Multiple support excitations of open-plane frames by a filtered white noise and soil-structure interaction

Seismic structural design is essentially the estimation of structural response to a forced motion, which may be deterministic or stochastic, imposed on the ground. The assumption that the same ground motion acts at every point of the base of the structure (or at every support) is not always justifiable; particularly in case of very large structures when considerable spatial variability in ground motion can exist over significant distances example long span bridges. This variability is partly due to the delay in arrival of the excitation at different supports (which is called the wave passage effect) and due to heterogeneity in the ground medium which results in incoherency and local effects. The current study examines the influence of the wave passage effect (in terms of delay in arrival of horizontal ground excitation at different supports and neglecting transmission through the structure) on the response of a few open-plane frame building structures with soil-structure interaction. The ground acceleration has been modeled by a suitably filtered white noise. As a special case, the ground excitation at different supports has also been treated as statistically independent to model the extreme case of incoherence due to local effects and due to modifications to the ground motion resulting from wave reflections and refractions in heterogeneous soil media. The results indicate that, even for relatively short spanned building frames, wave passage effect can be significant. In the absence of soil-structure interaction, it can significantly increase the root mean square (rms) value of the shear in extreme end columns for the stiffer frames but has negligible effect on the flexible frames when total displacements are considered. It is seen that pseudo-static displacements increasingly contribute to the rms value of column shear as the time delay increases both for the stiffer and for the more flexible frames. When soil-structure interaction is considered, wave passage effect (in terms of total displacements) is significant only for low soil shear modulus, G. values (where soil-structure interaction significantly lowers the fundamental frequency) and for stiff frames. The contribution of pseudo-static displacement to these rms values is found to decrease with increase in G. In general, wave passage effect for most interactive frames is insignificant compared to the attenuating effect a decrease in G, has on the response of the interactive structure to uniform support excitation. When the excitations at different supports are statistically independent, it is seen that for both the stiff and flexible frames, the rms value of the column shear in extreme end columns is several times larger (more for the stiffer frames) than the value corresponding to uniform base excitation with the pseudo-static displacements contributing over 99% of the rms value of column shear. Soil-structure interaction has an attenuating effect on the rms value of the column shear, the effect decreasing with increase in G,. Here too, the pseudo-static displacements contribute very largely to the column shear. The influence of the wave passage effect on the response of three 2-bay frames with and without soil-structure interaction to a recorded horizontal accelerogram is also examined. (C) 2010 Elsevier Ltd. All rights reserved.

Effect of coordinated ions on structure and flexibility of parallel G-quadruplexes: A molecular dynamics study

ingle tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G(7)) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the O6 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. There quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 Angstrom from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Nai counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. in the absence of any coordinated ion. due to strong mutual repulsion, O6 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures.

Solution structure of O-glycosylated C-terminal leucine zipper domain of human salivary mucin (MUC7)

Solution structures of a 23 residue glycopeptide II (KIS* RFLLYMKNLLNRIIDDMVEQ, where * denotes the glycan Gal-beta-(1-3)-alpha-GalNAc) and its deglycosylated counterpart I derived from the C-terminal leucine zipper domain of low molecular weight human salivary mucin (MUC7) were studied using CD, NMR spectroscopy and molecular modeling. The peptide I was synthesized using the Fmoc chemistry following the conventional procedure and the glycopeptide II was synthesized incorporating the O-glycosylated building block (N alpha-Fmoc-Ser-[Ac-4,-beta-D-Gal-(1,3)-Ac(2)alpha-D-GalN(3)]-OPfp) at the appropriate position in stepwise assembly of peptide chain. Solution structures of these glycosylated and nonglycosylated peptides were studied in water and in the presence of 50% of an organic cosolvent, trifluoroethanol (TFE) using circular dichroism (CD), and in 50% TFE using two-dimensional proton nuclear magnetic resonance (2D H-1 NMR) spectroscopy. CD spectra in aqueous medium indicate that the apopeptide I adapts, mostly, a beta-sheet conformation whereas the glycopeptide II assumes helical structure. This transition in the secondary structure, upon glycosylation, demonstrates that the carbohydrate moiety exerts significant effect on the peptide backbone conformation. However, in 50% TFE both the peptides show pronounced helical structure. Sequential and medium range NOEs, C alpha H chemical shift perturbations, (3)J(NH:C alpha H) couplings and deuterium exchange rates of the amide proton resonances in water containing 50% TFE indicate that the peptide I adapts alpha-helical structure from Ile2-Val21 and the glycopeptide II adapts alpha-helical structure from Ser3-Glu22. The observation of continuous stretch of helix in both the peptides as observed by both NMR and CD spectroscopy strongly suggests that the C-terminal domain of MUC7 with heptad repeats of leucines or methionine residues may be stabilized by dimeric leucine zipper motif. The results reported herein may be invaluable in understanding the aggregation (or dimerization) of MUC7 glycoprotein which would eventually have implications in determining its structure-function relationship.

Structure and dynamics of benzene in one-dimensional channels

Molecular dynamics investigation of benzene in one-dimensional channel systems A1PO(4)-5, VPI-5, and carbon nanotube is reported. The results suggest that, in all the three host systems, the plane of benzene is almost perpendicular to the channel axis when the molecule is near the center of the channel and the plane of benzene is parallel to the channel axis when the molecule is near the wall of the channel. The density distribution of benzene as a function of channel length, z and the radial distance, r, from the channel axis is also different in the three host structures. Anisotropy in translational diffusion coefficient, calculated in body-fixed frame of benzene, suggests that benzene prefers to move with its plane parallel to the direction of motion in A1PO(4)-5 and VPI-5 whereas in carbon nanotube the motion occurs predominantly with the plane of the benzene perpendicular to the direction of motion.;Anisotropy associated with the rotational motion is seen to alter significantly in confinement as compared to liquid benzene. In A1PO(4)-5, the rotational anisotropy is reversed as compared to liquid benzene thereby suggesting that anisotropy arising out of molecular geometry can be reduced. Reorientational correlation times for C-6 and C-2 axes Of benzene are reported. Apart from the inertial decay of reorientational correlation function due to free, rotation, two other distinct regimes of decay are observed in narrower channels (AIPO(4)-5 and carbon nanotube): (i) an initial fast decay (0.5-2 ps) and (ii) a slower decay (>2 ps) of reorientational correlation function where C-6 decays slower than C-2 Similar to what is observed in liquid benzene. In the initial fast decay, it is seen that the decay for C-6 is faster than C-2 which is in contrast to what is observed in liquid benzene or for benzene confined in VPI-5.

X-Ray structure of a ternary complex, copper(II)–lnosine 5-monophosphate–benzimidazole. The first example for the absence of direct metal–nucleotide interaction

The unprecedented absence of direct metal–nucleotide interaction has been observed in the X-ray structure of the ternary metal nucleotide system [Cu(bzim)(H2O)5]2+[IMP]2–·3H2O [IMP = inosine 5-monophosphate(2–), bzim = benzimidazole). The complex crystallizes in the space group P21 with a= 7.013(2), b= 13.179(9), c= 14.565(9)Å, = 94.82(4)°, and Z= 2. The structure was solved by the heavy-atom method and refined by full-matrix least squares on the basis of 1 761 observed (I? 3i) reflections to final R and R values of 0.034 and 0.036 respectively. The CuII has a distorted octahedral co-ordination with a nitrogen of the bzim ligand [Cu–N 1.947(5)Å] and three oxygens of water molecules in the basal plane [mean Cu–O 2.017(3)Å] and two more water oxygens at axial positions [Cu–O 2.194(6) and 2.732(5)Å]. The nucleotide base stacks with the bzim ligand at an average distance of 3.5 Å and an angle of 22°. In the lattice, N(7) of the base is linked to a lattice water through a hydrogen bond, while all the phosphate oxygens are involved in hydrogen bonds with co-ordinated as well as lattice water molecules. The co-ordination behaviour of IMP to CuII is compared in structures containing different -aromatic amines in order to assess the influence of the ternary ligand in complex formation. The present results indicate that, apart from the commonly observed phosphate binding, other modes of co-ordination are possible, these being influenced mainly by the -accepting properties of the ternary ligand.