BarraCUDA - a fast short read sequence aligner using graphics processing units.

BACKGROUND: With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. FINDINGS: Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. CONCLUSIONS: BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology.BarraCUDA is currently available from http://seqbarracuda.sf.net.

High velocity vortex channeling in vicinal YBCO thin films

We report on electrical transport measurements at high current densities on optimally doped YBa 2Cu 3O 7-δ thin films grown on vicinal SrTiO 3 substrates. Data were collected by using a pulsed-current technique in a four-probe arrangement, allowing to extend the current-voltage characteristics to high supercritical current densities (up to 24 MA cm -2) and high electric fields (more than 20 V/cm), in the superconducting state at temperatures between 30 and 80 K. The electric measurements were performed on tracks perpendicular to the vicinal step direction, such that the current crossed between ab planes, under magnetic field rotated in the plane defined by the crystallographic c axis and the current density. At magnetic field orientation parallel to the cuprate layers, evidence for the sliding motion along the ab planes (vortex channeling) was found. The signature of vortex channeling appeared to get enhanced with increasing electric field, due to the peculiar depinning features in the kinked vortex range. They give rise to a current-voltage characteristics steeper than in the more off-plane rectilinear vortex orientations, in the electric field range below approximately 1 V/cm. Roughly above this value, the high vortex channeling velocities (up to 8.6 km/s) could be ascribed to the flux flow, although the signature of ohmic transport appeared to be altered by unavoidable macroscopic self-heating and hot-electron-like effects. © 2012 Elsevier B.V. All rights reserved.

Measurements and calculations of transport AC loss in second generation high temperature superconducting pancake coils

Theoretical and experimental AC loss data on a superconducting pancake coil wound using second generation (2 G) conductors are presented. An anisotropic critical state model is used to calculate critical current and the AC losses of a superconducting pancake coil. In the coil there are two regions, the critical state region and the subcritical region. The model assumes that in the subcritical region the flux lines are parallel to the tape wide face. AC losses of the superconducting pancake coil are calculated using this model. Both calorimetric and electrical techniques were used to measure AC losses in the coil. The calorimetric method is based on measuring the boil-off rate of liquid nitrogen. The electric method used a compensation circuit to eliminate the inductive component to measure the loss voltage of the coil. The experimental results are consistent with the theoretical calculations thus validating the anisotropic critical state model for loss estimations in the superconducting pancake coil. © 2011 American Institute of Physics.

Statistics and dynamics of turbulence-flame alignment in premixed combustion

The geometric alignment of turbulent strain-rate structures with premixed flames greatly influences the results of the turbulence-flame interaction. Here, the statistics and dynamics of this alignment are experimentally investigated in turbulent premixed Bunsen flames using high-repetition-rate stereoscopic particle image velocimetry. In all cases, the statistics showed that the most extensive principal strain-rate associated with the turbulence preferentially aligned such that it was more perpendicular than parallel to the flame surface normal direction. The mean turbulence-flame alignment differed between the flames, with the stronger flames (higher laminar flame speed) exhibiting stronger preferential alignment. Furthermore, the preferential alignment was greatest on the reactant side of the mean flame brush. To understand these differences, individual structures of fluid-dynamic strain-rate were tracked through time in a Lagrangian manner (i.e., by following the fluid elements). It was found that the flame surface affected the orientation of the turbulence structures, with the majority of structures rotating as they approached the flame such that their most extensive principal strain-rate was perpendicular to the flame normal. The maximum change in turbulent structure orientation was found to decrease with the strength of the structure, increase with the strength of the flame, and exhibit similar trends when the structure strength and flame strength were represented by a Karlovitz number. The mean change in orientation decreased from the unburnt to burnt side of the flame brush and appears to be influenced by the overall flame shape. © 2011 The Combustion Institute.

Silver paint as a soldering agent for DyBaCuO single-domains welding

Silver paint has been tested as a soldering agent for DyBaCuO single-domain welding. Junctions have been manufactured on Dy-Ba-Cu-O single-domains cut either along planes parallel to the c-axis or along the ab-planes. Microstructural and superconducting characterisations of the samples have been performed. For both types of junctions, the microstructure in the joined area is very clean: no secondary phase or Ag particles segregation has been observed. Electrical and magnetic measurements for all configurations of interest are reported $\rho(T)$ curves, and Hall probe mapping). The narrow resistive superconducting transition reported for all configurations shows that the artificial junction does not affect significantly the measured superconducting properties of the material.

Magnetic properties and anisotropy of orthorhombic DyMnO3 single crystal

An orthorhombic DyMnO3 single crystal has been studied in magnetic fields up to 14 T and between 3 K and room temperature. The field dependent ordering temperature of Dy moments is deduced. The paramagnetic Curie Weiss behavior is related mainly to the Dy3+sublattice whereas the Mn sublattice contribution plays a secondary role. DC magnetization measurements show marked anisotropic features, related to the anisotropic structure of a cubic system stretched along a body diagonal, with a magnetic easy axis parallel to the crystallographic b axis. A temperature and field dependent spin flop transition is observed below 9 K, when relatively weak magnetocrystalline anisotropy is overcome by magnetic fields up to 1.6 T. © 2013 Elsevier B.V.

DC and AC Shielding properties of bulk high-tc

We have studied numerically and experimentally the magnetic flux penetration in high-Tc superconducting tube subjected to a uniform magnetic field parallel to its long axis. This study is carried in view of designing low-frequency magnetic shields by exploiting the diamagnetic properties of high-Tc superconducting ceramics. We have measured the field attenuation for applied magnetic fields in the frequency range 5 mHz-0.1 Hz by Hall probe measurements and at audio frequencies using a sensing coil. A simple 1D analysis using the Kim critical state model was found to be able to reproduce the experimental data satisfactorily. We have also determined the phase shift between the internal and the applied field both experimentally and numerically. Finally, we have studied the sweep rate dependence of the magnetic shielding properties, using data recorded either at several constant sweep rates dB /dt or at several AC fields of various amplitudes and frequencies. Both methods agree with each other and lead to a n-value of the E ∼ Jn law equal to ∼40 at 77 K. © 2009 IEEE.

Anisotropic behaviour in the magnetic field dependence of the low temperature electrical resistance of calcium-doped lanthanum manganate thin films grown by RF magnetron sputtering

We report about the magnetoresistive properties of calcium-doped lanthanum manganate thin films grown by RF magnetron sputtering on single crystalline LaAlO3 and MgO substrates. Two orientations of the magnetic field with respect to the electrical current have been studied: (i) magnetic field in the plane of the film and parallel to the electrical current, and (ii) magnetic field perpendicular to the plane of the film. The film grown on LaAlO 3 is characterised by an unusual magnetoresistive behaviour when the magnetic field is applied perpendicular to the film plane: the appearance of two bumps in the field dependence of the resistance is shown to be related to the occurrence of anisotropic magnetoresistive effects in manganate films. © 2004 Elsevier B.V. All rights reserved.

Photoconductive hybrid films via directional self-assembly of C 60 on aligned carbon nanotubes

Hybrid nanostructured materials can exhibit different properties than their constituent components, and can enable decoupled engineering of energy conversion and transport functions. Novel means of building hybrid assemblies of crystalline C 60 and carbon nanotubes (CNTs) are presented, wherein aligned CNT films direct the crystallization and orientation of C 60 rods from solution. In these hybrid films, the C 60 rods are oriented parallel to the direction of the CNTs throughout the thickness of the film. High-resolution imaging shows that the crystals incorporate CNTs during growth, yet grazing-incidence X-ray diffraction (GIXD) shows that the crystal structure of the C 60 rods is not perturbed by the CNTs. Growth kinetics of the C 60 rods are enhanced 8-fold on CNTs compared to bare Si, emphasizing the importance of the aligned, porous morphology of the CNT films as well as the selective surface interactions between C 60 and CNTs. Finally, it is shown how hybrid C 60-CNT films can be integrated electrically and employed as UV detectors with a high photoconductive gain and a responsivity of 10 5 A W -1 at low biases (± 0.5 V). The finding that CNTs can induce rapid, directional crystallization of molecules from solution may have broader implications to the science and applications of crystal growth, such as for inorganic nanocrystals, proteins, and synthetic polymers. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Plastic limit solution for the response of plate anchors under combined translational and torsional undrained loading

Plate anchors are increasingly being used to moor large floating offshore structures in deep and ultradeep water. These facilities impart substantial vertical uplift loading to plate anchors. However, extreme operating conditions such as hurricane loading often result in partial system failures, with significant change in the orientation of the remaining intact mooring lines. The purpose of this study is to investigate the undrained pure translational (parallel to plate) and torsional bearing capacity of anchor plates idealized as square and rectangular shaped plates. Moreover, the interaction response of plate anchors under combined translational and torsional loading is studied using a modified plastic limit analysis (PLA) approach. The previous PLA formulation which did not account for shear-normal force interaction on the vertical end faces of the plate provides an exact solution to the idealized problem of an infinitely thin plate but only an approximate solution to the problem of a plate of finite thickness. This is also confirmed by the three-dimensional finite element (FE) results, since the PLA values exceed FE results as the thickness of the plate increases. By incorporating the shear-normal interaction relationship in the modified solution, the torsional bearing capacity factors, as well as the plate interaction responses are enhanced as they show satisfactory agreement with the FE results. The interaction relationship is then obtained for square and rectangular plates of different aspect ratios and thicknesses. The new interaction relationships could also be used as an associated plastic failure locus for combined shear and torsional loading to predict plastic displacements and rotations in translational and torsional loading modes as well. Copyright © 2011 by the International Society of Offshore and Polar Engineers (ISOPE).

Polarization and temperature dependence of photoluminescence from zincblende and wurtzite InP nanowires

We use polarization-resolved and temperature-dependent photoluminescence of single zincblende (ZB) (cubic) and wurtzite (WZ) (hexagonal) InP nanowires to probe differences in selection rules and bandgaps between these two semiconductor nanostructures. The WZ nanowires exhibit a bandgap 80 meV higher in energy than the ZB nanowires. The temperature dependence of the PL is similar but not identical for the WZ and ZB nanowires. We find that ZB nanowires exhibit strong polarization parallel to the nanowire axis, while the WZ nanowires exhibit polarized emission perpendicular to the nanowire axis. This behavior is interpreted in terms of the different selection rules for WZ and ZB crystal structures. © 2007 American Institute of Physics.

Shear transfer across a diagonal crack in reinforced concrete strengthened with externally bonded FRP fabric

Aging concrete infrastructure in developed economies and more recently constructed concrete infrastructure in the developing world are frequently found to be deficient in structural strength relative to current needs. This can be attributed to a variety of factors including deterioration, construction defects, accidental damage, changes in understanding and failure to design for future loading requirements. Strengthening existing concrete structures can be a cost and carbon effective alternative to replacement. A competitive option for the strengthening of concrete slab-on-beam structures that are deficient in shear capacity is the U-wrapping of the down-stand beam portion of the shear span with externally bonded FRP fabric. While guidance exists for the strengthening of reinforced concrete by U-wrapping, the interaction between internal steel reinforcement, concrete and external FRP in the presence of a dominant diagonal shear crack is not well understood. An approach adopted in previous work has been to explore this interaction through conventional push-off testing. In conventional push-off testing, unlike in a beam, the shear plane is parallel to the direction of loading and perpendicular to the principal fibre orientation. This paper presents a novel push-off test variation in which the shear plane is inclined at 45° to the direction of loading and the principal fibre orientation. A variety of reinforcement ratios, FRP thicknesses and FRP end conditions are modelled. The implications of inclined cracking on debonding of FRP are investigated. The suitability and relevance of inclined push-off tests for further work in this area is also assessed. © 2013, NetComposite Limited.

Measurement of Residual Stresses in Ferroelectric Pb(Zr

The residual stresses in Pb(Zr0.3Ti0.7)O3thin films were measured by the \sin^{2}\Psi method using the normal X-ray incidence. The spacing of different planes (hkl) parallel to the film surface were converted to the spacing of a set of inclined planes (100). The angles between (100) and (hkl) were equivalent to the tilting angles of (100) from the normal of film surface. The residual stresses were extracted from the linear slope of the strain difference between the equivalent inclined direction and normal direction with respect to the \sin^{2}\Psi. The results were in consistency with that derived from the conventional \sin^{2}\Psi method.

Friction between carbon fibre reinforced polymers: Experiments and modelling

Carbon fibre reinforced polymers (CFRP) are well-known for the excellent combination of mechanical and thermal properties with light weight. However, their tribological properties are still largely uncovered. In this work an experimental study of friction between two CFRP at weak normal load (inferior to 20 N) was performed. Two effects were scrutinuously studied during the experiments: fibre volume friction and fibre orientation. In addition to this experimental work, a modelling of a contact between two FRP was realized. It is supposed that the real area of contact consists of a multitude of microcontacts of three types: fibre-fibre, fibre-matrix and matrix-matrix. The experimental work has shown a small rise in friction coefficient with the change of fibre orientation of two composites from parallel to perpendicular relative to the sliding direction. In parallel, the proposed analytical model predicts a independence of this angle. Regarding the influence of the fibre volume fraction, Vf, the experiments reveal a decrease in friction coefficient of 50% with a change of Vf from 0% to 62%. This observation corresponds to the qualitative dependence depicted with the model. © 2012 EDP Sciences.

Measurement of residual stresses in ferroelectric Pb(Zr 0.3Ti0.7)O3 thin films by X-ray diffraction

The residual stresses in Pb(Zr0.3Ti0.7)O3 thin films were measured by the sin2 Ψ method using the normal X-ray incidence. The spacing of different planes (hkl) parallel to the film surface were converted to the spacing of a set of inclined planes (100). The angles between (100) and (hkl) were equivalent to the tilting angles of (100) from the normal of film surface. The residual stresses were extracted from the linear slope of the strain difference between the equivalent inclined direction and normal direction with respect to the sin2 Ψ. The results were in consistency with that derived from the conventional sin2 Ψ method. © 2013 The Japan Society of Applied Physics.