Five-fold quasiperiodic tilings generated by inflated rhombuses with identical boundaries: possible application to the growth of quasicrystals

In order to generate normal Penrose tilings by inflation/deflation, decisions have to be made regarding the matching of the rhombuses/tilings with their neighbours. We show here that this decision-making problem can be avoided by adopting a deflation/inflation procedure which uses the decorated rhombuses with identical boundaries. The procedure enables both kinds of inflated rhombuses to match in any orientation along their edges. The tilings so generated are quasiperiodic. These structures appear to have a close relationship with the growth mechanism of quasicrystals.

HELANAL: A program to characterise helix geometry in proteins,

A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their C-alpha atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

Ultimate Strength of RC Wall Panels with Openings

Test results of 12 reinforced concrete (RC) wall panels with openings are presented. The panels have been subjected to in-plane vertical loads applied at an eccentricity to represent possible accidental eccentricity that occurs in practice due to constructional imperfections. The 12 specimens consist of two identical groups of six panels each. One group of panels is tested in one-way in-plane action (i.e., supported at top and bottom edges against lateral displacement). The second group of panels is tested in two-way in-plane action (i.e., supported on all the four edges against lateral displacement). Openings in the panels represent typical door and window openings. Cracking loads, ultimate loads, crack patterns, and lateral deflections of the panels are studied. Empirical methods have been developed for the prediction of ultimate load. Also, lateral deflections, cracking loads, and ultimate loads of identical loads tested under one-way and two-way action are compared.

Dislocation characterization in crystals of potash alum grown by seeded solution growth under conditions of low supersaturation

An analysis has been carried out of the genesis and character of growth dislocations present in all growth sectors of single crystals of potash alum. The crystals, grown from seeded solutions by the temperature lowering method under conditions of low supersaturation, presented the well-developed forms: {111} dominant, {100} and {110}. Growth dislocations formed predominately during refacetting of the edges and corners of the seed, rounded during preparation and insertion into the supersaturated solution. From here they become refracted into the {111} sectors which proved to be the most defective. Smaller numbers of dislocations form at the {111}, {100} and {110} seed interfaces and propagate in these sectors. In crystals of inferior quality, a number of inclusions were found predominantly in the fast growing {100} sectors which become the source of additional dislocations. Dislocations present in the original seed did not propagate across the interface into the developing crystal. Dislocations of all characters were observed. The principal Burgers vectors were found to be left angle bracket100right-pointing angle bracket, left angle bracket110right-pointing angle bracket and left angle bracket111right-pointing angle bracket.

Maximum-entropy calculation of the electron density at 4 A resolution of Pf1 filamentous bacteriophage

A 4 A electron-density map of Pf1 filamentous bacterial virus has been calculated from x-ray fiber diffraction data by using the maximum-entropy method. This method produces a map that is free of features due to noise in the data and enables incomplete isomorphous-derivative phase information to be supplemented by information about the nature of the solution. The map shows gently curved (banana-shaped) rods of density about 70 A long, oriented roughly parallel to the virion axis but slewing by about 1/6th turn while running from a radius of 28 A to one of 13 A. Within these rods, there is a helical periodicity with a pitch of 5 to 6 A. We interpret these rods to be the helical subunits of the virion. The position of strongly diffracted intensity on the x-ray fiber pattern shows that the basic helix of the virion is right handed and that neighboring nearly parallel protein helices cross one another in an unusual negative sense.

Armchair or Zigzag? A tool for characterizing graphene edge

Electronic, magnetic, and structural properties of graphene flakes depend sensitively upon the type of edge atoms. We present a simple software tool for determining the type of edge atoms in a honeycomb lattice. The algorithm is based on nearest neighbor counting. Whether an edge atom is of armchair or zigzag type is decided by the unique pattern of its nearest neighbors. Particular attention is paid to the practical aspects of using the tool, as additional features such as extracting out the edges from the lattice could help in analyzing images from transmission microscopy or other experimental probes. Ultimately, the tool in combination with density-functional theory or tight-binding method can also be helpful in correlating the properties of graphene flakes with the different armchair-to-zigzag ratios. Program summary Program title: edgecount Catalogue identifier: AEIA_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEIA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 66685 No. of bytes in distributed program, including test data, etc.: 485 381 Distribution format: tar.gz Programming language: FORTRAN 90/95 Computer: Most UNIX-based platforms Operating system: Linux, Mac OS Classification: 16.1, 7.8 Nature of problem: Detection and classification of edge atoms in a finite patch of honeycomb lattice. Solution method: Build nearest neighbor (NN) list; assign types to edge atoms on the basis of their NN pattern. Running time: Typically similar to second(s) for all examples. (C) 2010 Elsevier B.V. All rights reserved.

Paleoseismological evidence of surface faulting along the northeastern Himalayan front, India: Timing, size, and spatial extent of great earthquakes

The similar to 2500 km long Himalayan arc has experienced three large to great earthquakes of M-w 7.8 to 8.4 during the past century, but none produced surface rupture. Paleoseismic studies have been conducted during the last decade to begin understanding the timing, size, rupture extent, return period, and mechanics of the faulting associated with the occurrence of large surface rupturing earthquakes along the similar to 2500 km long Himalayan Frontal Thrust (HFT) system of India and Nepal. The previous studies have been limited to about nine sites along the western two-thirds of the HFT extending through northwest India and along the southern border of Nepal. We present here the results of paleoseismic investigations at three additional sites further to the northeast along the HFT within the Indian states of West Bengal and Assam. The three sites reside between the meizoseismal areas of the 1934 Bihar-Nepal and 1950 Assam earthquakes. The two westernmost of the sites, near the village of Chalsa and near the Nameri Tiger Preserve, show that offsets during the last surface rupture event were at minimum of about 14 m and 12 m, respectively. Limits on the ages of surface rupture at Chalsa (site A) and Nameri (site B), though broad, allow the possibility that the two sites record the same great historical rupture reported in Nepal around A.D. 1100. The correlation between the two sites is supported by the observation that the large displacements as recorded at Chalsa and Nameri would most likely be associated with rupture lengths of hundreds of kilometers or more and are on the same order as reported for a surface rupture earthquake reported in Nepal around A.D. 1100. Assuming the offsets observed at Chalsa and Nameri occurred synchronously with reported offsets in Nepal, the rupture length of the event would approach 700 to 800 km. The easternmost site is located within Harmutty Tea Estate (site C) at the edges of the 1950 Assam earthquake meizoseismal area. Here the most recent event offset is relatively much smaller (<2.5 m), and radiocarbon dating shows it to have occurred after A.D. 1100 (after about A.D. 1270). The location of the site near the edge of the meizoseismal region of the 1950 Assam earthquake and the relatively lesser offset allows speculation that the displacement records the 1950 M-w 8.4 Assam earthquake. Scatter in radiocarbon ages on detrital charcoal has not resulted in a firm bracket on the timing of events observed in the trenches. Nonetheless, the observations collected here, when taken together, suggest that the largest of thrust earthquakes along the Himalayan arc have rupture lengths and displacements of similar scale to the largest that have occurred historically along the world's subduction zones.

New Approximation Algorithms for Minimum Cycle Bases of Graphs

We consider the problem of computing an approximate minimum cycle basis of an undirected non-negative edge-weighted graph G with m edges and n vertices; the extension to directed graphs is also discussed. In this problem, a {0,1} incidence vector is associated with each cycle and the vector space over F-2 generated by these vectors is the cycle space of G. A set of cycles is called a cycle basis of G if it forms a basis for its cycle space. A cycle basis where the sum of the weights of the cycles is minimum is called a minimum cycle basis of G. Cycle bases of low weight are useful in a number of contexts, e.g. the analysis of electrical networks, structural engineering, chemistry, and surface reconstruction. Although in most such applications any cycle basis can be used, a low weight cycle basis often translates to better performance and/or numerical stability. Despite the fact that the problem can be solved exactly in polynomial time, we design approximation algorithms since the performance of the exact algorithms may be too expensive for some practical applications. We present two new algorithms to compute an approximate minimum cycle basis. For any integer k >= 1, we give (2k - 1)-approximation algorithms with expected running time O(kmn(1+2/k) + mn((1+1/k)(omega-1))) and deterministic running time O(n(3+2/k) ), respectively. Here omega is the best exponent of matrix multiplication. It is presently known that omega < 2.376. Both algorithms are o(m(omega)) for dense graphs. This is the first time that any algorithm which computes sparse cycle bases with a guarantee drops below the Theta(m(omega) ) bound. We also present a 2-approximation algorithm with expected running time O(M-omega root n log n), a linear time 2-approximation algorithm for planar graphs and an O(n(3)) time 2.42-approximation algorithm for the complete Euclidean graph in the plane.

Edge Stabilities of Hexagonal Boron Nitride Nanoribbons: A First-Principles Study

We investigate the comparative stability of sp(2) bonded planar hexagonal boron nitride (h-BN) nanoribbon (BNNR) edges, using first principles calculations. We find that the pristine armchair edges have the highest degree of stability. Pristine zigzag edges are metastable, favoring planar reconstructions in the form of 5-7 rings] that minimizes the energy. Our investigation further reveals that the pristine zigzag edges can be stabilized against 5-7 reconstructions by passivating the dangling bonds at the edges by other elements, such as hydrogen (H) atoms. Electronic and magnetic properties of nanoribbons depend on the edge shapes and are strongly affected by edge reconstructions.

Chloroplastic glutamine synthetase from normal and water stressed safflower (Carthamus tinctorius L.) leaves

The chloroplastic isoform of glutamine synthetase (GS(2), EC 6.3.1.2) from normal and water stressed safflower (Carthamus tinctorius L. cv.A-300) leaves has been purified to apparent electrophoretic homogeneity by a procedure involving anion-exchange, hydrophobic and size-exclusion chromatography followed by electroelution of the protein from preparative polyacrylamide gels. The observed molecular weight of the native protein varied from 305-330 kDa depending on the sizing column employed. The native protein is composed of 44 kDa subunits. Under conditions of saturating ammonium and at ATP levels of 0.1-10 mM, double-reciprocal plots with respect to glutamate are biphasic and concave downward at high concentrations of the varied substrate for normal enzyme but are linear for enzyme from water-stressed plants. Under subsaturating ATP levels, K-Glu is over 18-fold lower for enzyme from stressed leaves. The K-m, (ATP) varies with Mg2+ levels in the assay mixture. Double-reciprocal plots of initial velocity with respect to ATP at changing fixed levels of NH4+ are linear for normal enzyme but are curved upwards for enzyme from stressed leaves. Initial velocity data of 1/v vs. 1/ammonium for the enzyme from both the sources are non-linear (curved upwards) when ATP is saturating. At subsaturating ATP levels, the data are linear for normal enzyme but are still non-linear for the enzyme from stressed leaves. The results obtained suggest positively cooperative binding of NH4+ A V-max(/2) value of 3.6 mM for Mg2+ was obtained at 5 mM ATP. The isoelectric point of the native protein from normal and stressed leaves was determined to be, respectively, 5.6 and 6.1. The mixed competitive and competitive inhibitors, methionine sulfoximine and ADP and K-i values of 0.086 mM (0.017 for the enzyme from stressed leaves) and 2.15 mM (1.70 for the enzyme from stressed leaves), respectively. Enzyme from stressed leaves is not inhibited by 5 mM proline. The observed kinetic constants of GS(2) from normal and water stressed safflower seedlings are discussed in relation to the known water-stress tolerance of this crop plant.

On Network-Error Correcting Convolutional Codes under the BSC Edge Error Model

Convolutional network-error correcting codes (CNECCs) are known to provide error correcting capability in acyclic instantaneous networks within the network coding paradigm under small field size conditions. In this work, we investigate the performance of CNECCs under the error model of the network where the edges are assumed to be statistically independent binary symmetric channels, each with the same probability of error pe(0 <= p(e) < 0.5). We obtain bounds on the performance of such CNECCs based on a modified generating function (the transfer function) of the CNECCs. For a given network, we derive a mathematical condition on how small p(e) should be so that only single edge network-errors need to be accounted for, thus reducing the complexity of evaluating the probability of error of any CNECC. Simulations indicate that convolutional codes are required to possess different properties to achieve good performance in low p(e) and high p(e) regimes. For the low p(e) regime, convolutional codes with good distance properties show good performance. For the high p(e) regime, convolutional codes that have a good slope ( the minimum normalized cycle weight) are seen to be good. We derive a lower bound on the slope of any rate b/c convolutional code with a certain degree.

Non-uniform slot injection (suction) or wall enthalpy into a steady nonsimilar compressible laminar boundary layer

Steady two-dimensional and axisymmetric compressible nonsimilar laminar boundary-layer flows with non-uniform slot injection (or suction) and non-uniform wall enthalpy have been studied from the starting point of the streamwise co-ordinate to the exact point of separation. The effect of different free stream Mach number has also been considered. The finite discontinuities arising at the leading and trailing edges of the slot for the uniform slot injection (suction) or wall enthalpy are removed by choosing appropriate non-uniform slot injection (suction) or wall enthalpy. The difficulties arising at the starting point of the streamwise co-ordinate, at the edges of the slot and at the point of separation are overcome by applying the method of quasilinear implicit finite difference scheme with an appropriate selection of finer step size along the streamwise direction. It is observed that the non-uniform slot injection moves the point of separation downstream but the non-uniform slot suction has the reverse effect. The increase of Mach number shifts the point of separation upstream due to the adverse pressure gradient. The increase of total enthalpy at the wall causes the separation to occur earlier while cooling delays it. The non-uniform total enthalpy at the wall (i.e., the cooling or heating of the wall in a slot) along the streamwise co-ordinate has very little effect on the skin friction and thus on the point of separation.

The structure of amorphous platinum disulfide as studied by anomalous x-ray-scattering

Anomalous X-ray scattering (AXS) has been applied to study the structure of amorphous platinum disulfide, Pt1-xS2, prepared by the precipitation process. The local atomic arrangement in amorphous Pt1-xS2 was determined by the least-squares variational method so as to reproduce the experimental differential interference function at the Pt L(III) absorption edge by the AXS method as well as the ordinary interference function by MoK alpha. The structural unit in amorphous Pt1-xS2 is found to be a PtS6 octahedron, similar to that in crystalline PtS2. These octahedra share both their corners and edges, while only edge-sharing linkages occur in crystalline PtS2.

Anomalous X-ray scattering study of local structures in the superionic conducting class (CuI)(0.3)(Cu2O)(0.35)(MoO3)(0.35)

The anomalous X-ray scattering (AXS) method using Cu and Mo K absorption edges has been employed for obtaining the local structural information of superionic conducting glass having the composition (CuI)(0.3)(Cu2O)(0.35)(MoO3)(0.35). The possible atomic arrangements in near-neighbor region of this glass were estimated by coupling the results with the least-squares analysis so as to reproduce two differential intensity profiles for Cu and Mo as well as the ordinary scattering profile. The coordination number of oxygen around Mo is found to be 6.1 at the distance of 0.187 nm. This implies that the MoO6 octahedral unit is a more probable structural entity in the glass rather than MoO4 tetrahedra which has been proposed based on infrared spectroscopy. The pre-peak shoulder observed at about 10 nm(-1) may be attributed to density fluctuation originating from the MoO6 octahedral units connected with the corner sharing linkage, in which the correlation length is about 0.8 nm. The value of the coordination number of I- around Cu+ is estimated as 4.3 at 0.261 nm, suggesting an arrangement similar to that in molten CuI.

Analysis of a long thick orthotropic circular cylindrical shell panel

An exact three-dimensional elasticity solution has been obtained for an infinitely long, thick transversely isotropic circular cylindrical shell panel, simply supported along the longitudinal edges and subjected to a radial patch load. Using a set of three displacement functions, the boundary value problem is reduced to Bessel's differential equation. Numerical results are presented for different thickness to mean radius ratios and semicentral angles of the shell panel. Classical and first-order shear deformation orthotropic shell theories have been examined in comparison with the present elasticity solution.