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.

Time-domain-finite-wave analysis of the engine exhaust system by means of the stationary-frame method of characteristics. Part I. Theory

Time-domain-finite-wave analysis of the engine exhaust system is usually done using the method of characteristics. This makes use of either the moving frame method, or the stationary frame method. The stationary frame method is more convenient than its counterpart inasmuch as it avoids the tedium of graphical computations. In this paper (part I), the stationary-frame computational scheme along with the boundary conditions has been implemented. The analysis of a uniform tube, cavity-pipe junction including the engine and the radiation ends, and also the simple area discontinuities has been presented. The analysis has been done accounting for wall friction and heat-transfer for a one-dimensional unsteady flow. In the process, a few inconsistencies in the formulations reported in the literature have been pointed out and corrected. In the accompanying paper (part II) results obtained from the simulation are shown to be in good agreement with the experimental observations.

Post-transcriptional Repair of a Split Heat Shock Protein 90 Gene by mRNA trans-Splicing

Heat shock protein 90 participates in diverse biological processes ranging from protein folding, cell cycle, signal transduction and development to evolution in all eukaryotes. It is also critically involved in regulating growth of protozoa such as Dictyostelium discoideum, Leishmania donovani, Plasmodium falciparum, Trypanosoma cruzi, and Trypanosoma evansi. Selective inhibition of Hsp90 has also been explored as an intervention strategy against important human diseases such as cancer, malaria, or trypanosomiasis. Giardia lamblia, a simple protozoan parasite of humans and animals, is an important cause of diarrheal disease with significant morbidity and some mortality in tropical countries. Here we show that the G. lamblia cytosolic hsp90 ( glhsp90) is split in two similar sized fragments located 777 kb apart on the same scaffold. Intrigued by this unique arrangement, which appears to be specific for the Giardiinae, we have investigated the biosynthesis of GlHsp90. We used genome sequencing to confirm the split nature of the giardial hsp90. However, a specific antibody raised against the peptide detected a product with a mass of about 80 kDa, suggesting a post-transcriptional rescue of the genomic defect. We show evidence for the joining of the two independent Hsp90 transcripts in-trans to one long mature mRNA presumably by RNA splicing. The splicing junction carries hallmarks of classical cis-spliced introns, suggesting that the regular cis-splicing machinery may be sufficient for repair of the open reading frame. A complementary 26-nt sequence in the ``intron'' regions adjacent to the splice sites may assist in positioning the two pre-mRNAs for processing. This is the first example of post-transcriptional rescue of a split gene by trans-splicing.

CAITG sequence at the 5' end of Oligo(A)-tracts strongly modulates DNA curvature

An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5' end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAACCCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5' and 3' ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing of the sequences with AC/GT and CA/TG doublet junctions gives a similar cutting pattern in the A-tracts, which is quite different from that in the C-tracts, indicating that the oligo(A)-tracts have similar structures in the two oligomers. KMnO4 probing shows that the oligomer with a CA/TG doublet junction forms a kink that is responsible for its inherent curvature and unusual electrophoretic mobility. UV melting shows a reduced thermal stability of the duplex with CA/TG doublet junction, and circular dichroism (CD) studies indicate that a premelting transition occurs in the oligomer with CA/TG doublet step before global melting but not in the oligomer with AC/GT doublet step, which may correspond to thermally induced unbending of the oligomer. These observations indicate that the CA/TG doublet junction at the 5' end of the oligo(A)-tract has a crucial role in modulating the overall curvature in DNA.

Conductance of Tomonaga-Luttinger liquid wires and junctions with resistances

We study the effect that resistive regions have on the conductance of a quantum wire with interacting electrons which is connected to Fermi liquid leads. Using the bosonization formalism and a Rayleigh dissipation function to model the power dissipation, we use both scattering theory and Green's function techniques to derive the DC conductance. The resistive regions are generally found to lead to incoherent transport. For a single wire, we find that the resistance adds in series to the contact resistance of h/e(2) for spinless electrons, and the total resistance is independent of the Luttinger parameter K-W of the wire. We numerically solve the bosonic equations to illustrate what happens when a charge density pulse is incident on the wire; the results depend on the parameters of the resistive and interacting regions in interesting ways. For a junction of Tomonaga-Luttinger liquid wires, we use a dissipationless current splitting matrix to model the junction. For a junction of three wires connected to Fermi liquid leads, there are two families of such matrices; we find that the conductance matrix generally depends on K-W for one family but is independent of K-W for the other family, regardless of the resistances present in the system. Copyright (c) EPLA, 2011

Bayesian Decentralized Spectrum Sensing in Cognitive Radio Networks

This paper considers the problem of spectrum sensing, i.e., the detection of whether or not a primary user is transmitting data by a cognitive radio. The Bayesian framework is adopted, with the performance measure being the probability of detection error. A decentralized setup, where N sensors use M observations each to arrive at individual decisions that are combined at a fusion center to form the overall decision is considered. The unknown fading channel between the primary sensor and the cognitive radios makes the individual decision rule computationally complex, hence, a generalized likelihood ratio test (GLRT)-based approach is adopted. Analysis of the probabilities of false alarm and miss detection of the proposed method reveals that the error exponent with respect to M is zero. Also, the fusion of N individual decisions offers a diversity advantage, similar to diversity reception in communication systems, and a tight bound on the error exponent is presented. Through an analysis in the low power regime, the number of observations needed as a function of received power, to achieve a given probability of error is determined. Monte-Carlo simulations confirm the accuracy of the analysis.

DNA polymerase alpha-primase complex from the silk glands of the non-mulberry silkworm Philosamia ricini.

The DNA content in the silk glands of the non-mulberry silkworm Philosamia ricini increases continuously during the fourth and fifth instars of larval development indicating high levels of DNA replication in this terminally differentiated tissue. Concomitantly, the DNA polymerase alpha activity also increases in the middle and the posterior silk glands during development, reaching maximal levels in the middle of the fifth larval instar. A comparable level of DNA polymerase delta/epsilon was also observed in this highly replicative tissue. The DNA polymerase alpha-primase complex from the silk glands of P. ricini has been purified to homogeneity by conventional column chromatography as well as by immunoaffinity techniques. The molecular mass of the native enzyme is 560 kDa and the enzyme comprises six non-identical subunits. The identity of the enzyme as DNA polymerase alpha has been established by its sensitivity to inhibitors such as aphidicolin, N-ethylmaleimide, butylphenyl-dGTP, butylanilino-dATP and antibodies to polymerase alpha. The enzyme possesses primase activity capable of initiating DNA synthesis on single-stranded DNA templates. The tight association of polymerase and primase activities at a constant ratio of 6:1 is observed through all the purification steps. The 180 kDa subunit harbours the polymerase activity, while the primase activity is associated with the 45 kDa subunit.

Growth and applications of superconducting and nonsuperconducting oxide epitaxial films

Growth and characterization of high-temperature-superconducting YBa2Cu3O7 and several metallic-oxide thin films by pulsed laser deposition is described here. An overview of substrates employed for epitaxial growth of perovskite-related oxides is presented. Ag-doped YBa2Cu3O7 films grown on bare sapphire are shown to give T-c = 90 K, critical current > 10(6) A/cm(2) at 77 K and surface resistance = 450 mu Omega. Application of epitaxial metallic LaNiO3 thin films as an electrode for ferroelectric oxide and as a normal metal layer barrier in the superconductor-normal metal-superconductor (SNS) Josephson junction is presented. Observation of giant magnetoresistance (GMR) in the metallic La0-6Pb0-4MnO3 thin films up to 50% is highlighted.

Integrated Magnetics-Based Multisource Quality AC Power Supply

This paper proposes a method of sharing power/energy between multiple sources and multiple loads using an integrated magnetic circuit as a junction between sources and sinks. It also presents a particular use of the magnetic circuit as an ac power supply, delivering sinusoidal voltage to load irrespective of the presence of the grid, taking only active power from the grid. The proposed magnetic circuit is a three-energy-port unit, viz.: 1) power/energy from grid; 2) power energy from battery-inverter unit; and 3) power/energy delivery to the load in its particular application as quality ac power supply (QPS). The product provides sinusoidal regulated output voltage, input power-factor correction, electrical isolation between the sources and loads, low battery voltage, and control simplicity. Unlike conventional series-shunt-compensated uninterruptible power supply topologies with low battery voltage, the isolation is provided using a single magnetic circuit that results in a smaller size and lower cost. The circuit operating principles and analysis, as well as simulation and experimental results, are presented for this QPS.

Layered Tabu Search Algorithm for Large-MIMO Detection and a Lower Bound on ML Performance

In this paper, we are concerned with low-complexity detection in large multiple-input multiple-output (MIMO) systems with tens of transmit/receive antennas. Our new contributions in this paper are two-fold. First, we propose a low-complexity algorithm for large-MIMO detection based on a layered low-complexity local neighborhood search. Second, we obtain a lower bound on the maximum-likelihood (ML) bit error performance using the local neighborhood search. The advantages of the proposed ML lower bound are i) it is easily obtained for MIMO systems with large number of antennas because of the inherent low complexity of the search algorithm, ii) it is tight at moderate-to-high SNRs, and iii) it can be tightened at low SNRs by increasing the number of symbols in the neighborhood definition. Interestingly, the proposed detection algorithm based on the layered local search achieves bit error performances which are quite close to this lower bound for large number of antennas and higher-order QAM. For e. g., in a 32 x 32 V-BLAST MIMO system, the proposed detection algorithm performs close to within 1.7 dB of the proposed ML lower bound at 10(-3) BER for 16-QAM (128 bps/Hz), and close to within 4.5 dB of the bound for 64-QAM (192 bps/Hz).

The Shannon Cipher System With a Guessing Wiretapper: General Sources

The Shannon cipher system is studied in the context of general sources using a notion of computational secrecy introduced by Merhav and Arikan. Bounds are derived on limiting exponents of guessing moments for general sources. The bounds are shown to be tight for i.i.d., Markov, and unifilar sources, thus recovering some known results. A close relationship between error exponents and correct decoding exponents for fixed rate source compression on the one hand and exponents for guessing moments on the other hand is established.

A numerical study of division of flow in open channels

A two-dimensional numerical model which employs the depth-averaged forms of continuity and momentum equations along with k-e turbulence closure scheme is used to simulate the flow at the open channel divisions. The model is generalised to flows of arbitrary geometries and MacCormack finite volume method is used for solving governing equations. Application of cartesian version of the model to analyse the flow at right-angled junction is presented. The numerical predictions are compared with experimental data of earlier investigators and measurements made as part of the present study. Performance of the model in predicting discharge distribution, surface profiles, separation zone parameters and energy losses is evaluated and discussed in detail. To illustrate the application of the numerical model to analyse the flow in acute angled offtakes and streamlined branch entries, a few computational results are presented.

Modification of photochemical reactivity on formation of inclusion complexes: photorearrangement of benzyl phenyl ethers and methyl phenoxyacetates

The photorearrangement of benzyl phenyl ethers and methyl phenoxyacetates was investigated in methanol and in complexes with cyclodextrin in both the solid state and aqueous solutions. Irradiation in cyclodextrin media leads to a large change in product distribution with a very significant ortho selectivity different from that found in methanol where the reaction is non-selective. For meta-substituted ethers and phenoxyacetates, an impressive regioselectivity between the two ortho-rearranged isomers is observed and this is significantly enhanced by increasing the substituent chain length which acts as a spacer to induce a tight fit between the host and the guest. The observed results are rationalized on the basis of specific orientations of the unsubstituted and meta-substituted ethers and phenoxyacetates in the cyclodextrin cavity.

''Phase reversal'' of non-resonant microwave absorption in superconducting YBaCuO/CuO powder mixtures

Non-resonant microwave absorption is studied as a function of temperature and composition in superconducting YBa2Cu3O7/CuO ceramic composite samples. In pure YBa2Cu3O7 only normal field dependence of the absorption is observed, where as in composites an anomalous non-monotonic field dependence is seen. The results are explained using an extended resistively shunted junction model and invoking the occurrence of junctions with phase difference psi(0) such that pi/2 < psi(0) < 3 pi/2. Copyright (C) 1996 Elsevier Science Ltd

On Walkup's class K (d) and a minimal triangulation of (S-3 (sic) S-1)(#3)

For d >= 2, Walkup's class K (d) consists of the d-dimensional simplicial complexes all whose vertex-links are stacked (d - 1)-spheres. Kalai showed that for d >= 4, all connected members of K (d) are obtained from stacked d-spheres by finitely many elementary handle additions. According to a result of Walkup, the face vector of any triangulated 4-manifold X with Euler characteristic chi satisfies f(1) >= 5f(0) - 15/2 chi, with equality only for X is an element of K(4). Kuhnel observed that this implies f(0)(f(0) - 11) >= -15 chi, with equality only for 2-neighborly members of K(4). Kuhnel also asked if there is a triangulated 4-manifold with f(0) = 15, chi = -4 (attaining equality in his lower bound). In this paper, guided by Kalai's theorem, we show that indeed there is such a triangulation. It triangulates the connected sum of three copies of the twisted sphere product S-3 (sic) S-1. Because of Kuhnel's inequality, the given triangulation of this manifold is a vertex-minimal triangulation. By a recent result of Effenberger, the triangulation constructed here is tight. Apart from the neighborly 2-manifolds and the infinite family of (2d + 3)-vertex sphere products Sd-1 X S-1 (twisted for d odd), only fourteen tight triangulated manifolds were known so far. The present construction yields a new member of this sporadic family. We also present a self-contained proof of Kalai's result. (C) 2011 Elsevier B.V. All rights reserved.