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.

Fast-switching phase gratings using in-plane addressed short-pitch polymer stabilized chiral nematic liquid crystals

We demonstrate a fast-switching (sub-millisecond) phase grating based upon a polymer stabilized short-pitch chiral nematic liquid crystal that is electrically addressed using in-plane electric fields. The combination of the short-pitch and the polymer stabilization enables the diffraction pattern to be switched on and off reversibly in 600 μs. Results are presented on the far-field diffraction pattern along with the intensity of the diffraction orders as a function of the applied electric field and the response times. © 2011 American Institute of Physics.

Gaussian processes for fast policy optimisation of POMDP-based dialogue managers

Modelling dialogue as a Partially Observable Markov Decision Process (POMDP) enables a dialogue policy robust to speech understanding errors to be learnt. However, a major challenge in POMDP policy learning is to maintain tractability, so the use of approximation is inevitable. We propose applying Gaussian Processes in Reinforcement learning of optimal POMDP dialogue policies, in order (1) to make the learning process faster and (2) to obtain an estimate of the uncertainty of the approximation. We first demonstrate the idea on a simple voice mail dialogue task and then apply this method to a real-world tourist information dialogue task. © 2010 Association for Computational Linguistics.

Ferroelectric liquid crystal over silicon devices

Over the past 20 years, ferroelectric liquid crystal over silicon (FLCOS) devices have made a wide impact on applications as diverse as optical correlation and holographic projection. To cover the entire gamut of this technology would be difficult and long winded; hence, this paper describes the significant developments of FLCOS within the Engineering Department at the University of Cambridge.The purpose of this paper is to highlight the key issues in fabricating silicon backplane spatial light modulators (SLMs) and to indicate ways in which the technology can be fabricated using cheap, low-density production and manufacturability. Three main devices have been fabricated as part of several research programmes and are documented in this paper. The fast bitplane SLM and the reconfigurable optical switches for aerospace and telecommunications systems (ROSES) SLM will form the basis of a case study to outline the overall processes involved. There is a great deal of commonality in the fabrication processes for all three devices, which indicates their potential strength and demonstrates that these processes can be made independent of the SLMs that are being assembled. What is described is a generic process that can be applied to any silicon backplane SLM on a die-by-die basis. There are hundreds of factors that can affect the yield in a manufacturing process and the purpose of a good process design procedure is to minimise these factors. One of the most important features in designing a process is fabrication experience, as so many of the lessons in this business can only be learned this way. We are working with the advantage of knowing the mistakes already made in the flat panel display industry, but we are also faced with the fact that those mistakes took many years and many millions of dollars to make.The fabrication process developed here originates and adapts earlier processes from various groups around the world. There are also a few totally new processes that have now been adopted by others in the field. Many, such as the gluing process, are still on-going and have to be worked on more before they will fully suit 'manufacturability'. © 2012 Copyright Taylor and Francis Group, LLC.

Spatial correlation of heat release rate and sound emission from turbulent premixed flames

The two-point spatial correlation of the rate of change of fluctuating heat release rate is central to the sound emission from open turbulent flames, and a few attempts have been made to address this correlation in recent studies. In this paper, the two-point correlation and its role in combustion noise are studied by analysing direct numerical simulation (DNS) data of statistically multi-dimensional turbulent premixed flames. The results suggest that this correlation function depends on the separation distance and direction but, not on the positions inside the flame brush. This correlation can be modelled using a combination of Hermite-Gaussian functions of zero and second order, i.e. functions of the form (1-Ax2)e-Bx2 for constants A and B, to include its possible negative values. The integral correlation volume obtained using this model is about 0.2δL3 with the length scale obtained from its cube root being about 0.6δ L, where δ L is the laminar flame thermal thickness. Both of the values are slightly larger than the values reported in an earlier study because of the anisotropy observed for the correlation. This model together with the turbulence-dependent parameter K, the ratio of the root-mean-square (RMS) value of the rate of change of reaction rate to the mean reaction rate, derived from the DNS data is applied to predict the far-field sound emitted from open flames. The calculated noise levels agree well with recently reported measurements and show a sensitivity to K values. © 2012 The Combustion Institute.

Safety implications of reactivity variations in fast thorium ADSRs

Nuclear power generation offers a reliable, low-impact and large-scale alternative to fossil fuels. However, concerns exist over the safety and sustainability of this method of power production, and it remains unpopular with some governments and pressure groups throughout the world. Fast thorium fuelled accelerator-driven sub-critical reactors (ADSRs) offer a possible route to providing further re-assurance regarding these concerns on account of their properties of enhanced safety through sub-critical operation combined with reduced actinide waste production from the thorium fuel source. The appropriate sub-critical margin at which these reactors should operate is the subject of continued debate. Commercial interests favour a small sub-critical margin in order to minimise the size of the accelerator needed for a given power output, whilst enhanced safety would be better satisfied through larger sub-critical margins to further minimise the possibility of a criticality excursion. Against this background, this paper examines some of the issues affecting reactor safety inherent within thorium fuel sources resulting from the essential Th90232→Th90233→Pa91233→U92233 breeding chain. Differences in the decay half-lives and fission and capture cross-sections of 233Pa and 233U can result in significant changes in the reactivity of the fuel following changes in the reactor power. Reactor operation is represented using a homogeneous lumped fast reactor model that can simulate the evolution of actinides and reactivity variations to first-order accuracy. The reactivity of the fuel is shown to increase significantly following a loss of power to the accelerator. Where the sub-critical operating margins are small this can result in a criticality excursion unless some form of additional intervention is made, for example through the insertion of control rods. © 2012 Elsevier Ltd. All rights reserved.

Particle Image Velocimetry analysis in dynamic centrifuge tests

The Particle Image Velocimetry (PIV) technique is an image processing tool to obtain instantaneous velocity measurements during an experiment. The basic principle of PIV analysis is to divide the image into small patches and calculate the locations of the individual patches in consecutive images with the help of cross correlation functions. This paper focuses on the application of the PIV analysis in dynamic centrifuge tests on small scale tunnels in loose, dry sand. Digital images were captured during the application of the earthquake loading on tunnel models using a fast digital camera capable of taking digital images at 1000 frames per second at 1 Megapixel resolution. This paper discusses the effectiveness of the existing methods used to conduct PIV analyses on dynamic centrifuge tests. Results indicate that PIV analysis in dynamic testing requires special measures in order to obtain reasonable deformation data. Nevertheless, it was possible to obtain interesting mechanisms regarding the behaviour of the tunnels from PIV analyses. © 2010 Taylor & Francis Group, London.

Micromachining of glassy carbon toolsets for micro embossing applications

Laser micro machining is fast gaining popularity as a method of fabricating micro scale structures. Lasers have been utilised for micro structuring of metals, ceramics and glass composites and with advances in material science, new materials are being developed for micro/nano products used in medical, optical, and chemical industries. Due to its favourable strength to weight ratio and extreme resistance to chemical attack, glassy carbon is a new material that offers many unique properties for micro devices. The laser machining of SIGRADUR® G grade glassy carbon was characterised using a 1065 nm wavelength Ytterbium doped pulsed fiber laser. The laser system has a selection of 25 preset waveforms with optimised peak powers for different pulsing frequencies. The optics provide spot diameter of 40 μm at the focus. The effect of fluence, transverse overlap and pulsing frequency (as waveform) on glassy carbon was investigated. Depth of removal and surface roughness were measured as machining quality indicators. The damage threshold fluence was determined to be 0.29 J/cm2 using a pulsing frequency of 250 kHz and a pulse width of 18 ns (waveform 3). Ablation rates of 17 < V < 300 μm3/pulse were observed within a fluence range of 0.98 < F < 2.98 J/cm2. For the same fluence variation, 0.6 μm to 6.8 μm deep trenches were machined. Trench widths varied from 29 μm at lower fluence to 47 μm at the higher fluence. Square pockets, 1 mm wide, were machined to understand the surface machining or milling. The depth of removal using both waveform 3 and 5 showed positive correlation with fluence, with waveform 5 causing more removal than waveform 3 for the same fluence. Machined depths varied from less than 1 μm to nearly 40 μm. For transverse overlap variation using waveform 3, the best surface finish with Rz = 1.1 μm was obtained for fluence 0.792 J/cm2 for transverse overlap of 1 μm, 6 μm, and 9 μm at machined depths of 22.9 μm, 6.6 μm, and 4.6 μm respectively. For fluence of 1.426 J/cm2, the best surface finish with Rz = 1.2 μm was obtained for transverse overlap of 6 μm, and 9 μm at machined depths of 12.46 μm, and 8.6 μm respectively. The experimental data was compiled as machining charts and utilised for fabricating a micro-embossing glassy carbon master toolsets as a capability demonstration.

A fast 600-V Tandem PiN Schottky (TPS) rectifier with ultra-low on-state voltage

The Tandem PiN Schottky (TPS) rectifier features lowly-doped p-layers in both active and termination regions, and is applied in 600-V rating for the first time. In the active region, the Schottky contact is in series connection with a transparent p-layer, leading to a superior forward performance than the conventional diodes. In addition, due to the benefit of moderate hole injection from the p-layer, the TPS offers a better trade-off between the on-state voltage and the switching speed. The active p-layer also helps to stabilise the Schottky contact, and hence the electrical data distributions are more concentrated. Regarding the floating p-layer in the termination region, its purpose is to reduce the peak electric fields, and the TPS demonstrates a high breakdown voltage with a compact termination width, less than 70% of the state-of-the-art devices on the market. Experimental results have shown that the 600-V TPS rectifier has an ultra-low on-state voltage of 0.98 V at 250 A/cm 2, a fast turn-off time of 75 ns by the standard RG1 test (I F=0.5A, I R=1A, and I RR=0.25A) and a breakdown voltage over 720 V. It is noteworthy that the p-layers in the active and termination regions can be formed at no extra cost for the use of self-alignment process. © 2012 IEEE.

The Silent Period of Evidence Integration in Fast Decision Making

In a typical experiment on decision making, one out of two possible stimuli is displayed and observers decide which one was presented. Recently, Stanford and colleagues (2010) introduced a new variant of this classical one-stimulus presentation paradigm to investigate the speed of decision making. They found evidence for "perceptual decision making in less than 30 ms". Here, we extended this one-stimulus compelled-response paradigm to a two-stimulus compelled-response paradigm in which a vernier was followed immediately by a second vernier with opposite offset direction. The two verniers and their offsets fuse. Only one vernier is perceived. When observers are asked to indicate the offset direction of the fused vernier, the offset of the second vernier dominates perception. Even for long vernier durations, the second vernier dominates decisions indicating that decision making can take substantial time. In accordance with previous studies, we suggest that our results are best explained with a two-stage model of decision making where a leaky evidence integration stage precedes a race-to-threshold process. © 2013 Rüter et al.

Towards a fast electro-thermo-mechanical IGBT/Diode simulation framework for design of reliable power electronic converters

This paper describes a methodology that enables fast and reasonably accurate prediction of the reliability of power electronic modules featuring IGBTs and p-i-n diodes, by taking into account thermo-mechanical failure mechanisms of the devices and their associated packaging. In brief, the proposed simulation framework performs two main tasks which are tightly linked together: (i) the generation of the power devices' transient thermal response for realistic long load cycles and (ii) the prediction of the power modules' lifetime based on the obtained temperature profiles. In doing so the first task employs compact, physics-based device models, power losses lookup tables and polynomials and combined material-failure and thermal modelling, while the second task uses advanced reliability tests for failure mode and time-to-failure estimation. The proposed technique is intended to be utilised as a design/optimisation tool for reliable power electronic converters, since it allows easy and fast investigation of the effects that changes in circuit topology or devices' characteristics and packaging have on the reliability of the employed power electronic modules. © 2012 IEEE.