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.

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.

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.

A fast detailed-chemistry modelling approach for simulating the SI-HCCI transition

An established Stochastic Reactor Model (SRM) is used to simulate the transition from Spark Ignition (SI) to Homogeneous Charge Compression Ignition (HCCI) combustion mode in a four cylinder in-line four-stroke naturally aspirated direct injection SI engine with cam profile switching. The SRM is coupled with GT-Power, a one-dimensional engine simulation tool used for modelling engine breathing during the open valve portion of the engine cycle, enabling multi-cycle simulations. The mode change is achieved by switching the cam profiles and phasing, resulting in a Negative Valve Overlap (NVO), opening the throttle, advancing the spark timing and reducing the fuel mass as well as using a pilot injection. A proven technique for tabulating the model is used to create look-up tables in both SI and HCCI modes. In HCCI mode several tables are required, including tables for the first NVO, transient valve timing NVO, transient valve timing HCCI and steady valve timing HCCI and NVO. This results in the ability to simulate the transition with detailed chemistry in very short computation times. The tables are then used to optimise the transition with the goal of reducing NO x emissions and fluctuations in IMEP. Copyright © 2010 SAE International.

Fast response CO2 sensor for automotive exhaust gas analysis

A fast response sensor for measuring carbon dioxide concentration has been developed for laboratory research and tested on a spark ignition engine. The sensor uses the well known infra-red absorption technique with a miniaturized detection system and short capillary sampling tubes, giving a time constant of approximately 5 milliseconds; this is sufficiently fast to observe changes in CO2 levels on a cycle-by-cycle basis under normal operating conditions. The sensor is easily located in the exhaust system and operates continuously. The sensor was tested on a standard production four cylinder spark-ignition engine to observe changes in CO2 concentration in exhaust gas under steady state and transient operating conditions. The processed sensor signal was compared to a standard air-to-fuel ratio (AFR) sensor in the exhaust stream and the results are presented here. The high frequency response CO2 measurements give new insights into both engine and catalyst transient operation. Copyright © 1999 Society of Automotive Engineers, Inc.

Time resolved measurement of cold start hc concentration using the fast FID

Understanding mixture formation phenomena during the first few cycles of an engine cold start is extremely important for achieving the minimum engine-out emission levels at the time when the catalytic converter is not yet operational. Of special importance is the structure of the charge (film, droplets and vapour) which enters the cylinder during this time interval as well as its concentration profile. However, direct experimental studies of the fuel behaviour in the inlet port have so far been less than fully successful due to the brevity of the process and lack of a suitable experimental technique. We present measurements of the hydrocarbon (HC) concentration in the manifold and port of a production SI engine using the Fast Response Flame Ionisation Detector (FRFID). It has been widely reported in the past few years how the FRFID can be used to study the exhaust and in-cylinder HC concentrations with a time resolution of a few degrees of crank angle, and the device has contributed significantly to the understanding of unburned HC emissions. Using the FRFID in the inlet manifold is difficult because of the presence of liquid droplets, and the low and fluctuating pressure levels, which leads to significant changes in the response time of the instrument. However, using recently developed procedures to correct for the errors caused by these effects, the concentration at the sampling point can be reconstructed to align the FRFID signal with actual events in the engine. © 1996 Society of Automotive Engineers, Inc.

Decay heat in fast reactors with transuranic fuels

In this work, we performed an evaluation of decay heat power of advanced, fast spectrum, lead and molten salt-cooled reactors, with flexible conversion ratio. The decay heat power was calculated using the BGCore computer code, which explicitly tracks over 1700 isotopes in the fuel throughout its burnup and subsequent decay. In the first stage, the capability of the BGCore code to accurately predict the decay heat power was verified by performing a benchmark calculation for a typical UO2 fuel in a Pressurized Water Reactor environment against the (ANSI/ANS-5.1-2005, "Decay Heat Power in Light Water Reactors," American National Standard) standard. Very good agreement (within 5%) between the two methods was obtained. Once BGCore calculation capabilities were verified, we calculated decay power for fast reactors with different coolants and conversion ratios, for which no standard procedure is currently available. Notable differences were observed for the decay power of the advanced reactor as compared with the conventional UO2 LWR. The importance of the observed differences was demonstrated by performing a simulation of a Station Blackout transient with the RELAP5 computer code for a lead-cooled fast reactor. The simulation was performed twice: using the code-default ANS-79 decay heat curve and using the curve calculated specifically for the studied core by BGCore code. The differences in the decay heat power resulted in failure to meet maximum cladding temperature limit criteria by ∼100 °C in the latter case, while in the transient simulation with the ANS-79 decay heat curve, all safety limits were satisfied. The results of this study show that the design of new reactor safety systems must be based on decay power curves specific to each individual case in order to assure the desired performance of these systems. © 2009 Elsevier B.V. All rights reserved.