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.

Floating-body SOI memory: Concepts, physics and challenges

We present an overview of the single-transistor memory cells (lT-DRAMs), which are based on floating-body effects in SOI MOSFETs. The typical device architectures, principles of operation and key mechanisms for programming are described. The various approaches (Z-RAM, MSDRAM, etc) are compared in terms of performance and potential for aggressive scaling. ©The Electrochemical Society.

Blue-phase templated fabrication of three-dimensional nanostructures for photonic applications.

A promising approach to the fabrication of materials with nanoscale features is the transfer of liquid-crystalline structure to polymers. However, this has not been achieved in systems with full three-dimensional periodicity. Here we demonstrate the fabrication of self-assembled three-dimensional nanostructures by polymer templating blue phase I, a chiral liquid crystal with cubic symmetry. Blue phase I was photopolymerized and the remaining liquid crystal removed to create a porous free-standing cast, which retains the chiral three-dimensional structure of the blue phase, yet contains no chiral additive molecules. The cast may in turn be used as a hard template for the fabrication of new materials. By refilling the cast with an achiral nematic liquid crystal, we created templated blue phases that have unprecedented thermal stability in the range -125 to 125 °C, and that act as both mirrorless lasers and switchable electro-optic devices. Blue-phase templated materials will facilitate advances in device architectures for photonics applications in particular.

Blue-phase templated fabrication of three-dimensional nanostructures for photonic applications

A promising approach to the fabrication of materials with nanoscale features is the transfer of liquid-crystalline structure to polymers. However, this has not been achieved in systems with full three-dimensional periodicity. Here we demonstrate the fabrication of self-assembled three-dimensional nanostructures by polymer templating blue phase I, a chiral liquid crystal with cubic symmetry. Blue phase I was photopolymerized and the remaining liquid crystal removed to create a porous free-standing cast, which retains the chiral three-dimensional structure of the blue phase, yet contains no chiral additive molecules. The cast may in turn be used as a hard template for the fabrication of new materials. By refilling the cast with an achiral nematic liquid crystal, we created templated blue phases that have unprecedented thermal stability in the range-125 to 125°C, and that act as both mirrorless lasers and switchable electro-optic devices. Blue-phase templated materials will facilitate advances in device architectures for photonics applications in particular. © 2012 Macmillan Publishers Limited. All rights reserved.

A unified circuit model for the polysilicon thin film transistor

This paper describes a unified approach to modelling the polysilicon thin film transistor (TFT) for the purposes of circuit design. The approach uses accurate methods of predicting the channel conductance and then fitting the resulting data with a polynomial. Two methods are proposed to find the channel conductance: a device model and measurement. The approach is suitable because the TFT does not have a well defined threshold voltage. The polynomial conductance is then integrated generally to find the drain current and channel charge, necessary for a complete circuit model. © 1991 The Japan Society of Applied Physics.

Unified analytic model for current-voltage behavior in amorphous oxide semiconductor TFTs

We present a simple and semi-physical analytical description of the current-voltage characteristics of amorphous oxide semiconductor thin-film transistors in the above-threshold and sub-threshold regions. Both regions are described by single unified expression that employs the same set of model parameter values directly extracted from measured terminal characteristics. The model accurately reproduces measured characteristics of amorphous semiconductor thin film transistors in general, yielding a scatter of < 4%. © 1980-2012 IEEE.

InGaN/GaN LEDs grown on Si(111): Dependence of device performance on threading dislocation density and emission wavelength

We demonstrate the growth of crack-free blue and greenemitting LED structures grown on 2-inch and 6-inch Si(111) substrates by metalorganic vapour phase epitaxy (MOVPE), using AlN nucleation layers and AlGaN buffer layers for stress management. LED device performance and its dependence on threading dislocation (TD) density and emission wavelength were studied. Despite the inherently low light extraction efficiency, an output power of 1.2 mW at 50 mA was measured from a 500 μm square planar device, emitting at 455 nm. The light output decreases dramatically as the emission wavelength increases from 455 nm to 510 nm. For LED devices emitting at similar wavelength, the light output was more than doubled when the TD density was reduced from 5×1 09 cm-2 to 2×109 cm-2. Our results clearly show that high TD density is detrimental to the overall light output, highlighting the need for further TD reduction for structures grown on Si. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA.

A surface acoustic wave-based immunosensing device using a nanocrystalline ZnO film on Si

The novelty of this study resides in the fabrication of a bio-sensing device, based on the surface acoustic wave (SAW) on a nanocrystalline ZnO film. The ZnO film was deposited using an rf magnetron sputtering at room temperature on silicon. The deposited films showed the c-axisoriented crystallite with grain size of ∼40 nm. The immunosensing device was fabricated using photolithographic protocols on the film. As a model biomolecular recognition and immunosensing, biospecific interaction between a 6-(2,4-dinitrophenyl) aminohexanoic acid (DNP) antigen and its antibody was employed, demonstrating the shifts of resonant frequencies on SAW immunosensing device. The device exhibited a linearity as a function of the antibody concentration in the range of 20∼20,000 ng/ml. © 2009 American Scientific Publishers. All rights reserved.