Three-dimensional structure of Saccharomyces cerevisiae inorganic pyrophosphatase complexed with cobalt and phosphate ions

Crystals of Saccharomyces cerevisiae inorganic pyrophosphatase suitable for X-ray diffraction study were grown by cocrystallization of the enzyme with cobalt chloride and imidodiphosphate. Saccharomyces cerevisiae is a metal-dependent enzyme which catalyzes hydrolysis of inorganic pyrophosphate to orthophosphate. The three-dimensional structure of this enzyme was solved by the molecular-replacement method and refined at 1.8 Å resolution to an R factor of 19.5%. Cobalt and phosphate ions were revealed in the active centers of both identical subunits (A and B) of the pyrophosphatase molecule. In subunit B, a water molecule was found between two cobalt ions. It is believed that this water molecule acts as an attacking nucleophile in the enzymatic cleavage of the pyrophosphate bond. It was demonstrated that cobalt ions and a phosphate group occupy only part of the potential binding sites (two chemically identical and crystallographically independent subunits have different binding sites). The arrangement of ligands and the structure of the nucleophile-binding site are discussed in relation to the mechanism of action of the enzyme and the nature of the metal activator.     

Elastic wave scattering around cavities in inhomogeneous continua by the BEM

This work examines elastic wave scattering around cavities embedded in a continuum with depth-dependent shear modulus and under conditions of plane strain. A restricted case of inhomogeneity is considered, where the Poisson ratio is fixed at 0.25 and where the density profile also varies, but proportionally to the shear modulus. For this specific case, the wave speeds remain macroscopically constant and it becomes possible to recover the exact Green functions by using an algebraic transformation method. These functions are subsequently used as kernels in a standard 2D boundary element formulation defined in the Laplace transform domain. The final step involves an inverse Laplace transformation, whereby the transient behavior of cavities in the aforementioned inhomogeneous continuum can be recovered. Two basic examples are solved, namely the circular cylindrical cavity under sudden internal explosion and under a pressure wave sweep. In the latter case, it is possible to investigate the effect that the angle of wave incidence has on the displacement and stress that develop along the cavity's perimeter, given the fact that the shear modulus is changing along the vertical direction. These examples serve to illustrate the present approach and to reveal some interesting differences that are observed in transient wave scattering phenomena between homogeneous and continuously inhomogeneous models, where the latter models yield a more realistic representation of geological formations.     

Hutchinson's shear coefficient for anisotropic beams

Timoshenko's theory of vibrating beams requires a shear correction factor to correctly take into account the effects of shear deformation for different beam cross-sections. This correction is crucial for a precise determination of the shear modulus from the resonant frequencies. Hutchinson's beam theory is used to derive a new shear correction coefficient for anisotropic materials. A comparison is made with other shear coefficients for anisotropic materials published in the literature. Computer-simulated spectra are used to validate the new anisotropic shear correction coefficient.     

Ion source with a cold magnetron cathode and magnetic plasma compression

The operating principles, design, and characteristics of an ion source with a cold magnetron cathode and magnetic plasma compression are described. The source is intended for the injector of a linear proton accelerator.     

The action of an electron beam on dust structures in a plasma

The action of an electron beam on ordered dust structures in glow and low-pressure RF discharges was studied experimentally. The electron beam produces destruction and dynamic displacement of the dust structure. In the center of a dust structure, an electron beam with a low electron energy (tens of eV) at currents up to 1 mA caused structural disordering and “melting” in the region of its action but did not excite external crystal regions. Local action of an electron beam with a high electron energy (25 keV) and a beam current above 10 mA caused deformation of the whole dust structure and shifted it in the horizontal direction so that it was carried away from the RF discharge zone. The effect of dust structure displacements can be used to locally remove particles from a plasma.     

Single-electron charging spectra: from natural to artificial atoms

We present a theoretical study of the charging spectra in natural and artificial atoms. We apply a model electrostatic potential created by a homogenously charged sphere. This model potential allows for a continuous passage from the Coulomb potential of the nucleus to parabolic confinement potential of quantum dots. We consider electron systems with N=1,…,10 electrons with the use of the Hartree–Fock method. We discuss the qualitative similarities and differences between the chemical potential spectrum of electron systems bound to nucleus and confined in quantum dots.     

Karhunen–Loeve representations of turbulent channel flows using the method of snapshots

For three‐dimensional flows with one inhomogeneous spatial coordinate and two periodic directions, the Karhunen–Loeve procedure is typically formulated as a spatial eigenvalue problem. This is normally referred to as the direct method (DM). Here we derive an equivalent formulation in which the eigenvalue problem is formulated in the temporal coordinate. It is shown that this so‐called method of snapshots (MOS) has some numerical advantages when compared to the DM. In particular, the MOS can be formulated purely as a matrix composed of scalars, thus avoiding the need to construct a matrix of matrices as in the DM. In addition, the MOS avoids the need for so‐called weight functions, which emerge in the DM as a result of the non‐uniform grid typically employed in the inhomogeneous direction. The avoidance of such weight functions, which may exhibit singular behaviour, guarantees satisfaction of the boundary conditions. The MOS is applied to data sets recently obtained from the direct simulation of turbulence in a channel in which viscoelasticity is imparted to the fluid using a Giesekus model. The analysis reveals a steep drop in the dimensionality of the turbulence as viscoelasticity is increased. This is consistent with the results that have been obtained with other viscoelastic models, thus revealing an essential generic feature of polymer‐induced drag reduced turbulent flows. Published in 2006 by John Wiley & Sons, Ltd.     

In-plane loading of a cracked elastic solid by a disc inclusion with a Mindlin-type constraint

The paper examines the problem related to the axisymmetric interaction between an external circular crack and a centrally placed penny-shaped rigid inclusion located in the plane of the crack. The interface between the inclusion and the elastic medium exhibits a Mindlin-type imperfect bi-lateral contact. Analytical results presented in the paper illustrate the manner in which the lateral translational stiffness of the inclusion and the stress intensity factor at the boundary of the external circular crack are influenced by the inclusion/crack radii ratio.     

Energetics of an adiabatically-loaded excited anharmonic oscillator

The dependence of the energy characteristics on an adiabatically slowly increasing external force is determined analytically for an anharmonic oscillator. The analytical results are confirmed by a numerical calculation. The nature of the force dependences of the energy characteristics are determined and discussed. Fiz. Tverd. Tela (St. Petersburg) 39, 153–157 (January 1997)