Network approach for capturing ligand-induced subtle global changes in protein structures

Ligand-induced conformational changes in proteins are of immense functional relevance. It is a major challenge to elucidate the network of amino acids that are responsible for the percolation of ligand-induced conformational changes to distal regions in the protein from a global perspective. Functionally important subtle conformational changes (at the level of side-chain noncovalent interactions) upon ligand binding or as a result of environmental variations are also elusive in conventional studies such as those using root-mean-square deviations (r.m.s.d.s). In this article, the network representation of protein structures and their analyses provides an efficient tool to capture these variations (both drastic and subtle) in atomistic detail in a global milieu. A generalized graph theoretical metric, using network parameters such as cliques and/or communities, is used to determine similarities or differences between structures in a rigorous manner. The ligand-induced global rewiring in the protein structures is also quantified in terms of network parameters. Thus, a judicious use of graph theory in the context of protein structures can provide meaningful insights into global structural reorganizations upon perturbation and can also be helpful for rigorous structural comparison. Data sets for the present study include high-resolution crystal structures of serine proteases from the S1A family and are probed to quantify the ligand-induced subtle structural variations.

The structures of bacteriorhodopsin with different retinal-Schiff base orientations--computer modeling and energy minimization studies

Bacteriorhodopsin has been the subject of intense study in order to understand its photochemical function. The recent atomic model proposed by Henderson and coworkers based on electron cryo-microscopic studies has helped in understanding many of the structural and functional aspects of bacteriorhodopsin. However, the accuracy of the positions of the side chains is not very high since the model is based on low-resolution data. In this study, we have minimized the energy of this structure of bacteriorhodopsin and analyzed various types of interactions such as - intrahelical and interhelical hydrogen bonds and retinal environment. In order to understand the photochemical action, it is necessary to obtain information on the structures adopted at the intermediate states. In this direction, we have generated some intermediate structures taking into account certain experimental data, by computer modeling studies. Various isomers of retinal with 13-cis and/or 15-cis conformations and all possible staggered orientations of Lys-216 side chain were generated. The resultant structures were examined for the distance between Lys-216-schiff base nitrogen and the carboxylate oxygen atoms of Asp-96 - a residue which is known to reprotonate the schiff base at later stages of photocycle. Some of the structures were selected on the basis of suitable retinal orientation and the stability of these structures were tested by energy minimization studies. Further, the minimized structures are analyzed for the hydrogen bond interactions and retinal environment and the results are compared with those of the minimized rest state structure. The importance of functional groups in stabilizing the structure of bacteriorhodopsin and in participating dynamically during the photocycle have been discussed.

Structures, Stabilities and Strain in C60 and C70 Derivatives Fullerenes, Nanotubes and Carbon Nanostructures

The stabilities of a number of small adducts as well as larger hydrides of C-60 and C-70 are reported using semiempirical MO methods. The data are shown to be consistent with the nature of bond alternation in the parent fullerenes and strain effects in the cage systems.

The role of strain rate response in plane strain abrasion of metals

Titanium flats were scribed by silicon carbide wedges over ranges of temperatures and applied strains and with lubrication. The response of the material to scribing was noted by recording the coefficient of friction, the surface morphology of track and the subsurface deformation. Additional data were obtained from (1) uniaxial compression of titanium, (2) scribing of oxygen-free high conductivity copper and (3) scribing of aluminium under dry and lubricated conditions to analyse and explain the observed variation in response of titanium to scribing with strain, temperature and lubrication.

Variability of sif and cod of stochastic structural systems

Stochastic structural systems having a stochastic distribution of material properties and stochastic external loadings in space are analysed when a crack of deterministic size is present. The material properties and external loadings are considered to constitute independent, two-dimensional, univariate, real, homogeneous stochastic fields. The stochastic fields are characterized by their means, variances, autocorrelation functions or the equivalent power spectral density functions, and scale fluctuations. The Young's modulus and Poisson's ratio are treated to be stochastic quantities. The external loading is treated to be a stochastic field in space. The energy release rate is derived using the method of virtual crack extension. The deterministic relationship is derived to represent the sensitivities of energy release rate with respect to both virtual crack extension and real system parameter fluctuations. Taylor series expansion is used and truncation is made to the first order. This leads to the determination of second-order properties of the output quantities to the first order. Using the linear perturbations about the mean values of the output quantities, the statistical information about the energy release rates, SIF and crack opening displacements are obtained. Both plane stress and plane strain cases are considered. The general expressions for the SIF in all the three fracture modes are derived and a more detailed analysis is conducted for a mode I situation. A numerical example is given.

Diphenylantimony(V) oxo/chloro carboxylates and phosphinates: crystal structures of {SbPh2Cl[O2P(C6H11)2]}2O and [SbPh2(O2CPh)2]2O

Reaction of SbPh(2)Cl(3) (1 mol) with the silver salt of dicyclohexylphosphinic acid (2 mol) afforded {SbPh(2)Cl[O2P(C6H11)(2)]}O-2 1, a similar reaction with AgO2P(C8H15)(2) gave a product formulated as {SbPh(2)Cl[O2P(C8H15)(2)]}O-2 2. Similar reactions with silver carboxylates (1:3 stoichiometry) led to the crystalline derivatives [SbPh(2)(O(2)CR)(2)]O-2 (R = Ph 3, CHPh(2) 4, 2,4,6-Me(3)C(6)H(2) 5, 2-MeC(6)H(4) 6 or 4-MeC(6)H(4) 7), whereas the 1:2 reaction afforded crystalline SbPh(2)Cl(O(2)CR)(2) (R = Ph 8, 2-MeC(6)H(4) 9 or 4-MeC(6)H(4) 10). Interconversion of the previously known compounds [SbPh(2)(O(2)CMe)(2)]O and Sb(4)Ph(8)O(6) . 3MeCO(2)H was achieved and established by H-1 NMR spectroscopy. Compounds 1 and 3 were further characterized by X-ray diffraction; the antimony in 1 is six-co-ordinated with bridging phosphinates whereas in 3 it is seven-co-ordinated with chelating benzoates. Short Sb-O (oxo) distances (1.923 Angstrom) and near linearity at the bridging ox

Direct Cartesian-Space Solutions of Generalized Bloch Equations in the Rotating Frame

Analytical solutions of the generalized Bloch equations for an arbitrary set of initial values of the x, y, and z magnetization components are given in the rotating frame. The solutions involve the decoupling of the three coupled differential equations such that a third-order differential equation in each magnetization variable is obtained. In contrast to the previously reported solutions given by Torrey, the present attempt paves the way for more direct physical insight into the behavior of each magnetization component. Special cases have been discussed that highlight the utility of the general solutions. Representative trajectories of magnetization components are given, illustrating their behavior with respect to the values of off-resonance and initial conditions. (C) 1995 Academic Press, Inc.

Vortex sheet simulation of a plane �canonical� mixing layer

Discrete vortex simulations of the mixing layer carried out in the past have usually involved large induced velocity fluctuations, and thus demanded rather long time-averaging to obtain satisfactory values of Reynolds stresses and third-order moments. This difficulty has been traced here, in part, to the use of discrete vortices to model what in actuality are continuous vortex sheets. We propose here a novel two-dimensional vortex sheet technique for computing mixing layer flow in the limit of infinite Reynolds number. The method divides the vortex sheet into constant-strength linear elements, whose motions are computed using the Biot-Savart law. The downstream far-field is modelled by a steady vorticity distribution derived by application of conical similarity from the solution obtained in a finite computational domain. The boundary condition on the splitter plate is satisfied rigorously using a doublet sheet. The computed large-scale roll-up of the vortex sheet is qualitatively similar to experimentally obtained shadow-graphs of the plane turbulent mixing layer. The mean streamwise velocity profile and the growth rate agree well with experimental data. The presently computed Reynolds stresses and third-order moments are comparable with experimental and previous vortex-dynamical results, without using any external parameter (such as the vortex core-size) of the kind often used in the latter. The computed autocorrelations are qualitatively similar to experimental results along the top and bottom edges of the mixing layer, and show a well-defined periodicity along the centreline. The accuracy of the present computation is independently established by demonstrating negligibly small changes in the five invariants (including the Hamiltonian) in vortex dynamics.

Hydrogen-Bond-Directed Nonlinear-Optical Organic Materials - Evidence For The Control Of 2nd-Harmonic Generation Activities From The X-Ray Crystal-Structures Of The Complexes Of L-Tartaric Acid With M-Anisidine and P-Toluidine

Several substituted anilines were converted to binary salts with L-tartaric acid. Second harmonic generation (SHG) activities of these salts were determined. The crystal packing in two structures, (i) m-anisidinium-L-tartrate monohydrate (i) and (ii) p-toluidinium-L-tartrate (2), studied using X-ray diffraction demonstrates that extensive hydrogen bonding steers the components into a framework which has a direct bearing on the SHG activity

Spectroscopic Observation of Oscillations in the Corona During the Total Solar Eclipse of 22 July 2009

We performed high resolution spectroscopy of the solar corona during the total solar eclipse of 22 July 2009 in two emission lines: the green line at 5303 due to Fe xiv and the red line at 6374 due to Fe x, simultaneously from Anji (latitude 30A degrees 28.1' N; longitude 119A degrees 35.4' E; elevation 890 m), China. A two-mirror coelostat with 100 cm focal length lens produced a 9.2 mm image of the Sun. The spectrograph using 140 cm focal length lens in Littrow mode and a grating with 600 lines per millimeter blazed at 2 mu m provided a dispersion of 30 m and 43 m per pixel in the fourth order around the green line and third order around the red line, respectively. Two Peltier cooled 1k x 1k CCD cameras, with a pixel size of 13 mu m square and 14-bit readout at 10 MHz operated in frame transfer mode, were used to obtain the time sequence spectra in two emission lines simultaneously. The duration of totality was 341 s, but we could get spectra for 270 s after a trial exposure at an interval of 5 s. We report here on the detection of intensity, velocity, and line width oscillations with periodicity in the range of 25 -50 s. These oscillations can be interpreted in terms of the presence of fast magnetoacoustic waves or torsional Alfv,n waves. The intensity ratios of green to red emission lines indicate the temperature of the corona to be 1.65 MK in the equatorial region and 1.40 MK in the polar region, relatively higher than the expected temperature during the low activity period. The width variation of the emission lines in different coronal structures suggests different physical conditions in different structures.

Lamination-dependent shear deformation models for bending of angle-ply laminated plates

Lamination-dependent shear corrective terms in the analysis of bending of laminated plates are derived from a priori assumed linear thicknesswise distributions for gradients of transverse shear stresses by using CLPT inplane stresses in the two in-plane equilibrium equations of elasticity in each ply. In the development of a general model for angle-ply laminated plates, special cases like cylindrical bending of laminates in either direction, symmetric laminates, cross-ply laminates, antisymmetric angle-ply laminates, homogeneous plates are taken into consideration. Adding these corrective terms to the assumed displacements in (i) Classical Laminate Plate Theory (CLPT) and (ii) Classical Laminate Shear Deformation Theory (CLSDT), two new refined lamination-dependent shear deformation models are developed. Closed form solutions from these models are obtained for antisymmetric angle-ply laminates under sinusoidal load for a type of simply supported boundary conditions. Results obtained from the present models and also from Ren's model (1987) are compared with each other.

Lamination-dependent shear deformation models for cylindrical bending of angle-ply laminates

Lamination-dependent shear corrective terms in the analysis of flexure of laminates are derived from a priori assumed linear thicknesswise distributions for gradients of transverse shear stresses and using them in the two in-plane equilibrium equations of elasticity in each ply. Adding these corrective terms to (i) Classical Laminate Plate Theory (CLPT) displacements and (ii) Classical Laminate Shear Deformation Theory (CLSDT) displacements, four new refined lamination-dependent shear deformation models for angle-ply laminates are developed. Performance of these models is evaluated by comparing the results from these models with those from exact elasticity solutions for antisymmetric 2-ply laminates and for 4-ply [15/-15](s) laminates. In general, the model with shear corrective terms based on CLPT and added to CLSDT displacements is sufficient and predicts good estimates, both qualitatively and quantitatively, for all displacements and stresses.

Modelling plane mixing layers using vortex points and sheets

We present here a critical assessment of two vortex approaches (both two-dimensional) to the modelling of turbulent mixing layers. In the first approach the flow is represented by point vortices, and in the second it is simulated as the evolution of a continuous vortex sheet composed of short linear elements or ''panels''. The comparison is based on fresh simulations using approximately the same number of elements in either model, paying due attention in both to the boundary conditions far downstream as well as those on the splitter plate from which the mixing layer issues. The comparisons show that, while both models satisfy the well-known invariants of vortex dynamics approximately to the same accuracy, the vortex panel model, although ultimately not convergent, leads to smoother roll-up and values of stresses and moments that are in closer agreement with the experiment, and has a higher computational efficiency for a given degree of convergence on moments. The point vortex model, while faster for a given number of elements, produces an unsatisfactory roll-up which (for the number of elements used) is rendered worse by the incorporation of the Van der Vooren correction for sheet curvature.

Novel Metastable Structures of WO3, MoO3 and W1-xMoxO3 Obtained by the Deintercalation of Layered Amine Adducts

Deintercalation of amines from the layered amine adducts of WO3, MoO3 and W1-xMoxO3 has been employed as a soft chemical route to produce unusual metastable structures of the oxides. After the adducts of WO3, MoO3 and W1-xMoxO3 (x = 0.25, 0.5, 0.75) with amines such as triethylamine (TEA), pyridine, n-butylamine and n-octylamine had been characterized, deintercalation was carried out thermally as well as by acid leaching. Thermal deintercalation yielded novel metastable structures of WO3 and MoO3 that were significantly different from the stable forms, which contain distorted metal-oxygen octahedra. Thus, ReO3-type cubic WO3 was obtained by the thermal deintercalation of WO3 . 0.5 TEA. Acid leaching of the amines gave metastable phases of WO3, MoO3 and W1-xMoxO3, which were different from those obtained thermally. All the metastable phases transformed to the corresponding stable forms at higher temperatures.

Use of finite wordlength FIR digital filter structures with improved magnitude and phase characteristics for reduction of muscle noise in EEG signals

One of the main disturbances in EEG signals is EMG artefacts generated by muscle movements. In the paper, the use of a linear phase FIR digital low-pass filter with finite wordlength precision coefficients is proposed, designed using the compensation procedure, to minimise EMG artefacts in contaminated EEG signals. To make the filtering more effective, different structures are used, i.e. cascading, twicing and sharpening (apart from simple low-pass filtering) of the designed FIR filter Modifications are proposed to twicing and sharpening structures to regain the linear phase characteristics that are lost in conventional twicing and sharpening operations. The efficacy of all these transformed filters in minimising EMG artefacts is studied, using SNR improvements as a performance measure for simulated signals. Time plots of the signals are also compared. Studies show that the modified sharpening structure is superior in performance to all other proposed methods. These algorithms have also been applied to real or recorded EMG-contaminated EEG signal. Comparison of time plots, and also the output SNR, show that the proposed modified sharpened structure works better in minimising EMG artefacts compared with other methods considered.