse-power-law interactions. The results presented here closely resemble earlier results for Lennard-Jones type liquids, demonstrating that the existence of strong correlations and isomorphs does...... not depend critically on the mathematical form of the repulsion being an inverse power law....

  14. Free energy evaluation in polymer translocation via Jarzynski equality

    Energy Technology Data Exchange (ETDEWEB)

    Mondaini, Felipe, E-mail: fmondaini@if.ufrj.br [Centro Federal de Educação Tecnológica Celso Suckow da Fonseca, Petrópolis, 25.620-003, RJ (Brazil); Moriconi, L., E-mail: moriconi@if.ufrj.br [Instituto de Física, Universidade Federal do Rio de Janeiro, C.P. 68528, 21945-970, Rio de Janeiro, RJ (Brazil)

    2014-05-01

    We perform, with the help of cloud computing resources, extensive Langevin simulations, which provide free energy estimates for unbiased three-dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite-size scaling properties.

  15. Size dependence of the contact angle of a nanodrop in a nanocavity: Density functional theory considerations

    Science.gov (United States)

    Berim, Gersh O.; Ruckenstein, Eli

    2011-02-01

    The dependence of the contact angles of nanodrops of Lennard-Jones type fluids in nanocavities on their sizes are calculated using a nonlocal density functional theory in a canonical ensemble. Cavities of various radii and depths, various temperatures, as well as various values of the energy parameter of the fluid-solid interactions were considered. It is argued that this dependence might affect strongly, for instance, the rate of heterogeneous nucleation on rough surfaces, which is usually calculated under the assumption of constant contact angle.

  16. Effect of pressure on the structure and lattice dynamics of fullerene crystal C60

    International Nuclear Information System (INIS)

    Prilutski, Yu.I.; Shapovalov, G.G.

    1997-01-01

    The low-temperature orientationally ordered crystalline phase of fullerene C 60 was investigated in dependence on the external pressure. An assumption was made that the energy of the lattice includes two contributions: a Lennard-Jones (12-6) potential and electrostatic interaction. The vibrational spectrum of C 60 crystal was calculated using the atom-atom potential method. The frequencies of intermolecular modes as functions of external pressure were studied. The sound velocities, elastic constants and bulk modulus are calculated. The dependence of sound velocities in fullerene crystal C 60 on the external pressure is investigated. The results obtained are in good agreement with the available experimental data. (orig.)

  17. Um modelo para a superfície líquida no estudo da dinâmica do espalhamento de Xe e Ne pelo esqualano

    Directory of Open Access Journals (Sweden)

    Leal Alexandre S.

    2004-01-01

    Full Text Available In this work we present a theoretical model to investigate the scattering of Xe and Ne by a liquid squalane surface. The liquid surface is modeled as a grid of harmonic oscillators with frequencies adjusted to experimental vibration as frequencies of the liquid squalane and the atom-surface interaction potential is modeled by a Lennard-Jones function. The three dimensional description of the dynamics of the process which occurs at the gas-liquid interface is obtained by the classical trajectory method. The general characteristics of the dynamics of the scattering process are in good agreement with experimental data.

  18. 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....

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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....

  5. 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.

  6. 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...

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation

    Science.gov (United States)

    Pandey, R. B.; Farmer, B. L.

    2009-01-01

    Energy, mobility, and structural profiles of residues in a specific sequence of human immunodeficiency virus (HIV)-1 protease chain and its global conformation and dynamics are studied by a coarse-grained computer simulation model on a cubic lattice. HIV-1 protease is described by a chain of 99 residues (nodes) in a specific sequence (1DIFA) with N- and C-terminals on the lattice, where empty lattice sites represent an effective solvent medium. Internal structures of the residues are ignored but their specificities are captured via an interaction (ɛij) matrix (residue-residue, residue-solvent) of the coefficient (fɛij) of the Lennard-Jones potential. Simulations are performed for a range of interaction strength (f ) with the solvent-residue interaction describing the quality of the solvent. Snapshots of the protein show considerable changes in the conformation of the protein on varying the interaction. From the mobility and energy profiles of the residues, it is possible to identify the active (and not so active) segments of the protein and consequently their role in proteolysis. Contrary to interaction thermodynamics, the hydrophobic residues possess higher configurational energy and lower mobility while the electrostatic and polar residues are more mobile despite their lower interaction energy. Segments of hydrophobic core residues, crucial for the structural evolution of the protein are identified—some of which are consistent with recent molecular dynamics simulation in context to possible clinical observations. Global energy and radius of gyration of the protein exhibit nonmonotonic dependence on the interaction strength (f) with opposite trends, e.g., rapid transition into globular structure with higher energy. Variations of the rms displacement of the protein and that of a tracer residue, Gly49, with the time steps show how they slow down on increasing the interaction strength.

  15. 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

  16. 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...

  17. 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

  18. "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…

  19. 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...

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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)

  9. 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.

  10. 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

  11. 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...

  12. 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.

  13. [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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. Droplet spreading driven by van der Waals force: a molecular dynamics study

    KAUST Repository

    Wu, Congmin

    2010-07-07

    The dynamics of droplet spreading is investigated by molecular dynamics simulations for two immiscible fluids of equal density and viscosity. All the molecular interactions are modeled by truncated Lennard-Jones potentials and a long-range van der Waals force is introduced to act on the wetting fluid. By gradually increasing the coupling constant in the attractive van der Waals interaction between the wetting fluid and the substrate, we observe a transition in the initial stage of spreading. There exists a critical value of the coupling constant, above which the spreading is pioneered by a precursor film. In particular, the dynamically determined critical value quantitatively agrees with that determined by the energy criterion that the spreading coefficient equals zero. The latter separates partial wetting from complete wetting. In the regime of complete wetting, the radius of the spreading droplet varies with time as R(t) ∼ √t, a behavior also found in molecular dynamics simulations where the wetting dynamics is driven by the short-range Lennard-Jones interaction between liquid and solid. © 2010 IOP Publishing Ltd.

  5. Droplet spreading driven by van der Waals force: a molecular dynamics study

    International Nuclear Information System (INIS)

    Wu Congmin; Qian Tiezheng; Sheng Ping

    2010-01-01

    The dynamics of droplet spreading is investigated by molecular dynamics simulations for two immiscible fluids of equal density and viscosity. All the molecular interactions are modeled by truncated Lennard-Jones potentials and a long-range van der Waals force is introduced to act on the wetting fluid. By gradually increasing the coupling constant in the attractive van der Waals interaction between the wetting fluid and the substrate, we observe a transition in the initial stage of spreading. There exists a critical value of the coupling constant, above which the spreading is pioneered by a precursor film. In particular, the dynamically determined critical value quantitatively agrees with that determined by the energy criterion that the spreading coefficient equals zero. The latter separates partial wetting from complete wetting. In the regime of complete wetting, the radius of the spreading droplet varies with time as R(t)∼√t, a behavior also found in molecular dynamics simulations where the wetting dynamics is driven by the short-range Lennard-Jones interaction between liquid and solid.

  6. 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)

  7. 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.

  8. Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields.

    Science.gov (United States)

    Van Vleet, Mary J; Misquitta, Alston J; Stone, Anthony J; Schmidt, J R

    2016-08-09

    Short-range repulsion within intermolecular force fields is conventionally described by either Lennard-Jones (A/r(12)) or Born-Mayer (A exp(-Br)) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of intermolecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.

  9. Collision Frequency for Energy Transfer in Unimolecular Reactions.

    Science.gov (United States)

    Matsugi, Akira

    2018-03-01

    Pressure dependence of unimolecular reaction rates is governed by the energy transfer in collisions of reactants with bath gas molecules. Pressure-dependent rate constants can be theoretically determined by solving master equations for unimolecular reactions. In general, master equation formulations describe energy transfer processes using a collision frequency and a probability distribution model of the energy transferred per collision. The present study proposes a novel method for determining the collision frequency from the results of classical trajectory calculations. Classical trajectories for collisions of several polyatomic molecules (ethane, methane, tetrafluoromethane, and cyclohexane) with monatomic colliders (Ar, Kr, and Xe) were calculated on potential energy surfaces described by the third-order density-functional tight-binding method in combination with simple pairwise interaction potentials. Low-order (including non-integer-order) moments of the energy transferred in deactivating collisions were extracted from the trajectories and compared with those derived using some probability distribution models. The comparison demonstrates the inadequacy of the conventional Lennard-Jones collision model for representing the collision frequency and suggests a robust method for evaluating the collision frequency that is consistent with a given probability distribution model, such as the exponential-down model. The resulting collision frequencies for the exponential-down model are substantially higher than the Lennard-Jones collision frequencies and are close to the (hypothetical) capture rate constants for dispersion interactions. The practical adequacy of the exponential-down model is also briefly discussed.

  10. 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).

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Accelerating Monte Carlo molecular simulations by reweighting and reconstructing Markov chains: Extrapolation of canonical ensemble averages and second derivatives to different temperature and density conditions

    KAUST Repository

    Kadoura, Ahmad Salim

    2014-08-01

    Accurate determination of thermodynamic properties of petroleum reservoir fluids is of great interest to many applications, especially in petroleum engineering and chemical engineering. Molecular simulation has many appealing features, especially its requirement of fewer tuned parameters but yet better predicting capability; however it is well known that molecular simulation is very CPU expensive, as compared to equation of state approaches. We have recently introduced an efficient thermodynamically consistent technique to regenerate rapidly Monte Carlo Markov Chains (MCMCs) at different thermodynamic conditions from the existing data points that have been pre-computed with expensive classical simulation. This technique can speed up the simulation more than a million times, making the regenerated molecular simulation almost as fast as equation of state approaches. In this paper, this technique is first briefly reviewed and then numerically investigated in its capability of predicting ensemble averages of primary quantities at different neighboring thermodynamic conditions to the original simulated MCMCs. Moreover, this extrapolation technique is extended to predict second derivative properties (e.g. heat capacity and fluid compressibility). The method works by reweighting and reconstructing generated MCMCs in canonical ensemble for Lennard-Jones particles. In this paper, system\\'s potential energy, pressure, isochoric heat capacity and isothermal compressibility along isochors, isotherms and paths of changing temperature and density from the original simulated points were extrapolated. Finally, an optimized set of Lennard-Jones parameters (ε, σ) for single site models were proposed for methane, nitrogen and carbon monoxide. © 2014 Elsevier Inc.

  16. 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.

  17. 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.

  18. Heat conduction in diatomic chains with correlated disorder

    Science.gov (United States)

    Savin, Alexander V.; Zolotarevskiy, Vadim; Gendelman, Oleg V.

    2017-01-01

    The paper considers heat transport in diatomic one-dimensional lattices, containing equal amounts of particles with different masses. Ordering of the particles in the chain is governed by single correlation parameter - the probability for two neighboring particles to have the same mass. As this parameter grows from zero to unity, the structure of the chain varies from regular staggering chain to completely random configuration, and then - to very long clusters of particles with equal masses. Therefore, this correlation parameter allows a control of typical cluster size in the chain. In order to explore different regimes of the heat transport, two interatomic potentials are considered. The first one is an infinite potential wall, corresponding to instantaneous elastic collisions between the neighboring particles. In homogeneous chains such interaction leads to an anomalous heat transport. The other one is classical Lennard-Jones interatomic potential, which leads to a normal heat transport. The simulations demonstrate that the correlated disorder of the particle arrangement does not change the convergence properties of the heat conduction coefficient, but essentially modifies its value. For the collision potential, one observes essential growth of the coefficient for fixed chain length as the limit of large homogeneous clusters is approached. The thermal transport in these models remains superdiffusive. In the Lennard-Jones chain the effect of correlation appears to be not monotonous in the limit of low temperatures. This behavior stems from the competition between formation of long clusters mentioned above, and Anderson localization close to the staggering ordered state.

  19. Searching for globally optimal functional forms for interatomic potentials using genetic programming with parallel tempering.

    Science.gov (United States)

    Slepoy, A; Peters, M D; Thompson, A P

    2007-11-30

    Molecular dynamics and other molecular simulation methods rely on a potential energy function, based only on the relative coordinates of the atomic nuclei. Such a function, called a force field, approximately represents the electronic structure interactions of a condensed matter system. Developing such approximate functions and fitting their parameters remains an arduous, time-consuming process, relying on expert physical intuition. To address this problem, a functional programming methodology was developed that may enable automated discovery of entirely new force-field functional forms, while simultaneously fitting parameter values. The method uses a combination of genetic programming, Metropolis Monte Carlo importance sampling and parallel tempering, to efficiently search a large space of candidate functional forms and parameters. The methodology was tested using a nontrivial problem with a well-defined globally optimal solution: a small set of atomic configurations was generated and the energy of each configuration was calculated using the Lennard-Jones pair potential. Starting with a population of random functions, our fully automated, massively parallel implementation of the method reproducibly discovered the original Lennard-Jones pair potential by searching for several hours on 100 processors, sampling only a minuscule portion of the total search space. This result indicates that, with further improvement, the method may be suitable for unsupervised development of more accurate force fields with completely new functional forms. Copyright (c) 2007 Wiley Periodicals, Inc.

  20. Diffusion of Supercritical Fluids through Single-Layer Nanoporous Solids: Theory and Molecular Simulations.

    Science.gov (United States)

    Oulebsir, Fouad; Vermorel, Romain; Galliero, Guillaume

    2018-01-16

    With the advent of graphene material, membranes based on single-layer nanoporous solids appear as promising devices for fluid separation, be it liquid or gaseous mixtures. The design of such architectured porous materials would greatly benefit from accurate models that can predict their transport and separation properties. More specifically, there is no universal understanding of how parameters such as temperature, fluid loading conditions, or the ratio of the pore size to the fluid molecular diameter influence the permeation process. In this study, we address the problem of pure supercritical fluids diffusing through simplified models of single-layer porous materials. Basically, we investigate a toy model that consists of a single-layer lattice of Lennard-Jones interaction sites with a slit gap of controllable width. We performed extensive equilibrium and biased molecular dynamics simulations to document the physical mechanisms involved at the molecular scale. We propose a general constitutive equation for the diffusional transport coefficient derived from classical statistical mechanics and kinetic theory, which can be further simplified in the ideal gas limit. This transport coefficient relates the molecular flux to the fluid density jump across the single-layer membrane. It is found to be proportional to the accessible surface porosity of the single-layer porous solid and to a thermodynamic factor accounting for the inhomogeneity of the fluid close to the pore entrance. Both quantities directly depend on the potential of mean force that results from molecular interactions between solid and fluid atoms. Comparisons with the simulations data show that the kinetic model captures how narrowing the pore size below the fluid molecular diameter lowers dramatically the value of the transport coefficient. Furthermore, we demonstrate that our general constitutive equation allows for a consistent interpretation of the intricate effects of temperature and fluid loading

  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. 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.

  7. 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

  8. 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.

  9. 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)

  10. 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 ...

  11. 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.

  12. 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 ...

  13. 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

  14. 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

  15. 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 ...

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Blood Clotting Inspired Polymer Physics

    Science.gov (United States)

    Sing, Charles Edward

    The blood clotting process is one of the human body's masterpieces in targeted molecular manipulation, as it requires the activation of the clotting cascade at a specific place and a specific time. Recent research in the biological sciences have discovered that one of the protein molecules involved in the initial stages of the clotting response, von Willebrand Factor (vWF), exhibits counterintuitive and technologically useful properties that are driven in part by the physical environment in the bloodstream at the site of a wound. In this thesis, we take inspiration from initial observations of the vWF in experiments, and aim to describe the behaviors observed in this process within the context of polymer physics. By understanding these physical principles, we hope to harness nature's ability to both direct molecules in both spatial and conformational coordinates. This thesis is presented in three complementary sections. After an initial introduction describing the systems of interest, we first describe the behavior of collapsed Lennard-Jones polymers in the presence of an infinite medium. It has been shown that simple bead-spring homopolymer models describe vWF quite well in vitro. We build upon this previous work to first describe the behavior of a collapsed homopolymer in an elongational fluid flow. Through a nucleation-protrusion mechanism, scaling relationships can be developed to provide a clear picture of a first-order globule-stretch transition and its ramifications in dilute-solution rheology. The implications of this behavior and its relation to the current literature provides qualitative explanations for the physiological process of vasoconstriction. In an effort to generalize these observations, we present an entire theory on the behavior of polymer globules under influence of any local fluid flow. Finally, we investigate the internal dynamics of these globules by probing their pulling response in an analogous fashion to force spectroscopy. We elucidate

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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...

  9. 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.

  10. 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

  11. Cantilever-based sensing: the origin of surface stress and optimization strategies

    International Nuclear Information System (INIS)

    Godin, Michel; Tabard-Cossa, Vincent; Miyahara, Yoichi; Grutter, Peter; Monga, Tanya; Bruce Lennox, R; Williams, P J; Beaulieu, L Y

    2010-01-01

    Many interactions drive the adsorption of molecules on surfaces, all of which can result in a measurable change in surface stress. This article compares the contributions of various possible interactions to the overall induced surface stress for cantilever-based sensing applications. The surface stress resulting from adsorption-induced changes in the electronic density of the underlying surface is up to 2-4 orders of magnitude larger than that resulting from intermolecular electrostatic or Lennard-Jones interactions. We reveal that the surface stress associated with the formation of high quality alkanethiol self-assembled monolayers on gold surfaces is independent of the molecular chain length, supporting our theoretical findings. This provides a foundation for the development of new strategies for increasing the sensitivity of cantilever-based sensors for various applications.

  12. Digestion and Interaction of Starches with α-Amylases: I. Mutational analysis of Carbohydrate Binding Sites in barley. II. In Vitro Starch Digestion of Legumes

    DEFF Research Database (Denmark)

    Nielsen, Morten Munch

    2006-01-01

    the hydrolysis of internal 1,4-α-D-glucosidic bonds in starch and related polysaccharides. The present thesis concerns studies of two α-amylases: 1) secondary substrate binding sites in barley α-amylase 1 (AMY1), and 2) the involvement of anti-nutrients in in vitro digestion of starch in legumes by porcine......Starch is the primary energy storage of higher plants and an import nutrient for mammals, fungi and bacteria. The mobilization of starch is thus essential in both the germination of the barley grain and in human digestion of foods. α-Amylase (1,4-α-D-glucan glucanohydrolase, EC. 3.2.1.1) catalyzes...... pancreatic α-amylase. The degradation of insoluble polysaccharides by glycoside hydrolases is relative inefficient as the polysaccharide chains often are barely inaccessible to the active site of the enzymes. Many raw starch-degrading enzymes contain secondary carbohydrate binding sites on the catalytic...

  13. Integrated geochronology of Acheulian sites from the southern Latium (central Italy): Insights on human-environment interaction and the technological innovations during the MIS 11-MIS 10 period

    Science.gov (United States)

    Pereira, Alison; Nomade, Sébastien; Moncel, Marie-Hélène; Voinchet, Pierre; Bahain, Jean-Jacques; Biddittu, Italo; Falguères, Christophe; Giaccio, Biagio; Manzi, Giorgio; Parenti, Fabio; Scardia, Giancarlo; Scao, Vincent; Sottili, Gianluca; Vietti, Amina

    2018-05-01

    We have explored the multimethod approach combining 40Ar/39Ar on single crystal, ESR on bleached quartz, and ESR/U-series on teeth to improve the age of four neighbours "Acheulian" sites of the Frosinone Province (Latium, Italy): Fontana Ranuccio, Cava Pompi (Pofi), Isoletta, and Lademagne. Ages obtained by the three methods are in mutual agreement and confirm the potential of dating with confidence Middle Pleistocene sites of Italy using these methods. At Fontana Ranuccio, the 40Ar/39Ar age (408 ± 10 ka, full external error at 2σ) obtained for the archaeological level (unit FR4) and geochemical analyses of glass shards performed on the Unit FR2a layer allow us to attribute the studied volcanic material to the Pozzolane Nere volcanic series, a well-known caldera-forming event originated from the Colli Albani volcanic district. These new data ascribe the Fontana Ranuccio site, as well as the eponym faunal unit, to the climatic optimum of Marine Isotope Stage (MIS) 11. Ages obtained for the Cava Pompi, Isoletta, and Lademagne sites cover a relatively short period of time between 408 ka and 375 ka, spanning MIS 11 climatic optimum to the MIS 11-10 transition. Analysis of small collections of lithic industries, bifacial tools, and small cores technologies from Isoletta, Lademagne, and the neighbour site of Ceprano-Campogrande shows common technical strategies for the period comprised between MIS 11 and MIS 9 (410-325 ka), such as the elaboration of flaked elephant bone industries found over the whole Latium region. However, some features found only in the Frosinone province area, like large-sized bifaces, suggest particular regional behaviours. The presence of one Levallois core in the oldest layer of Lademagne (i.e. > 405 ± 9 ka) suggests a punctual practice of this technology, also proposed as early as MIS 10/11 in the neighbour site of Guado San Nicola (Molise) in central Italy.

  14. Site-directed mutagenesis of the histamine H1-receptor reveals a selective interaction of asparagine207 with subclasses of H1-receptor agonists

    NARCIS (Netherlands)

    Leurs, R; Smit, M J; Tensen, C P; Ter Laak, A M; Timmerman, H

    1994-01-01

    In this study we investigated the role of the threonine203 and the asparagine207 residues in the fifth transmembrane domain of the guinea-pig histamine H1-receptor by site-directed mutagenesis to non-functional alanines. Whereas the threonine203 residue is not important for the action of histamine,

  15. High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila

    NARCIS (Netherlands)

    Ramírez, Fidel; Lingg, Thomas; Toscano, Sarah; Lam, Kin Chung; Georgiev, Plamen; Chung, Ho-Ryun; Lajoie, Bryan R; de Wit, Elzo; Zhan, Ye; de Laat, Wouter; Dekker, Job; Manke, Thomas; Akhtar, Asifa

    2015-01-01

    Dosage compensation mechanisms provide a paradigm to study the contribution of chromosomal conformation toward targeting and spreading of epigenetic regulators over a specific chromosome. By using Hi-C and 4C analyses, we show that high-affinity sites (HAS), landing platforms of the male-specific

  16. New theories for smectic and nematic liquid crystalline polymers

    International Nuclear Information System (INIS)

    Dowell, F.

    1987-01-01

    A summary of results from new statistical-physics theories for both backbone and side-chain liquid crystalline polymers (LCPs) and for mixtures with LCPs is presented. Thermodynamic and molecular ordering properties (including odd-even effects) have been calculated as a function of pressure, density, temperature, and molecule chemical structures (including degree of polymerization and the following properties of the chemical structures of the repeat units: lengths and shapes, intra-chain rotation energies, dipole moments, site-site polarizabilities and Lennard-Jones potentials, etc.) in nematic and multiple smectic-A LC phases and in the isotropic liquid phase. These theories can also be applied to combined LCPs. Since these theories have no ad hoc or arbitrarily adjustable parameters, these theories have been used to design new LCPs and new solvents and to predict and explain properties

  17. New theories for smectic and nematic liquid-crystal polymers: Backbone LCPs [liquid crystalline polymers] and their mixtures and side-chain LCPs

    International Nuclear Information System (INIS)

    Dowell, F.

    1987-01-01

    A summary of predictions and explanations from statistical-physics theories for both backbone and side-chain liquid crystalline polymers (LCPs) and for mixtures with backbone LCPs are presented. Trends in the thermodynamic and molecular ordering properties have been calculated as a function of pressure, density, temperature, and molecule chemical structures (including degree of polymerization and the following properties of the chemical structures of the repeat units: lengths and shapes, intra-chain rotation energies, dipole moments, site-site polarizabilities and Lennard-Jones potentials, etc.) in nematic and multiple smectic-A LC phases and in the isotropic liquid phase. The theoretical results are found to be in good agreement with existing experimental data. These theories can also be applied to combined LCPs. Since these theories have no ad hoc or arbitrarily adjustable parameters, these theories can be used to design new LCPs and new solvents as well as to predict and explain properties. 27 refs., 4 tabs

  18. A study of the diffusion mechanism in glasses: a theoretical and experimental study of tracers diffusion in amorphous metallic alloys

    International Nuclear Information System (INIS)

    Loirat, Yanick

    1999-01-01

    The principal aims of this work are a better understanding of the experimental situation in amorphous metallic alloys and a tentative explanation of the role of collective mechanisms in matter transport. Self- and solute-diffusion of Hf, Au and Cu tracers in amorphous Ni Zr alloy have been studied. We study by SIMS analysis the broadening of the concentration profile with temperature and pressure, in thin amorphous layers which were prepared by sputtering and properly relaxed. The diffusion coefficient variation with temperature shows an Arrhenius behaviour for all of our tracers. The activation energy amount to 1.55 eV for Cu, 1.65 eV for Au and 1.78 eV for Hf and corresponds to nearly one half of the corresponding energy in crystalline zirconium. The diffusion coefficients variation with hydrostatic pressure yields an activation volume equal to one half of an average atomic volume of our matrix for medium and large sized tracers Au, Hf and a smaller activation volume for Cu. The second part of our work consists of numerical simulations of atomic displacements in a generic glass by two complementary methods. In a Lennard-Jones alloy with size effect, we observe by molecular dynamics (MD) some correlated displacements which consist of substitution cycles or chains. The associated energy of these collective events represents nearly 15 pc of that found in crystalline Lennard- Jones. The systematic exploration of energy surface in space configuration made with activation-relaxation technique ART yields energy distributions of stable and saddles positions and opens the way to an evaluation of diffusion coefficients. The events found by ART are qualitatively close to MD ones, but the averaged activation energy associated with these events represents only 10 pc of the crystalline one. This clearly points towards the limit of Lennard-Jones potential, which is not enough representative of actual glasses. This is the reason why an interaction model closer to amorphous

  19. Shape matters: The case for Ellipsoids and Ellipsoidal Water

    Science.gov (United States)

    Tillack, Andreas F.; Robinson, Bruce H.

    2017-11-01

    We describe the shape potentials used for the van der Waals interactions between soft-ellipsoids used to coarse-grain molecular moieties in Metropolis Monte-Carlo simulation software. The morphologies resulting from different expressions for these van der Waals interaction potentials are discussed for the case of a prolate spheroid system with a strong dipole at the center. We also show that the calculation of ellipsoids is, at worst, only about fivefold more expensive computationally when compared to a simple Lennard-Jones sphere. Finally, as an application of the ellipsoidal shape we parametrize water from the original SPC water model and observe – just through the difference in shape alone – a significant improvement of the O-O radial distribution function when compared to experimental data. ).

  20. Probing heterogeneous dynamics from spatial density correlation in glass-forming liquids.

    Science.gov (United States)

    Li, Yan-Wei; Zhu, You-Liang; Sun, Zhao-Yan

    2016-12-01

    We numerically investigate the connection between spatial density correlation and dynamical heterogeneity in glass-forming liquids. We demonstrate that the cluster size defined by the spatial aggregation of densely packed particles (DPPs) can better capture the difference between the dynamics of the Lennard-Jones glass model and the Weeks-Chandler-Andersen truncation model than the commonly used pair correlation functions. More interestingly, we compare the mobility of DPPs and loosely packed particles, and we find that high local density correlates well with slow dynamics in systems with relatively hard repulsive interactions but links to mobile ones in the system with soft repulsive interactions at one relaxation time scale. Our results show clear evidence that the above model dependence behavior stems from the hopping motion of DPPs at the end of the caging stage due to the compressive nature of soft repulsive spheres, which activates the dynamics of DPPs in the α relaxation stage.

  1. Shape matters: The case for Ellipsoids and Ellipsoidal Water

    Energy Technology Data Exchange (ETDEWEB)

    Tillack, Andreas F. [ORNL; Robinson, Bruce H. [University of Washington, Seattle

    2017-11-01

    We describe the shape potentials used for the van der Waals interactions between soft-ellipsoids used to coarse-grain molecular moieties in our Metropolis Monte-Carlo simulation software. The morphologies resulting from different expressions for these van der Waals interaction potentials are discussed for the case of a prolate spheroid system with a strong dipole at the ellipsoid center. We also show that the calculation of ellipsoids is, at worst, only about fivefold more expensive computationally when compared to a simple Lennard- Jones sphere. Finally, as an application of the ellipsoidal shape we parametrize water from the original SPC water model and observe – just through the difference in shape alone – a significant improvement of the O-O radial distribution function when compared to experimental data.

  2. 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 Lennard – Jones 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.

  3. The energy barrier to reorientational motion of the trifluoromethyl group in lithium trifluoromethanesulphonate and its complex with poly(ethylene oxide): a comparison between modelling and NMR relaxation measurements

    Science.gov (United States)

    Moore, Elaine A.; Mortimer, Michael; Wigglesworth, Christopher; Williams, Martin A. K.

    1999-07-01

    Molecular modelling is used to calculate the barrier heights to reorientation for the trifluoromethyl group, CF 3, in both lithium trifluoromethanesulphonate, LiCF 3SO 3, and the crystalline complex of this salt with poly(ethylene oxide), PEO. The calculated barrier heights are compared with those determined from 19F spin-lattice relaxation studies. In the case of LiCF 3SO 3, fluorine-fluorine non-bonded interactions are shown to play a dominant role in determining the barrier height to CF 3 group reorientation and optimised Lennard-Jones parameters for this interaction are determined. In the crystalline complex, PEO 3·LiCF 3SO 3, it is suggested that CF 3 group reorientation is strongly influenced by segmental motions of the PEO chain.

  4. Application of a non-integer Bessel uniform approximation to inelastic molecular collisions

    International Nuclear Information System (INIS)

    Connor, J.N.L.; Mayne, H.R.

    1979-01-01

    A non-integer Bessel uniform approximation has been used to calculate transition probabilities for collinear atom-oscillator collisions. The collision systems used are a harmonic oscillator interacting via a Lennard-Jones potential and a Morse oscillator interacting via an exponential potential. Both classically allowed and classically forbidden transitions have been treated. The order of the Bessel function is chosen by a physical argument that makes use of information contained in the final-action initial-angle plot. Limitations of this procedure are discussed. It is shown that the non-integer Bessel approximation is accurate for elastic 0 → 0 collisions at high collision energies, where the integer Bessel approximation is inaccurate or inapplicable. (author)

  5. Extension of the JCZ product species database

    Energy Technology Data Exchange (ETDEWEB)

    Hobbs, M.L.; Baer, M.R.; McGee, B.C.

    1998-09-01

    A database has been created for use with the Jacobs-Cowperthwaite-Zwisler-3 equation-of-state (JCZ3-EOS) to determine thermochemical equilibrium states for energetic materials. The JCZ3-EOS uses the exponential 6 intermolecular potential function to describe interactions between molecules. Product species are characterized by r{sup *}, the radius of the minimum pair potential energy, and {var_epsilon}/{kappa}, the well depth energy normalized by Boltzmann`s constant. These parameters constitute the JCZS (S for Sandia) database describing 750 gases listed in the JANNAF tables and were obtained by using literature values of the Lennard-Jones potential, a corresponding states theory, pure liquid shock Hugoniot data, and fit values to an empirical EOS. Detonation velocities predicted with the JCZS database for a wide variety of explosives are in good agreement with data. Improved predictions of low density explosives is attributed to a better description of molecular interactions at intermediate pressures.

  6. Buckling instability of circular double-layered graphene sheets.

    Science.gov (United States)

    Natsuki, Toshiaki; Shi, Jin-Xing; Ni, Qing-Qing

    2012-04-04

    In this paper, we study the buckling properties of circular double-layered graphene sheets (DLGSs), using plate theory. The two graphene layers are modeled as two individual sheets whose interactions are determined by the Lennard-Jones potential of the carbon-carbon bond. An analytical solution of coupled governing equations is proposed for predicting the buckling properties of circular DLGSs. Using the present theoretical approach, the influences of boundary conditions, plate sizes, and buckling-mode shapes on the buckling behaviors are investigated in detail. The buckling stability is significantly affected by the buckling-mode shapes. As a result of van der Waals interactions, the buckling stress of circular DLGSs is much larger for the anti-phase mode than for the in-phase mode. © 2012 IOP Publishing Ltd

  7. Mutations at the CXCR4 interaction sites for AMD3100 influence anti-CXCR4 antibody binding and HIV-1 entry

    DEFF Research Database (Denmark)

    Hatse, Sigrid; Princen, Katrien; Vermeire, Kurt

    2003-01-01

    The interaction of the CXCR4 antagonist AMD3100 with its target is greatly influenced by specific aspartate residues in the receptor protein, including Asp(171) and Asp(262). We have now found that aspartate-to-asparagine substitutions at these positions differentially affect the binding of four...

  8. The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions.

    Science.gov (United States)

    Smith, Eric E; Malik, Harmit S

    2009-05-01

    Apolipoprotein L1 (APOL1) is a human protein that confers immunity to Trypanosoma brucei infections but can be countered by a trypanosome-encoded antagonist SRA. APOL1 belongs to a family of programmed cell death genes whose proteins can initiate host apoptosis or autophagic death. We report here that all six members of the APOL gene family (APOL1-6) present in humans have rapidly evolved in simian primates. APOL6, furthermore, shows evidence of an adaptive sweep during recent human evolution. In each APOL gene tested, we found rapidly evolving codons in or adjacent to the SRA-interacting protein domain (SID), which is the domain of APOL1 that interacts with SRA. In APOL6, we also found a rapidly changing 13-amino-acid cluster in the membrane-addressing domain (MAD), which putatively functions as a pH sensor and regulator of cell death. We predict that APOL genes are antagonized by pathogens by at least two distinct mechanisms: SID antagonists, which include SRA, that interact with the SID of various APOL proteins, and MAD antagonists that interact with the MAD hinge base of APOL6. These antagonists either block or prematurely cause APOL-mediated programmed cell death of host cells to benefit the infecting pathogen. These putative interactions must occur inside host cells, in contrast to secreted APOL1 that trafficks to the trypanosome lysosome. Hence, the dynamic APOL gene family appears to be an important link between programmed cell death of host cells and immunity to pathogens.

  9. Mutations at the CXCR4 interaction sites for AMD3100 influence anti-CXCR4 antibody binding and HIV-1 entry

    DEFF Research Database (Denmark)

    Hatse, Sigrid; Princen, Katrien; Vermeire, Kurt

    2003-01-01

    The interaction of the CXCR4 antagonist AMD3100 with its target is greatly influenced by specific aspartate residues in the receptor protein, including Asp(171) and Asp(262). We have now found that aspartate-to-asparagine substitutions at these positions differentially affect the binding of four...... different anti-CXCR4 monoclonal antibodies as well as the infectivity of diverse human immunodeficiency virus type 1 (HIV-1) strains and clinical isolates. Mutation of Asp(262) strongly decreased the coreceptor efficiency of CXCR4 for wild-type but not for AMD3100-resistant HIV-1 NL4.3. Thus, resistance...... of HIV-1 NL4.3 to AMD3100 is associated with a decreased dependence of the viral gp120 on Asp(262) of CXCR4, pointing to a different mode of interaction of wild-type versus AMD3100-resistant virus with CXCR4....

  10. The chaperone and potential mannan-binding lectin (MBL) co-receptor calreticulin interacts with MBL through the binding site for MBL-associated serine proteases

    DEFF Research Database (Denmark)

    Pagh, Rasmus; Duus, Karen; Laursen, Inga

    2008-01-01

    was immobilized on a solid surface or bound to mannan on a surface. The binding was non-covalent and biphasic with an initial salt-sensitive phase followed by a more stable salt-insensitive interaction. For plasma-derived MBL, known to be complexed with MBL-associated serine proteases (MASPs), no binding...... with calreticulin. Comparative analysis of MBL with complement component C1q, its counterpart of the classical pathway, revealed that they display similar binding characteristics for calreticulin, providing further indication that calreticulin is a common co-receptor/chaperone for both proteins. In conclusion......The chaperone calreticulin has been suggested to function as a C1q and collectin receptor. The interaction of calreticulin with mannan-binding lectin (MBL) was investigated by solid-phase binding assays. Calreticulin showed saturable and time-dependent binding to recombinant MBL, provided that MBL...

  11. Interactions of dopaminergic agonists and antagonists with dopaminergic D3 binding sites in rat striatum. Evidence that [3H]dopamine can label a high affinity agonist-binding state of the D1 dopamine receptor

    International Nuclear Information System (INIS)

    Leff, S.E.; Creese, I.

    1985-01-01

    The interactions of dopaminergic agonists and antagonists with 3 H-agonist labeled D3 dopaminergic binding sites of rat striatum have been characterized by radioligand-binding techniques. When the binding of [ 3 H]dopamine and [ 3 H]apomorphine to D2 dopamine receptors is blocked by the inclusion of D2 selective concentrations of unlabeled spiroperidol or domperidone, these ligands appear to label selectively the previously termed D3 binding site. Antagonist/[ 3 H]dopamine competition curves are of uniformly steep slope (nH . 1.0), suggesting the presence of a single D3 binding site. The relative potencies of antagonists to inhibit D3 specific [ 3 H]dopamine binding are significantly correlated with their potencies to block D1 dopamine receptors as measured by the inhibition of both dopamine-stimulated adenylate cyclase and [ 3 H]flupentixol-binding activities. The affinities of agonists to inhibit D3 specific [ 3 H]dopamine binding are also correlated with estimates of these agonists affinities for the high affinity binding component of agonist/[ 3 H]flupentixol competition curves. Both D3 specific [ 3 H] dopamine binding and the high affinity agonist-binding component of dopamine/[ 3 H]flupentixol competition curves show a similar sensitivity to guanine nucleotides. Taken together, these data strongly suggest that the D3 binding site is related to a high affinity agonist-binding state of the D1 dopamine receptor

  12. The structure of the solid-liquid interface: atomic size effect; La structure de l'interface solide-liquide: effet de taille atomique

    Energy Technology Data Exchange (ETDEWEB)

    Geysermans, P.; Pontikis, V. [Centre National de la Recherche Scientifique (CNRS), 94 - Vitry-sur-Seine (France). Centre d' Etudes de Chimie Metallurgique

    2002-09-01

    The atomic structure of the solid-liquid heterophase interface was investigated by using molecular dynamics. Two kinds of systems were studied; the first one was crystalline copper with (100) and (111) surface terminations in contact with liquid aluminium, while in the second one the interface was modelled by two systems in contact made of Lennard-Jones particles with different size ({sigma}) and energy ({epsilon}) parameters. We found that at the interface the liquid was layered whatever the crystallographic orientation of the surface. The layering of the liquid is still preserved when the ratio of particles sites ({chi}={sigma}{sub 1}/{sigma}{sub 2}) changes while an epitaxial relationship is always found between the crystal and the first liquid layer. The average density of the latter is closely related to the {chi} value. (authors)

  13. Communication: Predicting virial coefficients and alchemical transformations by extrapolating Mayer-sampling Monte Carlo simulations

    Science.gov (United States)

    Hatch, Harold W.; Jiao, Sally; Mahynski, Nathan A.; Blanco, Marco A.; Shen, Vincent K.

    2017-12-01

    Virial coefficients are predicted over a large range of both temperatures and model parameter values (i.e., alchemical transformation) from an individual Mayer-sampling Monte Carlo simulation by statistical mechanical extrapolation with minimal increase in computational cost. With this extrapolation method, a Mayer-sampling Monte Carlo simulation of the SPC/E (extended simple point charge) water model quantitatively predicted the second virial coefficient as a continuous function spanning over four orders of magnitude in value and over three orders of magnitude in temperature with less than a 2% deviation. In addition, the same simulation predicted the second virial coefficient if the site charges were scaled by a constant factor, from an increase of 40% down to zero charge. This method is also shown to perform well for the third virial coefficient and the exponential parameter for a Lennard-Jones fluid.

  14. Time-dependent density functional theory (TD-DFT) coupled with reference interaction site model self-consistent field explicitly including spatial electron density distribution (RISM-SCF-SEDD)

    Science.gov (United States)

    Yokogawa, D.

    2016-09-01

    Theoretical approach to design bright bio-imaging molecules is one of the most progressing ones. However, because of the system size and computational accuracy, the number of theoretical studies is limited to our knowledge. To overcome the difficulties, we developed a new method based on reference interaction site model self-consistent field explicitly including spatial electron density distribution and time-dependent density functional theory. We applied it to the calculation of indole and 5-cyanoindole at ground and excited states in gas and solution phases. The changes in the optimized geometries were clearly explained with resonance structures and the Stokes shift was correctly reproduced.

  15. Transient Inverse Calibration of Site-Wide Groundwater Model to Hanford Operational Impacts from 1943 to 1996--Alternative Conceptual Model Considering Interaction with Uppermost Basalt Confined Aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Vermeul, Vincent R.; Cole, Charles R.; Bergeron, Marcel P.; Thorne, Paul D.; Wurstner, Signe K.

    2001-08-29

    The baseline three-dimensional transient inverse model for the estimation of site-wide scale flow parameters, including their uncertainties, using data on the transient behavior of the unconfined aquifer system over the entire historical period of Hanford operations, has been modified to account for the effects of basalt intercommunication between the Hanford unconfined aquifer and the underlying upper basalt confined aquifer. Both the baseline and alternative conceptual models (ACM-1) considered only the groundwater flow component and corresponding observational data in the 3-Dl transient inverse calibration efforts. Subsequent efforts will examine both groundwater flow and transport. Comparisons of goodness of fit measures and parameter estimation results for the ACM-1 transient inverse calibrated model with those from previous site-wide groundwater modeling efforts illustrate that the new 3-D transient inverse model approach will strengthen the technical defensibility of the final model(s) and provide the ability to incorporate uncertainty in predictions related to both conceptual model and parameter uncertainty. These results, however, indicate that additional improvements are required to the conceptual model framework. An investigation was initiated at the end of this basalt inverse modeling effort to determine whether facies-based zonation would improve specific yield parameter estimation results (ACM-2). A description of the justification and methodology to develop this zonation is discussed.

  16. The differential interference in collisional quantum interference on rotational energy transfer

    International Nuclear Information System (INIS)

    Yang Xin; Wang Weili

    2012-01-01

    The collisional quantum interference (CQI) on rotational energy transfer was observed in the experiment of the static cell, and the integral interference angles were measured. To obtain more accurate information, the experiment in the molecular beam should be taken, from which the differential interference angle can be obtained. Based on the first-Born approximation of time-dependent perturbation theory, the theoretical model of CQI is developed in an atom-diatom collision system in the condition of the molecular beam. The model has taken into account the Lennard-Jones interaction potentials and 'straight-line' trajectory approximation. The effect factors that the interference angle depend on are investigated. The changing tendencies of the differential interference angle with the impact parameter, velocity, and collision partner are discussed. This theoretical model is important to understand or perform the experiment in the molecular beam. (authors)

  17. Role of the first coordination shell in determining the equilibrium structure and dynamics of simple liquids

    DEFF Research Database (Denmark)

    Toxværd, Søren; Dyre, J. C.

    2011-01-01

    . Lett. 103, 170601 (2009);10.1103/PhysRevLett.103.170601 J. Chem. Phys. 134, 214503 (2011)10.1063/1.3592709] . We present simulations of the standard Lennard-Jones liquid at several condensed-fluid state points, including a fairly low density state and a very high density state, as well as simulations......The traditional view that the physical properties of a simple liquid are determined primarily by its repulsive forces was recently challenged by Berthier and Tarjus, who showed that in some cases ignoring the attractions leads to large errors in the dynamics [L. Berthier and G. Tarjus, Phys. Rev...... are included in the simulations. What matters is whether or not interactions are included from all particles within the first coordination shell – the attractive forces can thus be ignored, but only at extremely high densities. The recognition of the importance of a local shell in condensed fluids goes back...

  18. Permeation, diffusion and dissolution of hydrogen isotopes, methane and inert gases through/in a tetrafluoroethylene film

    International Nuclear Information System (INIS)

    Matsuyama, M.; Miyake, H.; Ashida, K.; Watanabe, K.

    1982-01-01

    Tetrafluoroethylene (TFE) is widely used for conventional tritium handling systems such as vacuum seals, tubing and so on. We measured the permeation of the three hydrogen isotopes, methane and the inert gases through a TFE film at room temperature by means of the time-lag method in order to establish the physicochemical properties which determine the solubility and diffusivity of those gases. It was found that the diffusion constant of the inert gases changed exponentially with the heat of vaporization and the solubility was an exponential function of the Lennard-Jones force constant of the gases. On the other hand, hydrogen isotopes and methane deviated from these relations. It is concluded that chemical interactions between the solute and the solvent play an important role for the dissolution and the diffusion of these gases in TFE. (orig.)

  19. Simulation of wetting and drying at solid-fluid interfaces on the Delft molecular dynamics processor

    International Nuclear Information System (INIS)

    Sikkenk, J.H.; Indekeu, J.O.; van Leeuwen, J.M.J.; Vossnack, E.O.; Bakker, A.F.

    1988-01-01

    The adsorption is studied of a fluid at a structured solid substrate by means of computer simulations on the Delft Molecular Dynamics Processor. Two types of particles are present, 2904 of one type for building a three-layer substrate and about 8500 of another type for composing the fluid. Interactions between like and unlike atoms are modeled by pair potentials of Lennard-Jones form cut off at 2.5σ. Simulations are performed at constant temperature and variable ratio of substrate-adsorbate to adsorbate-adsorbate attraction. On the basis of measurements of density profiles, coverages, surface tensions, and contact angles, a wetting as well as a drying phase transition have been identified. Both transitions are of first order

  20. Theoretical study of the frequency shift in bimodal FM-AFM by fractional calculus.

    Science.gov (United States)

    Herruzo, Elena T; Garcia, Ricardo

    2012-01-01

    Bimodal atomic force microscopy is a force-microscopy method that requires the simultaneous excitation of two eigenmodes of the cantilever. This method enables the simultaneous recording of several material properties and, at the same time, it also increases the sensitivity of the microscope. Here we apply fractional calculus to express the frequency shift of the second eigenmode in terms of the fractional derivative of the interaction force. We show that this approximation is valid for situations in which the amplitude of the first mode is larger than the length of scale of the force, corresponding to the most common experimental case. We also show that this approximation is valid for very different types of tip-surface forces such as the Lennard-Jones and Derjaguin-Muller-Toporov forces.

  1. Theoretical study of the frequency shift in bimodal FM-AFM by fractional calculus

    Directory of Open Access Journals (Sweden)

    Elena T. Herruzo

    2012-03-01

    Full Text Available Bimodal atomic force microscopy is a force-microscopy method that requires the simultaneous excitation of two eigenmodes of the cantilever. This method enables the simultaneous recording of several material properties and, at the same time, it also increases the sensitivity of the microscope. Here we apply fractional calculus to express the frequency shift of the second eigenmode in terms of the fractional derivative of the interaction force. We show that this approximation is valid for situations in which the amplitude of the first mode is larger than the length of scale of the force, corresponding to the most common experimental case. We also show that this approximation is valid for very different types of tip–surface forces such as the Lennard-Jones and Derjaguin–Muller–Toporov forces.

  2. Computer simulations of nanoindentation in Mg-Cu and Cu-Zr metallic glasses

    DEFF Research Database (Denmark)

    Paduraru, Anca; Andersen, Ulrik Grønbjerg; Thyssen, Anders

    2010-01-01

    The formation of shear bands during plastic deformation of Cu0.50Zr0.50 and Mg0.85Cu0.15 metallic glasses is studied using atomic-scale computer simulations. The atomic interactions are described using realistic many-body potentials within the effective medium theory, and are compared with similar...... simulations using a Lennard-Jones description of the material. The metallic glasses are deformed both in simple shear and in a simulated nanoindentation experiment. Plastic shear localizes into shear bands with a width of approximately 5 nm in CuZr and 8 nm in MgCu. In simple shear, the shear band formation...... is very clear, whereas only incipient shear bands are seen in nanoindentation. The shear band formation during nanoindentation is sensitive to the indentation velocity, indenter radius and the cooling rate during the formation of the metallic glass. For comparison, a similar nanoindentation simulation...

  3. Anomalous diffusion and diffusion anomaly in confined Janus dumbbells.

    Science.gov (United States)

    B Krott, Leandro; Gavazzoni, Cristina; Bordin, José Rafael

    2016-12-28

    Self-assembly and dynamical properties of Janus nanoparticles have been studied by molecular dynamic simulations. The nanoparticles are modeled as dimers and they are confined between two flat parallel plates to simulate a thin film. One monomer from the dumbbells interacts by a standard Lennard-Jones potential and the other by a two-length scales shoulder potential, typically used for anomalous fluids. Here, we study the effects of removing the Brownian effects, typical from colloidal systems immersed in aqueous solution, and consider a molecular system, without the drag force and the random collisions from the Brownian motion. Self-assembly and diffusion anomaly are preserved in relation to the Brownian system. Additionally, a superdiffusive regime associated to a collective reorientation in a highly structured phase is observed. Diffusion anomaly and anomalous diffusion are explained in the two length scale framework.

  4. Atomistic simulation of processes in Ni-base alloys with account for local relaxations

    International Nuclear Information System (INIS)

    Bursik, Jiri

    2007-01-01

    Ordering in Ni-base superalloys is the crucial process controlling the development of the characteristic two-phase microstructure and subsequently the mechanical properties. Systems containing up to six alloying elements typical of advanced Ni-based superalloys are modelled in this work using a Monte Carlo approach with phenomenological Lennard-Jones pair potentials and interactions up to the third coordination sphere. Three-dimensional crystal block is used with over 10 5 atoms. Molecular dynamics approach is used to relax local atomic positions in course of ordering processes under applied stress. The importance of taking into account both relaxation of modelled block dimensions and relaxation of local atomic positions is discussed

  5. Thermophysical properties and some parameters of liquid sodium

    International Nuclear Information System (INIS)

    Rapeanu, S.; Padureanu, I.; Rotarescu, G.; Craciun, C.; Ion, M.

    1982-07-01

    In the paper are reported some results on the thermophysical properties of the liquid sodium obtained by means of the neutron scattering and of the theories existing for various physical parameters. The results are based on hard sphere approach and neutron diffraction experiments performed in the region of the small momentum transfer. From this measurement extrapolated at Q → 0, the packing fraction eta as a function of temperature in the range 100-600 deg is obtained. Knowing the parameter eta, the structure factor S(Q) and the radial distribution function g(r) are calculated. To calculate various physical parameters of the liquid sodium like: electrical resistivity, thermoelectric power, viscosity coefficient, electrical conductivity etc., S(Q), g(r) and a Lennard Jones interaction potential phi(r) are used. (authors)

  6. Anomalous diffusion and diffusion anomaly in confined Janus dumbbells

    Science.gov (United States)

    Krott, Leandro B.; Gavazzoni, Cristina; Bordin, José Rafael

    2016-12-01

    Self-assembly and dynamical properties of Janus nanoparticles have been studied by molecular dynamic simulations. The nanoparticles are modeled as dimers and they are confined between two flat parallel plates to simulate a thin film. One monomer from the dumbbells interacts by a standard Lennard-Jones potential and the other by a two-length scales shoulder potential, typically used for anomalous fluids. Here, we study the effects of removing the Brownian effects, typical from colloidal systems immersed in aqueous solution, and consider a molecular system, without the drag force and the random collisions from the Brownian motion. Self-assembly and diffusion anomaly are preserved in relation to the Brownian system. Additionally, a superdiffusive regime associated to a collective reorientation in a highly structured phase is observed. Diffusion anomaly and anomalous diffusion are explained in the two length scale framework.

  7. Sub- and super-Maxwellian evaporation of simple gases from liquid water

    International Nuclear Information System (INIS)

    Kann, Z. R.; Skinner, J. L.

    2016-01-01

    Non-Maxwellian evaporation of light atoms and molecules (particles) such as He and H 2 from liquids has been observed experimentally. In this work, we use simulations to study systematically the evaporation of Lennard-Jones particles from liquid water. We find instances of sub- and super-Maxwellian evaporation, depending on the mass of the particle and the particle-water interaction strength. The observed trends are in qualitative agreement with experiment. We interpret these trends in terms of the potential of mean force and the effectiveness and frequency of collisions during the evaporation process. The angular distribution of evaporating particles is also analyzed, and it is shown that trends in the energy from velocity components tangential and normal to the liquid surface must be understood separately in order to interpret properly the angular distributions.

  8. Computational study of heat transport in compositionally disordered binary crystals

    International Nuclear Information System (INIS)

    Lyver, John W.; Blaisten-Barojas, Estela

    2006-01-01

    The thermal conductivity of compositionally disordered binary crystals with atoms interacting through Lennard-Jones potentials has been studied as a function of temperature. The two species in the crystal differ in mass, hard-core atomic diameter, well depth and relative concentration. The isobaric Monte Carlo was used to equilibrate the samples at near-zero pressure. The isoenergy molecular dynamics combined with the Green-Kubo approach was taken to calculate the heat current time-dependent autocorrelation function and determine the lattice thermal conductivity of the sample. The inverse temperature dependence of the lattice thermal conductivity was shown to fail at low temperatures when the atomic diameters of the two species differ. Instead, the thermal conductivity was nearly a constant across temperatures for species with different atomic diameters. Overall, it is shown that there is a dramatic decrease of the lattice thermal conductivity with increasing atomic radii ratio between species and a moderate decrease due to mass disorder

  9. A New Simplified Local Density Model for Adsorption of Pure Gases and Binary Mixtures

    Science.gov (United States)

    Hasanzadeh, M.; Dehghani, M. R.; Feyzi, F.; Behzadi, B.

    2010-12-01

    Adsorption modeling is an important tool for process simulation and design. Many theoretical models have been developed to describe adsorption data for pure and multicomponent gases. The simplified local density (SLD) approach is a thermodynamic model that can be used with any equation of state and offers some predictive capability with adjustable parameters for modeling of slit-shaped pores. In previous studies, the SLD model has been utilized with the Lennard-Jones potential function for modeling of fluid-solid interactions. In this article, we have focused on application of the Sutherland potential function in an SLD-Peng-Robinson model. The advantages and disadvantages of using the new potential function for adsorption of methane, ethane, carbon dioxide, nitrogen, and three binary mixtures on two types of activated carbon are illustrated. The results have been compared with previous models. It is shown that the new SLD model can correlate adsorption data for different pressures and temperatures with minimum error.

  10. Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model.

    Science.gov (United States)

    Mohebifar, Mohamad; Johnson, Erin R; Rowley, Christopher N

    2017-12-12

    London dispersion interactions play an integral role in materials science and biophysics. Force fields for atomistic molecular simulations typically represent dispersion interactions by the 12-6 Lennard-Jones potential using empirically determined parameters. These parameters are generally underdetermined, and there is no straightforward way to test if they are physically realistic. Alternatively, the exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields. In this work, the XDM model was used to obtain the London dispersion coefficients of 88 organic molecules relevant to biochemistry and pharmaceutical chemistry and the values compared with those derived from the Lennard-Jones parameters of the CGenFF, GAFF, OPLS, and Drude polarizable force fields. The molecular dispersion coefficients for the CGenFF, GAFF, and OPLS models are systematically higher than the XDM-calculated values by a factor of roughly 1.5, likely due to neglect of higher order dispersion terms and premature truncation of the dispersion-energy summation. The XDM dispersion coefficients span a large range for some molecular-mechanical atom types, suggesting an unrecognized source of error in force-field models, which assume that atoms of the same type have the same dispersion interactions. Agreement with the XDM dispersion coefficients is even poorer for the Drude polarizable force field. Popular water models were also examined, and TIP3P was found to have dispersion coefficients similar to the experimental and XDM references, although other models employ anomalously high values. Finally, XDM-derived dispersion coefficients were used to parametrize molecular-mechanical force fields for five liquids-benzene, toluene, cyclohexane, n-pentane, and n-hexane-which resulted in improved accuracy in the

  11. Lethal action of ultraviolet and visible (blue violet) radiations at defined wavelengths on human lymphoblastoid cells; action spectra and interaction sites

    Energy Technology Data Exchange (ETDEWEB)

    Tyrrell, R.M.; Werfelli, P.; Moraes, E.C. (Institut Suisse de Recherches Experimentales sur le Cancer, Lausanne)

    1984-02-01

    The repair proficient human lymphoblastoid line (TK6) has been employed to construct an action spectrum for the lethal action of ultraviolet (UV) radiation in the range 254 to 434 nm and to examine possible interactions between longer (334, 365 and 405 nm) and shorter wavelength (254 and 313 nm) radiations. The action spectrum follows a DNA absorption spectrum fairly closely out to 360 nm. As in previously determined lethal action spectra for procaryotic and eucaryotic cell populations, there is a broad shoulder in the 334 to 405 nm region which could reflect the existence of either (a) a non-DNA chromophore or (b) a unique photochemical reaction in the DNA over this region. Pre-treatment with radiation at 334 or 365 nm causes either a slight sensitivity to (low fluences) or protection from (higher fluences) subsequent exposure to radiation at a shorter wavelength (254 or 313 nm). Pre-irradiation at a visible wavelength (405 nm) at all fluence levels employed sensitizes the populations to treatment with 254 or 313 nm radiations. These interactions will influence the lethal outcome of cellular exposure to broad-band radiation sources.

  12. Alternative Hamiltonian for molecular dynamics simulations in the grand canonical ensemble

    International Nuclear Information System (INIS)

    Lo, C.; Palmer, B.

    1995-01-01

    An alternative to the Hamiltonian of Cagin and Pettitt for performing molecular dynamics simulations in the grand canonical ensemble is presented and used as the basis for a new algorithm. The algorithm is tested on the ideal gas and the truncated and shifted Lennard-Jones fluid. Simulations are used to calculate the vapor--liquid coexistence points for the Lennard-Jones system and are found to be in agreement with previous calculations using Gibbs ensemble calculations and with the Nicolas equation of state. Simulations are also performed on the Lennard-Jones solid

  13. Kinetic analysis of ligand binding to the Ehrlich cell nucleoside transporter: Pharmacological characterization of allosteric interactions with the sup 3 Hnitrobenzylthioinosine binding site

    Energy Technology Data Exchange (ETDEWEB)

    Hammond, J.R. (Department of Pharmacology and Toxicology, University of Western Ontario, London (Canada))

    1991-06-01

    Kinetic analysis of the binding of {sup 3}Hnitrobenzylthioinosine ({sup 3}H NBMPR) to Ehrlich ascites tumor cell plasma membranes was conducted in the presence and absence of a variety of nucleoside transport inhibitors and substrates. The association of {sup 3}H NBMPR with Ehrlich cell membranes occurred in two distinct phases, possibly reflecting functional conformation changes in the {sup 3}HNBMPR binding site/nucleoside transporter complex. Inhibitors of the equilibrium binding of {sup 3}HNBMPR, tested at submaximal inhibitory concentrations, generally decreased the rate of association of {sup 3}HNBMPR, but the magnitude of this effect varied significantly with the agent tested. Adenosine and diazepam had relatively minor effects on the association rate, whereas dipyridamole and mioflazine slowed the rate dramatically. Inhibitors of nucleoside transport also decreased the rate of dissociation of {sup 3}HNBMPR, with an order of potency significantly different from their relative potencies as inhibitors of the equilibrium binding of {sup 3}HNBMPR. Dilazep, dipyridamole, and mioflazine were effective inhibitors of both {sup 3}HNBMPR dissociation and equilibrium binding. The lidoflazine analogue R75231, on the other hand, had no effect on the rate of dissociation of {sup 3}HNBMPR at concentrations below 300 microM, even though it was one of the most potent inhibitors of {sup 3}HNBMPR binding tested (Ki less than 100 nM). In contrast, a series of natural substrates for the nucleoside transport system enhanced the rate of dissociation of {sup 3}HNBMPR with an order of effectiveness that paralleled their relative affinities for the permeant site of the transporter. The most effective enhancers of {sup 3}HNBMPR dissociation, however, were the benzodiazepines diazepam, chlordiazepoxide, and triazolam.

  14. Site Features

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of various site features from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times...

  15. Bioluminescence of beetle luciferases with 6'-amino-D-luciferin analogues reveals excited keto-oxyluciferin as the emitter and phenolate/luciferin binding site interactions modulate bioluminescence colors.

    Science.gov (United States)

    Viviani, Vadim R; Neves, Deimison Rodrigues; Amaral, Danilo Trabuco; Prado, Rogilene A; Matsuhashi, Takuto; Hirano, Takashi

    2014-08-19

    Beetle luciferases produce different bioluminescence colors from green to red using the same d-luciferin substrate. Despite many studies of the mechanisms and structural determinants of bioluminescence colors with firefly luciferases, the identity of the emitters and the specific active site interactions responsible for bioluminescence color modulation remain elusive. To address these questions, we analyzed the bioluminescence spectra with 6'-amino-D-luciferin (aminoluciferin) and its 5,5-dimethyl analogue using a set of recombinant beetle luciferases that naturally elicit different colors and different pH sensitivities (pH-sensitive, Amydetes vivianii λmax=538 nm, Macrolampis sp2 λmax=564 nm; pH-insensitive, Phrixotrix hirtus λmax=623 nm, Phrixotrix vivianii λmax=546 nm, and Pyrearinus termitilluminans λmax=534 nm), a luciferase-like enzyme (Tenebrionidae, Zophobas morio λmax=613 nm), and mutants of C311 (S314). The green-yellow-emitting luciferases display red-shifted bioluminescence spectra with aminoluciferin in relation to those with D-luciferin, whereas the red-emitting luciferases displayed blue-shifted spectra. Bioluminescence spectra with 5,5-dimethylaminoluciferin, in which enolization is blocked, were almost identical to those of aminoluciferin. Fluorescence probing using 2-(4-toluidino)naphthalene-6-sulfonate and inference with aminoluciferin confirm that the luciferin binding site of the red-shifted luciferases is more polar than in the case of the green-yellow-emitting luciferases. Altogether, the results show that the keto form of excited oxyluciferin is the emitter in beetle bioluminescence and that bioluminescence colors are essentially modulated by interactions of the 6'-hydroxy group of oxyluciferin and basic moieties under the influence of the microenvironment polarity of the active site: a strong interaction between a base moiety and oxyluciferin phenol in a hydrophobic microenvironment promotes green-yellow emission, whereas a more polar

  16. An Unaltered Orthosteric Site and a Network of Long-Range Allosteric Interactions for PNU-120596 in α7 Nicotinic Acetylcholine Receptors.

    Science.gov (United States)

    Marotta, Christopher B; Lester, Henry A; Dougherty, Dennis A

    2015-08-20

    Nicotinic acetylcholine receptors (nAChRs) are vital to neuronal signaling, are implicated in important processes such as learning and memory, and are therapeutic targets for neural diseases. The α7 nAChR has been implicated in Alzheimer's disease and schizophrenia, and allosteric modulators have become one focus of drug development efforts. We investigate the mode of action of the α7-selective positive allosteric modulator, PNU-120596, and show that the higher potency of acetylcholine in the presence of PNU-120596 is not due to an altered agonist binding site. In addition, we propose several residues in the gating interface and transmembrane region that are functionally important to transduction of allosteric properties, and link PNU-120596, the acetylcholine binding region, and the receptor gate. These results suggest global protein stabilization from a communication network through several key residues that alter the gating equilibrium of the receptor while leaving the agonist binding properties unperturbed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Interaction of benzo[a]pyrene diol epoxide isomers with human serum albumin: Site specific characterisation of adducts and associated kinetics

    Science.gov (United States)

    Motwani, Hitesh V.; Westberg, Emelie; Törnqvist, Margareta

    2016-11-01

    Carcinogenicity of benzo[a]pyrene {B[a]P, a polycyclic aromatic hydrocarbon (PAH)} involves DNA-modification by B[a]P diol epoxide (BPDE) metabolites. Adducts to serum albumin (SA) are not repaired, unlike DNA adducts, and therefore considered advantageous in assessment of in vivo dose of BPDEs. In the present work, kinetic experiments were performed in relation to the dose (i.e. concentration over time) of different BPDE isomers, where human SA (hSA) was incubated with respective BPDEs under physiological conditions. A liquid chromatography (LC) tandem mass spectrometry methodology was employed for characterising respective BPDE-adducts at histidine and lysine. This strategy allowed to structurally distinguish between the adducts from racemic anti- and syn-BPDE and between (+)- and (-)-anti-BPDE, which has not been attained earlier. The adduct levels quantified by LC-UV and the estimated rate of disappearance of BPDEs in presence of hSA gave an insight into the reactivity of the diol epoxides towards the N-sites on SA. The structure specific method and dosimetry described in this work could be used for accurate estimation of in vivo dose of the BPDEs following exposure to B[a]P, primarily in dose response studies of genotoxicity, e.g. in mice, to aid in quantitative risk assessment of PAHs.

  18. ALMA OBSERVATIONS OF A HIGH-DENSITY CORE IN TAURUS: DYNAMICAL GAS INTERACTION AT THE POSSIBLE SITE OF A MULTIPLE STAR FORMATION

    Energy Technology Data Exchange (ETDEWEB)

    Tokuda, Kazuki; Onishi, Toshikazu [Department of Physical Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531 (Japan); Saigo, Kazuya; Kawamura, Akiko [National Astronomical Observatory of Japan, Mitaka, Tokyo 181-8588 (Japan); Fukui, Yasuo; Inutsuka, Shu-ichiro; Tachihara, Kengo [Department of Physics, Nagoya University, Chikusa-ku, Nagoya 464-8602 (Japan); Matsumoto, Tomoaki [Faculty of Humanity and Environment, Hosei University, Fujimi, Chiyoda-ku, Tokyo 102-8160 (Japan); Machida, Masahiro N. [Department of Earth and Planetary Sciences, Kyushu University, Fukuoka 812-8581 (Japan); Tomida, Kengo, E-mail: s_k.tokuda@p.s.osakafu-u.ac.jp [Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544 (United States)

    2014-07-01

    Starless dense cores eventually collapse dynamically, forming protostars inside them, and the physical properties of the cores determine the nature of the forming protostars. We report ALMA observations of dust continuum emission and molecular rotational lines toward MC27 or L1521F, which is considered to be very close to the first protostellar core phase. We found a few starless high-density cores, one of which has a very high density of ∼10{sup 7} cm{sup –3}, within a region of several hundred AU around a very low-luminosity protostar detected by Spitzer. A very compact bipolar outflow with a dynamical timescale of a few hundred years was found toward the protostar. The molecular line observation shows several cores with an arc-like structure, possibly due to the dynamical gas interaction. These complex structures revealed in the present observations suggest that the initial condition of star formation is highly dynamical in nature, which is considered to be a key factor in understanding fundamental issues of star formation such as the formation of multiple stars and the origin of the initial mass function of stars.

  19. Magnetic and Structural Properties of A-Site Ordered Chromium Spinel Sulfides: Alternating Antiferromagnetic and Ferromagnetic Interactions in the Breathing Pyrochlore Lattice

    Science.gov (United States)

    Okamoto, Yoshihiko; Mori, Masaki; Katayama, Naoyuki; Miyake, Atsushi; Tokunaga, Masashi; Matsuo, Akira; Kindo, Koichi; Takenaka, Koshi

    2018-03-01

    We report a comprehensive study on the magnetic and structural properties of the spinel sulfides LiInCr4S8, LiGaCr4S8, and CuInCr4S8, where Li+/Cu+ and Ga3+/In3+ ions form a zinc-blende-type order. On the basis of synchrotron X-ray diffraction and magnetization data obtained using polycrystalline samples, these three sulfides are suggested to be breathing pyrochlore magnets with alternating antiferromagnetic and ferromagnetic interactions on the small and large tetrahedra, respectively. The measured magnetization processes of the three sulfides up to 72 T are significantly different. The magnetization curves of LiInCr4S8 and CuInCr4S8 have large hysteresis loops with different shapes, while there is no hysteresis in that of LiGaCr4S8. Geometrical frustration of the small tetrahedron is likely to give rise to a wide variety of ground states, indicating the rich physics in these antiferromagnetic-ferromagnetic breathing pyrochlore magnets.

  20. Molecular Insights into the Coding Region Determinant-binding Protein-RNA Interaction through Site-directed Mutagenesis in the Heterogeneous Nuclear Ribonucleoprotein-K-homology Domains*

    Science.gov (United States)

    Barnes, Mark; van Rensburg, Gerrit; Li, Wai-Ming; Mehmood, Kashif; Mackedenski, Sebastian; Chan, Ching-Man; King, Dustin T.; Miller, Andrew L.; Lee, Chow H.

    2015-01-01

    The ability of its four heterogeneous nuclear RNP-K-homology (KH) domains to physically associate with oncogenic mRNAs is a major criterion for the function of the coding region determinant-binding protein (CRD-BP). However, the particular RNA-binding role of each of the KH domains remains largely unresolved. Here, we mutated the first glycine to an aspartate in the universally conserved GXXG motif of the KH domain as an approach to investigate their role. Our results show that mutation of a single GXXG motif generally had no effect on binding, but the mutation in any two KH domains, with the exception of the combination of KH3 and KH4 domains, completely abrogated RNA binding in vitro and significantly retarded granule formation in zebrafish embryos, suggesting that any combination of at least two KH domains cooperate in tandem to bind RNA efficiently. Interestingly, we found that any single point mutation in one of the four KH domains significantly impacted CRD-BP binding to mRNAs in HeLa cells, suggesting that the dynamics of the CRD-BP-mRNA interaction vary over time in vivo. Furthermore, our results suggest that different mRNAs bind preferentially to distinct CRD-BP KH domains. The novel insights revealed in this study have important implications on the understanding of the oncogenic mechanism of CRD-BP as well as in the future design of inhibitors against CRD-BP function. PMID:25389298

  1. Aromatic aldehydes at the active site of aldehyde oxidoreductase from Desulfovibrio gigas: reactivity and molecular details of the enzyme-substrate and enzyme-product interaction.

    Science.gov (United States)

    Correia, Hugo D; Marangon, Jacopo; Brondino, Carlos D; Moura, Jose J G; Romão, Maria J; González, Pablo J; Santos-Silva, Teresa

    2015-03-01

    Desulfovibrio gigas aldehyde oxidoreductase (DgAOR) is a mononuclear molybdenum-containing enzyme from the xanthine oxidase (XO) family, a group of enzymes capable of catalyzing the oxidative hydroxylation of aldehydes and heterocyclic compounds. The kinetic studies reported in this work showed that DgAOR catalyzes the oxidative hydroxylation of aromatic aldehydes, but not heterocyclic compounds. NMR spectroscopy studies using (13)C-labeled benzaldehyde confirmed that DgAOR catalyzes the conversion of aldehydes to the respective carboxylic acids. Steady-state kinetics in solution showed that high concentrations of the aromatic aldehydes produce substrate inhibition and in the case of 3-phenyl propionaldehyde a suicide substrate behavior. Hydroxyl-substituted aromatic aldehydes present none of these behaviors but the kinetic parameters are largely affected by the position of the OH group. High-resolution crystallographic structures obtained from single crystals of active-DgAOR soaked with benzaldehyde showed that the side chains of Phe425 and Tyr535 are important for the stabilization of the substrate in the active site. On the other hand, the X-ray data of DgAOR soaked with trans-cinnamaldehyde showed a cinnamic acid molecule in the substrate channel. The X-ray data of DgAOR soaked with 3-phenyl propionaldehyde showed clearly how high substrate concentrations inactivate the enzyme by binding covalently at the surface of the enzyme and blocking the substrate channel. The different reactivity of DgAOR versus aldehyde oxidase and XO towards aromatic aldehydes and N-heterocyclic compounds is explained on the basis of the present kinetic and structural data.

  2. Interaction of the 268-282 region of glycoprotein Ibalpha with the heparin-binding site of thrombin inhibits the enzyme activation of factor VIII.

    Science.gov (United States)

    De Cristofaro, R; De Filippis, V

    2003-01-01

    Activation of factor VIII (FVIII) by thrombin plays a fundamental role in the amplification of the coagulation cascade and takes place through specific proteolytic cleavages at Arg(372), Arg(740) and Arg(1689). Full FVIII activation requires cleavage at Arg(372), a process involving the alpha-thrombin exosite-II; referred to as heparin-binding site (HBS). The present study was aimed at investigating the effect of glycoprotein Ibalpha (GpIbalpha; 1-282 fragment) binding to thrombin HBS on FVIII activation. Similar experiments were also performed using a synthetic peptide modelled on the 268-282 sequence of GpIbalpha, and sulphated successfully at all tyrosine residues present along its sequence, at positions 276, 278 and 279. Both GpIbalpha 1-282 and the sulphated GpIb 268-282 peptides induced a progressive decrease (up to 70%) in activated FVIII generation, assessed by coagulation and FXa-generation assays. Furthermore, SDS/PAGE and Western-blot experiments showed that the specific appearance of the 44 kDa A2 domain on cleavage of the FVIII Arg(372)-Ser(373) peptide bond was delayed significantly in the presence of either GpIbalpha 1-282 or GpIb 268-282 peptide. Moreover, the effect of the latter on thrombin-mediated hydrolysis of a peptide having the sequence 341-376 of FVIII was investigated using reverse-phase HPLC. The k (cat)/ K (m) values of the FVIII 341-376 peptide hydrolysis by thrombin decreased linearly as a function of the GpIbalpha 268-282 peptide concentration, according to a competitive inhibition effect. Taken together, these experiments suggest that the sulphated 268-282 region of GpIbalpha binds to thrombin HBS, and is responsible for the inhibition of the Arg(372)-Ser(373) bond cleavage and activation of FVIII. PMID:12689334

  3. Site decontamination

    International Nuclear Information System (INIS)

    Bicker, A.E.

    1981-01-01

    Among the several DOE sites that have been radiologically decontaminated under the auspices of the Nevada Operations Office are three whose physical characteristics are unique. These are the Tatum Dome Test Site (TDTS) near Hattiesburg, Mississippi; a location of mountainous terrain (Pahute Mesa) on the Nevada Test Site; and the GNOME site near Carlsbad, New Mexico. In each case the contamination, the terrain, and the climate conditions were different. This presentation includes a brief description of each site, the methods used to perform radiological surveys, the logistics required to support the decontamination (including health physics and sample analysis), and the specific techniques used to reduce or remove the contamination

  4. Molecular dynamics and information on possible sites of interaction of intramyocellular metabolites in vivo from resolved dipolar couplings in localized 1H NMR spectra

    Science.gov (United States)

    Schröder, Leif; Schmitz, Christian; Bachert, Peter

    2004-12-01

    Proton NMR resonances of the endogenous metabolites creatine and phosphocreatine ((P)Cr), taurine (Tau), and carnosine (Cs, β-alanyl- L-histidine) were studied with regard to residual dipolar couplings and molecular mobility. We present an analysis of the direct 1H- 1H interaction that provides information on motional reorientation of subgroups in these molecules in vivo. For this purpose, localized 1H NMR experiments were performed on m. gastrocnemius of healthy volunteers using a 1.5-T clinical whole-body MR scanner. We evaluated the observable dipolar coupling strength SD0 ( S = order parameter) of the (P)Cr-methyl triplet and the Tau-methylene doublet by means of the apparent line splitting. These were compared to the dipolar coupling strength of the (P)Cr-methylene doublet. In contrast to the aliphatic protons of (P)Cr and Tau, the aromatic H2 ( δ = 8 ppm) and H4 ( δ = 7 ppm) protons of the imidazole ring of Cs exhibit second-order spectra at 1.5 T. This effect is the consequence of incomplete transition from Zeeman to Paschen-Back regime and allows a determination of SD0 from H2 and H4 of Cs as an alternative to evaluating the multiplet splitting which can be measured directly in high-resolution 1H NMR spectra. Experimental data showed striking differences in the mobility of the metabolites when the dipolar coupling constant D0 (calculated with the internuclear distance known from molecular geometry in the case of complete absence of molecular dynamics and motion) is used for comparison. The aliphatic signals involve very small order parameters S ≈ (1.4 - 3) × 10 -4 indicating rapid reorientation of the corresponding subgroups in these metabolites. In contrast, analysis of the Cs resonances yielded S ≈ (113 - 137) × 10 -4. Thus, the immobilization of the Cs imidazole ring owing to an anisotropic cellular substructure in human m. gastrocnemius is much more effective than for (P)Cr and Tau subgroups. Furthermore, 1H NMR experiments on aqueous model

  5. Full-length cellular β-secretase has a trimeric subunit stoichiometry, and its sulfur-rich transmembrane interaction site modulates cytosolic copper compartmentalization.

    Science.gov (United States)

    Liebsch, Filip; Aurousseau, Mark R P; Bethge, Tobias; McGuire, Hugo; Scolari, Silvia; Herrmann, Andreas; Blunck, Rikard; Bowie, Derek; Multhaup, Gerd

    2017-08-11

    The β-secretase (BACE1) initiates processing of the amyloid precursor protein (APP) into Aβ peptides, which have been implicated as central players in the pathology of Alzheimer disease. BACE1 has been described as a copper-binding protein and its oligomeric state as being monomeric, dimeric, and/or multimeric, but the native cellular stoichiometry has remained elusive. Here, by using single-molecule fluorescence and in vitro cross-linking experiments with photo-activatable unnatural amino acids, we show that full-length BACE1, independently of its subcellular localization, exists as trimers in human cells. We found that trimerization requires the BACE1 transmembrane sequences (TMSs) and cytoplasmic domains, with residues Ala 463 and Cys 466 buried within the trimer interface of the sulfur-rich core of the TMSs. Our 3D model predicts that the sulfur-rich core of the trimeric BACE1 TMS is accessible to metal ions, but copper ions did not trigger trimerization. The results of functional assays of endogenous BACE1 suggest that it has a role in intracellular copper compartmentalization by transferring cytosolic copper to intracellular compartments, while leaving the overall cellular copper concentration unaltered. Adding to existing physiological models, our results provide novel insight into the atypical interactions between copper and BACE1 and into its non-enzymatic activities. In conclusion, therapeutic Alzheimer disease prevention strategies aimed at decreasing BACE1 protein levels should be regarded with caution, because adverse effects in copper homeostasis may occur. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Low anticoagulant heparin targets multiple sites of inflammation, suppresses heparin-induced thrombocytopenia, and inhibits interaction of RAGE with its ligands.

    Science.gov (United States)

    Rao, Narayanam V; Argyle, Brian; Xu, Xiaoyu; Reynolds, Paul R; Walenga, Jeanine M; Prechel, Margaret; Prestwich, Glenn D; MacArthur, Robert B; Walters, Bradford B; Hoidal, John R; Kennedy, Thomas P

    2010-07-01

    While heparin has been used almost exclusively as a blood anticoagulant, important literature demonstrates that it also has broad anti-inflammatory activity. Herein, using low anti-coagulant 2-O,3-O-desulfated heparin (ODSH), we demonstrate that most of the anti-inflammatory pharmacology of heparin is unrelated to anticoagulant activity. ODSH has low affinity for anti-thrombin III, low anti-Xa, and anti-IIa anticoagulant activities and does not activate Hageman factor (factor XII). Unlike heparin, ODSH does not interact with heparin-platelet factor-4 antibodies present in patients with heparin-induced thrombocytopenia and even suppresses platelet activation in the presence of activating concentrations of heparin. Like heparin, ODSH inhibits complement activation, binding to the leukocyte adhesion molecule P-selectin, and the leukocyte cationic granular proteins azurocidin, human leukocyte elastase, and cathepsin G. In addition, ODSH and heparin disrupt Mac-1 (CD11b/CD18)-mediated leukocyte adhesion to the receptor for advanced glycation end products (RAGE) and inhibit ligation of RAGE by its many proinflammatory ligands, including the advanced glycation end-product carboxymethyl lysine-bovine serum albumin, the nuclear protein high mobility group box protein-1 (HMGB-1), and S100 calgranulins. In mice, ODSH is more effective than heparin in reducing selectin-mediated lung metastasis from melanoma and inhibits RAGE-mediated airway inflammation from intratracheal HMGB-1. In humans, 50% inhibitory concentrations of ODSH for these anti-inflammatory activities can be achieved in the blood without anticoagulation. These results demonstrate that the anticoagulant activity of heparin is distinct from its anti-inflammatory actions and indicate that 2-O and 3-O sulfate groups can be removed to reduce anticoagulant activity of heparin without impairing its anti-inflammatory pharmacology.

  7. Site organization and site arrangement

    International Nuclear Information System (INIS)

    Boissonnet, B.; Macqueron, J.F.

    1976-01-01

    The present paper deals with criteria for the choice of a production unit or power plant site, the organization and development of a site in terms of its particular characteristics and takes into account personnel considerations in site organizations as well as the problem of integrating the architecture into the environment. (RW) [de

  8. Site assessment

    DEFF Research Database (Denmark)

    Villanueva, Héctor; Gómez Arranz, Paula

    This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed.......This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed....

  9. Site assessment

    DEFF Research Database (Denmark)

    Villanueva, Héctor; Vesth, Allan

    This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed......This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed...

  10. Electronic and thermoelectric properties of Ce{sub 3}Te{sub 4} and La{sub 3}Te{sub 4} computed with density functional theory with on-site Coulomb interaction correction

    Energy Technology Data Exchange (ETDEWEB)

    Vo, Trinh; Allmen, Paul von; Huang, Chen-Kuo; Ma, James; Bux, Sabah; Fleurial, Jean-Pierre [Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109 (United States)

    2014-10-07

    The electronic properties and Seebeck coefficients of Ce{sub 3}Te{sub 4} and La{sub 3}Te{sub 4} are computed using Density Functional Theory with on-site Coulomb interaction correction. We found that the Seebeck coefficients of Ce{sub 3}Te{sub 4} and La{sub 3}Te{sub 4} are almost equal at temperatures larger than the Curie temperature of Ce{sub 3}Te{sub 4}, and in good agreement with the measurements reported by May et al. [Phys. Rev. B 86, 035135 (2012)]. At temperatures below the Curie temperature, the Seebeck coefficient of Ce{sub 3}Te{sub 4} increases due to the ferromagnetic ordering, which leads the f-electron of Ce to contribute to the Seebeck coefficient in the relevant range of electron concentration.

  11. Confirming therapeutic target of protopine using immobilized β2 -adrenoceptor coupled with site-directed molecular docking and the target-drug interaction by frontal analysis and injection amount-dependent method.

    Science.gov (United States)

    Liu, Guangxin; Wang, Pei; Li, Chan; Wang, Jing; Sun, Zhenyu; Zhao, Xinfeng; Zheng, Xiaohui

    2017-07-01

    Drug-protein interaction analysis is pregnant in designing new leads during drug discovery. We prepared the stationary phase containing immobilized β 2 -adrenoceptor (β 2 -AR) by linkage of the receptor on macroporous silica gel surface through N,N'-carbonyldiimidazole method. The stationary phase was applied in identifying antiasthmatic target of protopine guided by the prediction of site-directed molecular docking. Subsequent application of immobilized β 2 -AR in exploring the binding of protopine to the receptor was realized by frontal analysis and injection amount-dependent method. The association constants of protopine to β 2 -AR by the 2 methods were (1.00 ± 0.06) × 10 5 M -1 and (1.52 ± 0.14) × 10 4 M -1 . The numbers of binding sites were (1.23 ± 0.07) × 10 -7 M and (9.09 ± 0.06) × 10 -7 M, respectively. These results indicated that β 2 -AR is the specific target for therapeutic action of protopine in vivo. The target-drug binding occurred on Ser 169 in crystal structure of the receptor. Compared with frontal analysis, injection amount-dependent method is advantageous to drug saving, improvement of sampling efficiency, and performing speed. It has grave potential in high-throughput drug-receptor interaction analysis. Copyright © 2017 John Wiley & Sons, Ltd.

  12. The 3.2 Å resolution structure of a receptor: CheA:CheW signaling complex defines overlapping binding sites and key residue interactions within bacterial chemosensory arrays.

    Science.gov (United States)

    Li, Xiaoxiao; Fleetwood, Aaron D; Bayas, Camille; Bilwes, Alexandrine M; Ortega, Davi R; Falke, Joseph J; Zhulin, Igor B; Crane, Brian R

    2013-06-04

    Bacterial chemosensory arrays are composed of extended networks of chemoreceptors (also known as methyl-accepting chemotaxis proteins, MCPs), the histidine kinase CheA, and the adaptor protein CheW. Models of these arrays have been developed from cryoelectron microscopy, crystal structures of binary and ternary complexes, NMR spectroscopy, mutational, data and biochemical studies. A new 3.2 Å resolution crystal structure of a Thermotoga maritima MCP protein interaction region in complex with the CheA kinase-regulatory module (P4-P5) and adaptor protein CheW provides sufficient detail to define residue contacts at the interfaces formed among the three proteins. As in a previous 4.5 Å resolution structure, CheA-P5 and CheW interact through conserved hydrophobic surfaces at the ends of their β-barrels to form pseudo 6-fold symmetric rings in which the two proteins alternate around the circumference. The interface between P5 subdomain 1 and CheW subdomain 2 was anticipated from previous studies, whereas the related interface between CheW subdomain 1 and P5 subdomain 2 has only been observed in these ring assemblies. The receptor forms an unexpected structure in that the helical hairpin tip of each subunit has "unzipped" into a continuous α-helix; four such helices associate into a bundle, and the tetramers bridge adjacent P5-CheW rings in the lattice through interactions with both P5 and CheW. P5 and CheW each bind a receptor helix with a groove of conserved hydrophobic residues between subdomains 1 and 2. P5 binds the receptor helix N-terminal to the tip region (lower site), whereas CheW binds the same helix with inverted polarity near the bundle end (upper site). Sequence comparisons among different evolutionary classes of chemotaxis proteins show that the binding partners undergo correlated changes at key residue positions that involve the lower site. Such evolutionary analyses argue that both CheW and P5 bind to the receptor tip at overlapping positions

  13. Experimental investigations and geochemical modelling of site-specific fluid-fluid and fluid-rock interactions in underground storage of CO2/H2/CH4 mixtures: the H2STORE project

    Science.gov (United States)

    De Lucia, Marco; Pilz, Peter

    2015-04-01

    work packages hosted at the German Research Centre for Geosciences (GFZ) focus on the fluid-fluid and fluid-rock interactions triggered by CO2, H2 and their mixtures. Laboratory experiments expose core samples to hydrogen and CO2/hydrogen mixtures under site-specific conditions (temperatures up to 200 °C and pressure up to 300 bar). The resulting qualitative and, whereas possible, quantitative data are expected to ameliorate the precision of predictive geochemical and reactive transport modelling, which is also performed within the project. The combination of experiments, chemical and mineralogical analyses and models is needed to improve the knowledge about: (1) solubility model and mixing rule for multicomponent gas mixtures in high saline formation fluids: no data are namely available in literature for H2-charged gas mixtures in the conditions expected in the potential sites; (2) chemical reactivity of different mineral assemblages and formation fluids in a broad spectrum of P-T conditions and composition of the stored gas mixtures; (3) thermodynamics and kinetics of relevant reactions involving mineral dissolution or precipitation. The resulting amelioration of site characterization and the overall enhancement in understanding the potential processes will benefit the operational reliability, the ecological tolerance, and the economic efficiency of future energy storing plants, crucial aspects for public acceptance and for industrial investors.

  14. Characteristics of persistent spin current components in a quasi-periodic Fibonacci ring with spin–orbit interactions: Prediction of spin–orbit coupling and on-site energy

    Energy Technology Data Exchange (ETDEWEB)

    Patra, Moumita; Maiti, Santanu K., E-mail: santanu.maiti@isical.ac.in

    2016-12-15

    In the present work we investigate the behavior of all three components of persistent spin current in a quasi-periodic Fibonacci ring subjected to Rashba and Dresselhaus spin–orbit interactions. Analogous to persistent charge current in a conducting ring where electrons gain a Berry phase in presence of magnetic flux, spin Berry phase is associated during the motion of electrons in presence of a spin–orbit field which is responsible for the generation of spin current. The interplay between two spin–orbit fields along with quasi-periodic Fibonacci sequence on persistent spin current is described elaborately, and from our analysis, we can estimate the strength of any one of two spin–orbit couplings together with on-site energy, provided the other is known. - Highlights: • Determination of Rashba and Dresselhaus spin–orbit fields is discussed. • Characteristics of all three components of spin current are explored. • Possibility of estimating on-site energy is given. • Results can be generalized to any lattice models.

  15. Characteristics of persistent spin current components in a quasi-periodic Fibonacci ring with spin–orbit interactions: Prediction of spin–orbit coupling and on-site energy

    International Nuclear Information System (INIS)

    Patra, Moumita; Maiti, Santanu K.

    2016-01-01

    In the present work we investigate the behavior of all three components of persistent spin current in a quasi-periodic Fibonacci ring subjected to Rashba and Dresselhaus spin–orbit interactions. Analogous to persistent charge current in a conducting ring where electrons gain a Berry phase in presence of magnetic flux, spin Berry phase is associated during the motion of electrons in presence of a spin–orbit field which is responsible for the generation of spin current. The interplay between two spin–orbit fields along with quasi-periodic Fibonacci sequence on persistent spin current is described elaborately, and from our analysis, we can estimate the strength of any one of two spin–orbit couplings together with on-site energy, provided the other is known. - Highlights: • Determination of Rashba and Dresselhaus spin–orbit fields is discussed. • Characteristics of all three components of spin current are explored. • Possibility of estimating on-site energy is given. • Results can be generalized to any lattice models.

  16. Site Calibration

    DEFF Research Database (Denmark)

    Kock, Carsten Weber; Vesth, Allan

    This Site Calibration report is describing the results of a measured site calibration for a site in Denmark. The calibration is carried out by DTU Wind Energy in accordance with Ref.[3] and Ref.[4]. The measurement period is given. The site calibration is carried out before a power performance...... measurement on a given turbine to clarify the influence from the terrain on the ratio between the wind speed at the center of the turbine hub and at the met mast. The wind speed at the turbine is measured by a temporary mast placed at the foundation for the turbine. The site and measurement equipment...... is detailed described in [1] and [2]. All parts of the sensors and the measurement system have been installed by DTU Wind Energy....

  17. Effect of electrostatic interactions on lubrication in polymeric and biological systems

    Science.gov (United States)

    Carrillo, Jan-Michael

    2012-02-01

    Many connective tissues, such as cartilage demonstrate excellent lubrication and wear characteristics. Cartilages in mammalian joints can withstand pressures of the order of ten atmospheres and have remarkably low friction coefficient in the range of 0.001-0.03. The surface of the cartilage is covered with bottle-brush-like polyelectrolyte layer consisting of glycoproteins. This brush layer, which faces a similar layer on the opposing cartilage, is sheared as two surfaces slide passing each other during joint motion. We have performed molecular dynamics simulations of charged and neutral bottle-brush macromolecules tethered to substrates to understand the role of the electrostatic and hydrodynamic coupling between brush layers on the lubricating properties in biological and polymeric systems. Glycoprotein layers were modeled as two opposing layers of highly charged bottle-brush macromolecules composed of Lennard-Jones particles grafted to a substrate. Simulations have shown that charged bottle-brush systems have lower friction under shear and weaker dependence of the disjoining pressure on substrate separation than neutral bottle-brush systems. This was explained by formation of lubricating layer with excess of counterions located in the middle between brush-bearing surfaces. In overlapping brush layers the disjoining pressure between brush-bearing surfaces is controlled by the bottle-brush bending rigidity. Under shear, the main deformation mode of the charged bottle-brush layers is associated with the bottle-brush backbone deformation resulting in backbone deformation ratio and shear viscosity being universal functions of the Weissenberg number. In the case of neutral bottle-brush systems there is coupling between backbone and side chain deformation. This violates universality in backbone deformation ratio and manifests itself in shear viscosity dependence on the shear rate. The shear viscosity as a function of the shear rate for the neutral bottle-brush systems

  18. The Golgi-Localized γ-Ear-Containing ARF-Binding (GGA Proteins Alter Amyloid-β Precursor Protein (APP Processing through Interaction of Their GAE Domain with the Beta-Site APP Cleaving Enzyme 1 (BACE1.

    Directory of Open Access Journals (Sweden)

    Bjoern von Einem

    Full Text Available Proteolytic processing of amyloid-β precursor protein (APP by beta-site APP cleaving enzyme 1 (BACE1 is the initial step in the production of amyloid beta (Aβ, which accumulates in senile plaques in Alzheimer's disease (AD. Essential for this cleavage is the transport and sorting of both proteins through endosomal/Golgi compartments. Golgi-localized γ-ear-containing ARF-binding (GGA proteins have striking cargo-sorting functions in these pathways. Recently, GGA1 and GGA3 were shown to interact with BACE1, to be expressed in neurons, and to be decreased in AD brain, whereas little is known about GGA2. Since GGA1 impacts Aβ generation by confining APP to the Golgi and perinuclear compartments, we tested whether all GGAs modulate BACE1 and APP transport and processing. We observed decreased levels of secreted APP alpha (sAPPα, sAPPβ, and Aβ upon GGA overexpression, which could be reverted by knockdown. GGA-BACE1 co-immunoprecipitation was impaired upon GGA-GAE but not VHS domain deletion. Autoinhibition of the GGA1-VHS domain was irrelevant for BACE1 interaction. Our data suggest that all three GGAs affect APP processing via the GGA-GAE domain.

  19. Tachykinin regulation of cholinergic transmission in the limbic/prefrontal territory of the rat dorsal striatum: implication of new neurokinine 1-sensitive receptor binding site and interaction with enkephalin/mu opioid receptor transmission.

    Science.gov (United States)

    Pérez, Sylvie; Tierney, Adrienne; Deniau, Jean-Michel; Kemel, Marie-Louise

    2007-12-01

    The tachykinin neurokinin 1 receptors (NK(1)Rs) regulation of acetylcholine release and its interaction with the enkephalin/mu opioid receptors (MORs) transmission was investigated in the limbic/prefrontal (PF) territory of the dorsal striatum. Using double immunohistochemistry, we first showed that in this territory, cholinergic interneurons contain tachykinin NK(1)Rs and co-express MORs in the last part of the light period (afternoon). In slices of the striatal limbic/PF territory, following suppression of the dopaminergic inhibitory control of acetylcholine release, application of the tachykinin NK(1)R antagonist, SSR240600, markedly reduced the NMDA-induced acetylcholine release in the morning but not in the afternoon when the enkephalin/MOR regulation is operational. In the afternoon, the NK(1)R antagonist response required the suppression of the enkephalin/MOR inhibitory control of acetylcholine release by betafunaltrexamine. The pharmacological profile of the tachykinin NK(1)R regulation tested by application of the receptor agonists [[Pro(9)]substance P, neurokinin A, neuropeptide K, and substance P(6-11)] and antagonists (SSR240600, GR205171, GR82334, and RP67580) indicated that the subtype of tachykinin NK(1)R implicated are the new NK(1)-sensitive receptor binding site. Therefore, in the limbic/PF territory of the dorsal striatum, endogenous tachykinin facilitates acetylcholine release via a tachykinin NK(1)R subtype. In the afternoon, the tachykinin/NK(1)R and the enkephalin/MOR transmissions interact to control cholinergic transmission.

  20. Mutagenesis of the Agrobacterium VirE2 single-stranded DNA-binding protein identifies regions required for self-association and interaction with VirE1 and a permissive site for hybrid protein construction.

    Science.gov (United States)

    Zhou, X R; Christie, P J

    1999-07-01

    The VirE2 single-stranded DNA-binding protein (SSB) of Agrobacterium tumefaciens is required for delivery of T-DNA to the nuclei of susceptible plant cells. By yeast two-hybrid and immunoprecipitation analyses, VirE2 was shown to self-associate and to interact with VirE1. VirE2 mutants with small deletions or insertions of a 31-residue oligopeptide (i31) at the N or C terminus or with an i31 peptide insertion at Leu236 retained the capacity to form homomultimers. By contrast, VirE2 mutants with modifications outside a central region located between residues 320 and 390 retained the capacity to interact with VirE1. These findings suggest the tertiary structure of VirE2 is important for homomultimer formation whereas a central domain mediates formation of a complex with VirE1. The capacity of VirE2 mutants to interact with full-length VirE2 in the yeast Saccharomyces cerevisiae correlated with the abundance of the mutant proteins in A. tumefaciens, suggesting that VirE2 is stabilized by homomultimerization in the bacterium. We further characterized the promoter and N- and C-terminal sequence requirements for synthesis of functional VirE2. A PvirB::virE2 construct yielded functional VirE2 protein as defined by complementation of a virE2 null mutation. By contrast, PvirE or Plac promoter constructs yielded functional VirE2 only if virE1 was coexpressed with virE2. Deletion of 10 or 9 residues from the N or C terminus of VirE2, respectively, or addition of heterologous peptides or proteins to either terminus resulted in a loss of protein function. However, an i31 peptide insertion at Tyr39 had no effect on protein function as defined by the capacity of the mutant protein to (i) interact with native VirE2, (ii) interact with VirE1, (iii) accumulate at abundant levels in A. tumefaciens, and (iv) restore wild-type virulence to a virE2 null mutant. We propose that Tyr39 of VirE2 corresponds to a permissive site for insertion of heterologous peptides or proteins of interest

  1. Pramana – Journal of Physics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    dimensional spatial inhomogeneity is parallel to the direction of propagation. pp 269-279 Research Articles. Structures and autocorrelation functions of liquid Al and Mg modelled via Lennard-Jones potential from molecular dynamics simulation.

  2. A free energy study of the liquid-liquid phase transition of the Jagla ...

    Indian Academy of Sciences (India)

    Appendix” preliminary free energy surface calculations for select parameterizations of the generalized family of Jagla potentials spanning from the original (anomalous,water-like) Jagla model to the Lennard-Jones model. These calculations ...

  3. QuickSiteSM, the Argonne expedited site characterization methodology

    International Nuclear Information System (INIS)

    Burton, J.C.; Meyer, W.T.

    1997-09-01

    Expedited site characterization (ESC), developed by Argonne National Laboratory, is an interactive, integrated process emphasizing the use of existing data of sufficient quality, multiple complementary characterization methods, and on-site decision making to optimize site investigations. The Argonne ESC is the basis for the provisional ESC standard of the ASTM (American Society for Testing and Materials). QuickSite SM is the implementation package developed by Argonne to facilitate ESC of sites contaminated with hazardous wastes. At various sites, Argonne has successfully implemented QuickSite SM and demonstrated the technical superiority of the ESC process over traditional methodologies guided by statistics and random-sampling approaches. For example, in a QuickSite SM characterization of a perched aquifer at the Pantex Plant in Texas, past data and geochemical analyses of existing wells were used to develop a model for recharge and contaminant movement. With the model as a guide, closure was achieved with minimal field work

  4. Site development

    International Nuclear Information System (INIS)

    Noack, J.

    1975-01-01

    The subject of this paper is a general view over all necessary considerations to develop the site after it has been chosen and before starting with the construction of a nuclear power plant. (orig./RW) [de

  5. Site selection

    International Nuclear Information System (INIS)

    Olsen, C.W.

    1983-07-01

    The conditions and criteria for selecting a site for a nuclear weapons test at the Nevada Test Site are summarized. Factors considered are: (1) scheduling of drill rigs, (2) scheduling of site preparation (dirt work, auger hole, surface casing, cementing), (3) schedule of event (when are drill hole data needed), (4) depth range of proposed W.P., (5) geologic structure (faults, Pz contact, etc.), (6) stratigraphy (alluvium, location of Grouse Canyon Tuff, etc.), (7) material properties (particularly montmorillonite and CO 2 content), (8) water table depth, (9) potential drilling problems (caving), (10) adjacent collapse craters and chimneys, (11) adjacent expended but uncollapsed sites, (12) adjacent post-shot or other small diameter holes, (13) adjacent stockpile emplacement holes, (14) adjacent planned events (including LANL), (15) projected needs of Test Program for various DOB's and operational separations, and (16) optimal use of NTS real estate

  6. Superfund Sites

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This layer represents active Superfund Sites published by the Environmental Protection Agency (EPA). These data were extracted from the Superfund Enterprise...

  7. Catalytic site interactions in yeast OMP synthase

    DEFF Research Database (Denmark)

    Hansen, Michael Riis; Barr, Eric W.; Jensen, Kaj Frank

    2014-01-01

    45 (2006) 5330-5342]. This behavior was investigated in the yeast enzyme by mutations in the conserved catalytic loop and 5-phosphoribosyl-1-diphosphate (PRPP) binding motif. Although the reaction is mechanistically sequential, the wild-type (WT) enzyme shows parallel lines in double reciprocal...

  8. Providing the climatic component in human-climate interaction studies: 550,000 years of climate history in the Chew Bahir basin, a key HSPDP site in southern Ethiopia.

    Science.gov (United States)

    Foerster, V. E.; Asrat, A.; Bronk Ramsey, C.; Chapot, M. S.; Cohen, A. S.; Dean, J. R.; Deocampo, D.; Deino, A. L.; Guenter, C.; Junginger, A.; Lamb, H. F.; Leng, M. J.; Roberts, H. M.; Schaebitz, F.; Trauth, M. H.

    2017-12-01

    As a contribution towards an enhanced understanding of human-climate interactions, the Hominin Sites and Paleolakes Drilling Project (HSPDP) has cored six predominantly lacustrine archives of climate change spanning much of the last 3.5 Ma in eastern Africa. All six sites in Ethiopia and Kenya are adjacent to key paleoanthropological sites encompassing diverse milestones in human evolution, dispersal, and technological innovation. The 280 m-long Chew Bahir sediment core, recovered from a tectonically-bound basin in the southern Ethiopian rift in late 2014, covers the past 550 ka of environmental history, an interval marked by intense climatic changes and includes the transition to the Middle Stone Age and the origin and dispersal of modern Homo sapiens. We present the outcome of lithologic and stratigraphic investigations, first interpretations of high resolution MSCL and XRF scanning data, and initial results of detailed multi-indicator analysis of the Chew Bahir cores. These analyses are based on more than 14,000 discrete samples, including grain size analyses and X-ray diffraction. An initial chronology, based on Ar/Ar and OSL dating, allows temporal calibration of our reconstruction of dry-wet cycles. Both geochemical and sedimentological data show that the Chew Bahir deposits are sensitive recorders of climate change on millennial to centennial timescales. Initial statistical analyses identify phases marked by abrupt climatic changes, whereas several long-term wet-dry oscillations reveal variations mostly in the precession ( 15-25 kyr), but also in the obliquity ( 40 kyr) and eccentricity frequency bands ( 90-120 kyr). The Chew Bahir record will help decode climate variation on several different time scales, as a consequence of orbitally-driven high-latitude glacial-interglacial shifts and variations in greenhouse gases, Indian and Atlantic Ocean sea-surface temperatures, as well as local solar irradiance. This 550 ka record of environmental change in eastern

  9. The interactions between soil-biosphere-atmosphere (ISBA) land surface model multi-energy balance (MEB) option in SURFEXv8 - Part 2: Introduction of a litter formulation and model evaluation for local-scale forest sites

    Science.gov (United States)

    Napoly, Adrien; Boone, Aaron; Samuelsson, Patrick; Gollvik, Stefan; Martin, Eric; Seferian, Roland; Carrer, Dominique; Decharme, Bertrand; Jarlan, Lionel

    2017-04-01

    Land surface models (LSMs) need to balance a complicated trade-off between computational cost and complexity in order to adequately represent the exchanges of energy, water and matter with the atmosphere and the ocean. Some current generation LSMs use a simplified or composite canopy approach that generates recurrent errors in simulated soil temperature and turbulent fluxes. In response to these issues, a new version of the interactions between soil-biosphere-atmosphere (ISBA) land surface model has recently been developed that explicitly solves the transfer of energy and water from the upper canopy and the forest floor, which is characterized as a litter layer. The multi-energy balance (MEB) version of ISBA is first evaluated for three well-instrumented contrasting local-scale sites, and sensitivity tests are performed to explore the behavior of new model parameters. Second, ISBA-MEB is benchmarked against observations from 42 forested sites from the global micro-meteorological network (FLUXNET) for multiple annual cycles.It is shown that ISBA-MEB outperforms the composite version of ISBA in improving the representation of soil temperature, ground, sensible and, to a lesser extent, latent heat fluxes. Both versions of ISBA give comparable results in terms of simulated latent heat flux because of the similar formulations of the water uptake and the stomatal resistance. However, MEB produces a better agreement with the observations of sensible heat flux than the previous version of ISBA for 87.5 % of the simulated years across the 42 forested FLUXNET sites. Most of this improvement arises owing to the improved simulation of the ground conduction flux, which is greatly improved using MEB, especially owing to the forest litter parameterization. It is also shown that certain processes are also modeled more realistically (such as the partitioning of evapotranspiration into transpiration and ground evaporation), even if certain statistical performances are neutral. The

  10. Structure and function of DnaA N-terminal domains: specific sites and mechanisms in inter-DnaA interaction and in DnaB helicase loading on oriC.

    Science.gov (United States)

    Abe, Yoshito; Jo, Takaaki; Matsuda, Yusaku; Matsunaga, Chika; Katayama, Tsutomu; Ueda, Tadashi

    2007-06-15

    DnaA forms a homomultimeric complex with the origin of chromosomal replication (oriC) to unwind duplex DNA. The interaction of the DnaA N terminus with the DnaB helicase is crucial for the loading of DnaB onto the unwound region. Here, we determined the DnaA N terminus structure using NMR. This region (residues 1-108) consists of a rigid region (domain I) and a flexible region (domain II). Domain I has an alpha-alpha-beta-beta-alpha-beta motif, similar to that of the K homology (KH) domain, and has weak affinity for oriC single-stranded DNA, consistent with KH domain function. A hydrophobic surface carrying Trp-6 most likely forms the interface for domain I dimerization. Glu-21 is located on the opposite surface of domain I from the Trp-6 site and is crucial for DnaB helicase loading. These findings suggest a model for DnaA homomultimer formation and DnaB helicase loading on oriC.

  11. Site selection

    CERN Multimedia

    CERN PhotoLab

    1968-01-01

    To help resolve the problem of site selection for the proposed 300 GeV machine, the Council selected "three wise men" (left to right, J H Bannier of the Netherlands, A Chavanne of Switzerland and L K Boggild of Denmark).

  12. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A

    2001-04-01

    The objectives, the programme, and the achievements of the Site Restoration Department of SCK-CEN in 2000 are summarised. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and activities related to the management of decommissioning projects. The department provides consultancy and services to external organisations.

  13. Site Restoration

    International Nuclear Information System (INIS)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A.

    2001-01-01

    The objectives, the programme, and the achievements of the Site Restoration Department of SCK-CEN in 2000 are summarised. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and activities related to the management of decommissioning projects. The department provides consultancy and services to external organisations

  14. Site calibration

    DEFF Research Database (Denmark)

    Gómez Arranz, Paula; Georgieva Yankova, Ginka

    between the wind speed at the center of the turbine hub and at the met mast. The wind speed at the turbine is measured by a temporary mast placed at the foundation for the turbine. The site and measurement equipment is detailed described in [2]. The possible measurement sector for power performance...

  15. Site Practice

    DEFF Research Database (Denmark)

    Wahedi, Haseebullah

    2016-01-01

    that the construction phase comprises several communities and practices, leading to various uses of the drawings. The results indicated that the craftsmen used drawings to position themselves in the correct location, and that the site managers and contract managers used them as management tools and legal documents...... different practices in the construction phase. The research is based on an ethnographic study of a case in Denmark. The empirical data were collected through direct observations and semi-structured interviews with site managers, contract managers, foremen and craftsmen. Findings revealed....... It is concluded that the drawings and the physical building play a vital role in relation to coordination within and across the various communities that are in play within the construction phas...

  16. Modeling a calixarene-crown-6 and its alkali complexes by means of a hybrid quantum mechanical/molecular mechanical method

    International Nuclear Information System (INIS)

    Lamare, V.; Golebiowski, J.; Ruiz-Lopez, M.F.; Martins-Costa, M.; Millot, C.

    2000-01-01

    Calixarene-crown-6s in 1,3-alternate conformation are compounds currently investigated for their ability to selectively extract traces of cesium from acidic or strong salinity aqueous solutions. Studies based on molecular modeling were undertaken on these systems to understand their behavior regarding cesium and other alkali cations, in particular sodium. In this work, a recently developed molecular modeling approach was used to investigate calixarene BC6 and its alkali complexes. The whole calixarene ligand is treated by the semiempirical AM1 quantum method (QM) whereas the cation and solvent are treated by a conventional force field (MM). The total energy of the system is the sum of the QM and MM sub-system contributions plus the QM/MM interaction energy. The latter includes the electrostatic interaction between QM charges (nuclei + electrons) and MM sites, and the non-electrostatic QM/MM van der Weals term, usually expressed by a Lennard-Jones potential. In the QM/MM method, van der Waals interactions between the QM and MM sub-systems are described by empirical Lennard-Jones parameters which must be adapted to the hybrid potential considered. Parameters on oxygen atoms were optimized. For the cations, two sets of Parameters were tested: Aqvist empirical parameters, derived to represent cation/water interactions in classical dynamics (set 2), and a new set of parameters which we calculated from dispersion coefficients available in the literature (set 1). The latter gave better results for the interactions with the crown. In the sodium complex, the cation interacts with only four oxygen atoms of the crown, whereas in the complex with cesium, the interaction involves six oxygen atoms. Distortion of the BC6 is therefore less with sodium and favors the corresponding complex by 4 kcal/mol. The cation/BC6 van der Waals energy is very weak for the two complexes. Hence the interaction between the cation and BC6 is primarily electrostatic. The BC6 polarization energy due

  17. Effect of on-site Coulomb interaction (U) on the electronic and magnetic properties of Fe{sub 2}MnSi, Fe{sub 2}MnAl and Co{sub 2}MnGe

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Sonu, E-mail: sonusharma@iitmandi.ac.in; Pandey, Sudhir K.

    2016-04-01

    The electronic band structures, density of states' plots and magnetic moments of Fe{sub 2}MnSi, Fe{sub 2}MnAl, and Co{sub 2}MnGe are studied by using the first principles calculation. The FM solutions using LSDA without U show the presence of half-metallic ferromagnetic (HFM) ground state in Fe{sub 2}MnSi, whereas the ground state of Fe{sub 2}MnAl is found to be metallic. In both compounds the maximum contribution to the total magnetic moment is from the Mn atom, while the Fe atom contributes very less. The electronic structures and magnetic moments of Fe-based compounds are affected significantly by U under around-the-mean-field (AMF) double counting scheme, whereas its effect is very less on Co{sub 2}MnGe. The magnetic moment of Fe atom in Fe{sub 2}MnSi (Fe{sub 2}MnAl) increased by ∼70% (∼75%) and in Mn atom it decreases by ∼50% (∼70%) when the value of U is increased from 1 to 5 eV. Hund's like exchange interactions are increasing in Fe atom while decreasing in Mn atom with increase in U. The Fe and Mn moments are ferromagnetically coupled in Fe{sub 2}MnSi for all values of U, whereas in Fe{sub 2}MnAl they are coupled antiferromagnetically below U=2 eV and ferromagnetically above it. Above U=2 eV the metallic ground state of Fe{sub 2}MnAl changes to semiconducting ground state and the ferromagnetic coupling between Fe and Mn atoms appears to be responsible for this. This shows that the validity of AFM double counting scheme is not robust for the entire range of U in the Fe{sub 2}MnAl compound. - Highlights: • The full-potential linearized augmented-plane wave methods have been employed. • On-site Coulomb interaction U under AMF double counting scheme has also considered. • The significant effect of U was observed on the properties of Fe{sub 2}-based compounds. • Very small effect of U under AMF scheme has been observed on Co{sub 2}MnGe. • The validity of the scheme is not robust for the entire range of U in Fe{sub 2}MnAl.

  18. Site Restoration

    International Nuclear Information System (INIS)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A.

    2002-01-01

    The objectives, the programme, and the achievements of SCK-CEN's Site Restoration Department for 2001 are described. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and the management of spent fuel and the flow of dismantled materials and the recycling of materials from decommissioning activities based on the smelting of metallic materials in specialised foundries. The department provides consultancy and services to external organisations and performs R and D on new techniques including processes for the treatment of various waste components including the reprocessing of spent fuel, the treatment of tritium, the treatment of liquid alkali metals into cabonates through oxidation, the treatment of radioactive organic waste and the reconditioning of bituminised waste products

  19. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A

    2002-04-01

    The objectives, the programme, and the achievements of SCK-CEN's Site Restoration Department for 2001 are described. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and the management of spent fuel and the flow of dismantled materials and the recycling of materials from decommissioning activities based on the smelting of metallic materials in specialised foundries. The department provides consultancy and services to external organisations and performs R and D on new techniques including processes for the treatment of various waste components including the reprocessing of spent fuel, the treatment of tritium, the treatment of liquid alkali metals into cabonates through oxidation, the treatment of radioactive organic waste and the reconditioning of bituminised waste products.

  20. Mochovce site

    International Nuclear Information System (INIS)

    1997-01-01

    In Mochovce site the construction of four units of WWER 440 NPP with V-213 type of reactor is being carried out. The financing of Mochovce units completion was resolved in April 1996. The completion work commenced at the construction site under leadership of SKODA Prague, the general supplier. The completion work on building part and tests of constructional electric distributions and lightning constructors started. The revisions in technological part were finished, and final protocols from revisions are the basis for starting of completion work. The assembly of transport container anchorage,ventilation system in hermetic areas and hermetic coverage of pools for stored spent nuclear fuel is being carried out. The pre-completion tests of instrumentation and control of ventilation systems, individual dosimetric control in medical station, and tests of nuclear programme according to commissioning and assembling work schedule at the equipment for physical protection of the NPP area started. Inspection activities at Mochovce were performed in accordance with inspection plan for 1996. Evaluation of routine inspections was performed by means of quarterly protocols. Main findings from the inspections performed in Mochovce were in the following areas: (a) deficiencies in the knowledge of the respective regulation and conditions from the Resolution of the state regulatory body, concerning selected employees; (b) training of the selected employees; (c) aim of the measures imposes by inspectors is to eliminate deficiencies in preparation of programmes for pre-completion and completion testing. NRA SR assessment activities at Mochovce NPP were focused mainly on approving and inspecting of design modification to approving programmes for pre-completion and completion testing of system s and equipment and on approving quality assurance programmes. The suggestions of international missions, which reviewed Mochovce safety in the years, were taken into consideration in the programme

  1. SITE-94. Radionuclide solubilities for SITE-94

    Energy Technology Data Exchange (ETDEWEB)

    Arthur, R.; Apted, M. [QuantiSci, Denver, CO (United States)

    1996-12-01

    In this report, solubility constraints are evaluated on radioelement source-term concentrations supporting the SITE-94 performance assessment. Solubility models are based on heterogeneous-equilibrium, mass- and charge-balance constraints incorporated into the EQ3/6 geochemical software package, which is used to calculate the aqueous speciation behavior and solubilities of U, Th, Pu, Np, Am, Ni, Ra, Se, Sn, Sr, Tc and Zr in site groundwaters and near-field solutions. The chemical evolution of the near field is approximated using EQ3/6 in terms of limiting conditions at equilibrium, or steady state, in three closed systems representing fully saturated bentonite, Fe{sup o} corrosion products of the canister, and spent fuel. The calculations consider both low-temperature (15 deg C) and high-temperature (80 deg C) conditions in the near field, and the existence of either reducing or strongly oxidizing conditions in each of the bentonite, canister, and spent-fuel barriers. Heterogeneities in site characteristics are evaluated through consideration of a range of initial groundwaters and their interactions with engineered barriers. Aqueous speciation models for many radioelements are constrained by thermodynamic data that are estimated with varying degrees of accuracy. An important question, however, is how accurate do these models need to be for purposes of estimating source-term concentrations? For example, it is unrealistic to expect a high degree of accuracy in speciation models if such models predict solubilities that are below the analytical detection limit for a given radioelement. From a practical standpoint, such models are irrelevant if calculated solubilities cannot be tested by direct comparison to experimental data. In the absence of models that are both accurate and relevant for conditions of interest, the detection limit could define a pragmatic upper limit on radioelement solubility 56 refs, 25 tabs, 10 figs

  2. Two interacting Hofstadter butterflies

    International Nuclear Information System (INIS)

    Barelli, A.; Bellissard, J.; Jacquod, P.

    1997-01-01

    The problem of two interacting particles in a quasiperiodic potential is addressed. Using analytical and numerical methods, we explore the spectral properties and eigenstates structure from the weak to the strong interaction case. More precisely, a semiclassical approach based on noncommutative geometry techniques is used to understand the intricate structure of such a spectrum. An interaction induced localization effect is furthermore emphasized. We discuss the application of our results on a two-dimensional model of two particles in a uniform magnetic field with on-site interaction. copyright 1997 The American Physical Society

  3. The binding site for regulatory 14-3-3 protein in plant plasma membrane H+-ATPase: Involvement of a region promoting phosphorylation-independent interaction in addition to the phosphorylation-dependent C-terminal end

    DEFF Research Database (Denmark)

    Fuglsang, Anja T; Borch, Jonas; Bych, Katrine

    2003-01-01

    14-3-3 proteins constitute a family of well conserved proteins interacting with a large number of phosphorylated binding partners in eukaryotic cells. The plant plasma membrane H+-ATPase is an unusual target in that a unique phosphothreonine motif (946YpTV, where pT represents phosphothreonine......, Thr-924 is important for interaction with 14-3-3 protein even when Thr-947 is phosphorylated. We suggest that the role of phosphorylation, which is accentuated by fusicoccin, is to stabilize protein-protein interaction between 14-3-3 protein and several residues of the H+-ATPase C-terminal domain....

  4. Emission of water clusters: molecular dynamic simulation

    International Nuclear Information System (INIS)

    Kutliev, U.O.; Kalandarov, K.S.

    2006-01-01

    SPC potential is able to reproduce many of the properties of bulk H 2 O [6]. In the SPC model, the molecular interaction potential U inter consists of an electrostatic component U electrostatic describing the charge-charge interaction between pairs of atoms in the two molecules. In order to describe the dispersion and repulsive interactions between the two oxygen sites, a Lennard- Jones function ULJ is included. The Au-Au interactions are represented by the MD/Monte Carlo corrected effective medium (MD/MC-CEM) potential function for fcc metals [7]. For metal- water systems has been developed a potential by Spohr [8]. The Spohr potential consist a Morse function combined with a corrugation term defining various surface sites for the oxygen-surface interaction and a repulsive term for the hydrogen -surface interaction. For our calculation we used modified Spo hr function. Because we need the metal atoms to move and interact the water molecules, we have modified the Spohr function so that the interactions are pairwise additive between the O and H atoms in the H 2 O molecule and the metal atoms. The process of sputtering water molecules from the metal surface have been investigated by computer simulation. For the 2 layers water molecules on the Au(III) have been obtained mass spectra secondary particles. The mass spectra consists peaks corresponding to the both water molecules and clusters. On the mass spectra also observed peaks of gold atoms. The visual observations shown that at the bombardment observed 'small icebergs' which can not registered by mass detectors. These results are of interest for mass spectrometry of molecules, study of surfaces, biological molecules and medical procedures. (author)

  5. Contaminated Sites in Iowa

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — Sites contaminated by hazardous materials or wastes. These sites are those administered by the Contaminated Sites Section of Iowa DNR. Many are sites which are...

  6. Re-assessment of plant carbon dynamics at the Duke free-air CO2 enrichment site: interactions of atmospheric [CO2] with nitrogen and water availability over stand development

    Science.gov (United States)

    Heather R. McCarthy; Ram Oren; Kurt H Johnsen; Anne Gallet-Budynek; Seth G. Pritchard; Charles W Cook; Shannon L. LaDeau; Robert B. Jackson; Adrien C. Finzi

    2010-01-01

    The potential for elevated [CO2]-induced changes to plant carbon (C) storage, through modifications in plant production and allocation of C among plant pools, is an important source of uncertainty when predicting future forest function. Utilizing 10 yr of data from the Duke free-air CO2 enrichment site, we evaluated the...

  7. The 5'HS2 of the globin locus control region enhances transcription through the interaction of a multimeric complex binding at two functionally distinct NF-E2 binding sites.

    NARCIS (Netherlands)

    D. Talbot; F.G. Grosveld (Frank)

    1991-01-01

    textabstractThe locus control region (LCR) of the human beta-globin locus consists of four hypersensitive regions (5'HS 1-4). One of these sites, 5'HS2, is active in both transient and stable transfection assays and transgenic mice. It has previously been shown that the jun/fos consensus binding

  8. Análise de interações solo-planta-clima em zonas diferenciadas de área de cultivo de milho Site-specific analysis of soil-plant-climate interactions on maize

    Directory of Open Access Journals (Sweden)

    Antonio O. Santos

    2002-04-01

    ao contraste espacial existente nas propriedades físicas do solo e no potencial produtivo dos cultivos.Taking into account the very large area of corn crop in Brazil along side the constant demand for the improvement of crop management, there is a need for further investigation into the new methodologies for the treatment of inputs required by the production system. Maize yield studies have demonstrated significant spatial and time-related variability along the growing seasons. The simulation of the crop development may serve while discussing the variability and its effects on yield, as well as for data integration, when looking for useful information. This happens, mainly when moving from a homogeneous treatment of cultivated field toward a site-specific based management; where the difference in potential yield is due to occur, inside the same cultivated area. In accordance with the Ceres-Maize model, soil, plant and climate data, were collected in a corn growing area, located around the Angatuba (Sao Paulo, Brazil, at the Vale do Parapanema region (23º33' S; 48º18' W; 670 m. The simulation of yield related properties, for a single growing season and for a medium term climatic series of data was performed, in three separate soil units. The Ceres-Maize model allows the simulation of corn development on a daily-step basis, based upon a balance of carbon, nitrogen and water, provided that key morphogenetic traits of a given cultivar are known. Soil, plant and climate interactions implied moderate differences in the pattern of simulated corn yield variability along years, for two separate zones, inside the same cultivated area. This caused the simulated rate of nitrogen for the maximum economic return, to be moderately different. The simulation process suggested that the use of the model as a "non-point" analytical tool is conditional to the level of spatial contrasts in soil physical properties and yield potential.

  9. Olkiluoto site description 2004

    International Nuclear Information System (INIS)

    2005-05-01

    This Olkiluoto Site Description 2004 is a description of the Olkiluoto site, in which the various disciplines have been integrated to produce a coherent picture, and is based on the data available prior to the start of the underground excavation of the ONKALO facility. This report is the first version of such a Site Report and supplements the site syntheses that have already been published. Further Site Reports will be produced on a regular basis and it is planned that the Site Report should form the geoscientific basis of the Safety Case in a future licence application. The report updates the Baseline report published in 2003 and is designed to produce an integrated site model, by focusing on interdisciplinary interactions, and also by including new data obtained during 2003 and 2004. The report has been produced by the OMTF (Olkiluoto Modelling Task Force), which covers the areas of geology, rock mechanics, hydrogeology and hydrogeochemistry. In addition to discussing the input from these four disciplines, the Site Report also includes a description of the surface conditions. Formally, the surface conditions are not within the remit of the OMTF, which is concentrating on modelling the bedrock around the ONKALO and the future repository. The influence of the surface conditions to the overall system and to the conditions at depth is recognised, however, and thus a summary of climate, ecosystems and overburden properties is also included in this report. Chapter 1 sets out the methodology to be used in the modelling, describes the various discipline-specific models which are developed and the modelled areas which are used, and also describes two important processes - the prediction/outcome studies and the uncertainty and confidence assessment. The difference between the estimate (the prediction) and the result (the outcome) indicates the level of knowledge and the prevailing uncertainties in the models. Chapter 2 presents the applied investigation data, which are

  10. A Global Survey 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): A Guide to Interactive Global Map Layers, Table Database, References and Notes

    Energy Technology Data Exchange (ETDEWEB)

    Tynan, Mark C. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Russell, Glenn P. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Perry, Frank V. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kelley, Richard E. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Champenois, Sean T. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2017-06-13

    These associated tables, references, notes, and report present a synthesis of some notable geotechnical and engineering information used to create four interactive layer maps for selected: 1) deep mines and shafts; 2) existing, considered or planned radioactive waste management deep underground studies 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 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 comprehensive, it is representative 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 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.

  11. A Global Survey 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): A Guide to Interactive Global Map Layers, Table Database, References and Notes

    International Nuclear Information System (INIS)

    Tynan, Mark C.; Russell, Glenn P.; Perry, Frank V.; Kelley, Richard E.; Champenois, Sean T.

    2017-01-01

    These associated tables, references, notes, and report present a synthesis of some notable geotechnical and engineering information used to create four interactive layer maps for selected: 1) deep mines and shafts; 2) existing, considered or planned radioactive waste management deep underground studies 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 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 comprehensive, it is representative 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 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.

  12. Ground water chemistry and geochemical modeling of water-rock interactions at the Osamu Utsumi mine and the Morro do Ferro analogue study sites, Poços de Caldas, Minas Gerais, Brazil

    Science.gov (United States)

    Nordstrom, D. Kirk; McNutt, R.H.; Puigdomenech, I.; Smellie, John A.T.; Wolf, M.

    1992-01-01

    Surface and ground waters, collected over a period of three years from the Osamu Utsumi uranium mine and the Morro do Ferro thorium/rare-earth element (Th/REE) deposits, were analyzed and interpreted to identify the major hydrogeochemical processes. These results provided information on the current geochemical evolution of ground waters for two study sites within the Poços de Caldas Natural Analogue Project.

  13. Kinesthetic Interaction

    DEFF Research Database (Denmark)

    Fogtmann, Maiken Hillerup; Fritsch, Jonas; Kortbek, Karen Johanne

    2008-01-01

    Within the Human-Computer Interaction community there is a growing interest in designing for the whole body in interaction design. The attempts aimed at addressing the body have very different outcomes spanning from theoretical arguments for understanding the body in the design process, to more...... practical examples of designing for bodily potential. This paper presents Kinesthetic Interaction as a unifying concept for describing the body in motion as a foundation for designing interactive systems. Based on the theoretical foundation for Kinesthetic Interaction, a conceptual framework is introduced...... to be utilized when analyzing existing designs, as well as developing designs exploring new ways of designing kinesthetic interactions....

  14. Selective screening of a large phage display library of plasminogen activator inhibitor 1 mutants to localize interaction sites with either thrombin or the variable region 1 of tissue-type plasminogen activator.

    Science.gov (United States)

    van Meijer, M; Roelofs, Y; Neels, J; Horrevoets, A J; van Zonneveld, A J; Pannekoek, H

    1996-03-29

    Phage display technology has been exploited to study in detail the interaction between plasminogen activator inhibitor 1 (PAI-1) and either thrombin or an essential positively charged "loop" of tissue-type plasminogen activator (t-PA), denoted variable region 1 (VR1). For this purpose, a PAI-1 mutant phage library was used that served as a reservoir of PAI-1 proteins potentially deficient in the interaction with either VR1 or thrombin. A stringent two-step selection procedure was developed. (i) A negative selection was performed by incubating the pComb3/PAI-1 mutant library with an excess of a thrombin mutant with its VR1 domain substituted with that of t-PA (thrombin-VR1). (ii) The remaining phages were complexed with t-PA (positive selection) and selected by panning with an immobilized anti-t-PA monoclonal antibody. Four consecutive panning rounds yielded an enrichment of pComb3/PAI-1 mutant phages of approximately 50-fold. Sequence analysis of 16 different cDNAs, encoding PAI-1 mutants that are hampered in the binding to thrombin-VR1, revealed the following mutations. Four independent variants share a mutation of the P4' residue (Glu350 --> Lys). Nine independent PAI-1 variants share a substitution of P1' (Met347 --> Lys), whereas three others share a P2 substitution (Ala345 --> Asp). Kinetic analysis of representative PAI-1 mutants provides evidence that the P4' residue is essential for the interaction with the VR1 domain, consistent with the data of Madison et al. (Madison, E.L., Goldsmith, E.J., Gething, M.J., Sambrook, J.F., and Gerard, R.D. (1990) J. Biol. Chem. 265, 21423-21426), whereas the P1' and P2 residues confer thrombin specificity. Concordant with the design of the selection procedure, mutants were obtained that inhibit thrombin-VR1 at least 100-fold slower than wild-type PAI-1, identifying residues that are central to the interaction with either thrombin or VR1. This study demonstrates that phage technology can be used to analyze large numbers of

  15. Cell differentiation by interaction of two HMG-box proteins: Mat1-Mc activates M cell-specific genes in S.pombe by recruiting the ubiquitous transcription factor Ste11 to weak binding sites

    DEFF Research Database (Denmark)

    Kjaerulff, S; Dooijes, D; Clevers, H

    1997-01-01

    The Schizosaccharomyces pombe mfm1 gene is expressed in an M cell-specific fashion. This regulation requires two HMG-box proteins: the ubiquitous Ste11 transcription factor and the M cell-controlling protein Mat1-Mc. Here we report that the mfm1 promoter contains a single, weak Stell-binding site...... of a complex containing both Ste11 and Mat1-Mc. A single copy of this fragment was sufficient to activate a heterologous promoter in an M-specific fashion, suggesting that these two boxes act in a synergistic manner....

  16. Ocean Disposal Site Monitoring

    Science.gov (United States)

    EPA is responsible for managing all designated ocean disposal sites. Surveys are conducted to identify appropriate locations for ocean disposal sites and to monitor the impacts of regulated dumping at the disposal sites.

  17. Promoting Your Web Site.

    Science.gov (United States)

    Raeder, Aggi

    1997-01-01

    Discussion of ways to promote sites on the World Wide Web focuses on how search engines work and how they retrieve and identify sites. Appropriate Web links for submitting new sites and for Internet marketing are included. (LRW)

  18. Interactive benchmarking

    DEFF Research Database (Denmark)

    Lawson, Lartey; Nielsen, Kurt

    2005-01-01

    We discuss individual learning by interactive benchmarking using stochastic frontier models. The interactions allow the user to tailor the performance evaluation to preferences and explore alternative improvement strategies by selecting and searching the different frontiers using directional...

  19. Weak interactions

    International Nuclear Information System (INIS)

    Chanda, R.

    1981-01-01

    The theoretical and experimental evidences to form a basis for Lagrangian Quantum field theory for Weak Interactions are discussed. In this context, gauge invariance aspects of such interactions are showed. (L.C.) [pt

  20. Hanford Site Development Plan

    Energy Technology Data Exchange (ETDEWEB)

    Rinne, C.A.; Curry, R.H.; Hagan, J.W.; Seiler, S.W.; Sommer, D.J. (Westinghouse Hanford Co., Richland, WA (USA)); Yancey, E.F. (Pacific Northwest Lab., Richland, WA (USA))

    1990-01-01

    The Hanford Site Development Plan (Site Development Plan) is intended to guide the short- and long-range development and use of the Hanford Site. All acquisition, development, and permanent facility use at the Hanford Site will conform to the approved plan. The Site Development Plan also serves as the base document for all subsequent studies that involve use of facilities at the Site. This revision is an update of a previous plan. The executive summary presents the highlights of the five major topics covered in the Site Development Plan: general site information, existing conditions, planning analysis, Master Plan, and Five-Year Plan. 56 refs., 67 figs., 31 tabs.