BarraCUDA – a Fast Sequence Mapping Software using Graphics Processing Units

High-throughput DNA sequencing (HTS) instruments today are capable of generating millions of sequencing reads in a short period of time, and this represents a serious challenge to current bioinformatics pipeline in processing such an enormous amount of data in a fast and economical fashion. Modern graphics cards are powerful processing units that consist of hundreds of scalar processors in parallel in order to handle the rendering of high-definition graphics in real-time. It is this computational capability that we propose to harness in order to accelerate some of the time-consuming steps in analyzing data generated by the HTS instruments. We have developed BarraCUDA, a novel sequence mapping software that utilizes the parallelism of NVIDIA CUDA graphics cards to map sequencing reads to a particular location on a reference genome. While delivering a similar mapping fidelity as other mainstream programs , BarraCUDA is a magnitude faster in mapping throughput compared to its CPU counterparts. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the mapping throughput. BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the mapping of millions of sequencing reads generated by HTS 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 at http://seqbarracuda.sf.net

Near-complete transuranic waste incineration in a thorium fuelled pressurised water reactor

The production of long-lived transuranic (TRU) waste is a major disadvantage of fission-based nuclear power. Incineration, and virtual elimination, of waste stockpiles is possible in a thorium (Th) fuelled critical or subcritical fast reactor. Fuel cycles producing a net decrease in TRUs are possible in conventional pressurised water reactors (PWRs). However, minor actinides (MAs) have a detrimental effect on reactivity and stability, ultimately limiting the quality and quantity of waste that can be incinerated. In this paper, we propose using a thorium-retained-actinides fuel cycle in PWRs, where the reactor is fuelled with a mixture of thorium and TRU waste, and after discharge all actinides are reprocessed and returned to the reactor. To investigate the feasibility and performance of this fuel cycle an assembly-level analysis for a one-batch reloading strategy was completed over 125 years of operation using WIMS 9. This one-batch analysis was performed for simplicity, but allowed an indicative assessment of the performance of a four-batch fuel management strategy. The build-up of 233U in the reactor allowed continued reactive and stable operation, until all significant actinide populations had reached pseudo-equilibrium in the reactor. It was therefore possible to achieve near-complete transuranic waste incineration, even for fuels with significant MA content. The average incineration rate was initially around 330 kg per GW th year and tended towards 250 kg per GW th year over several decades: a performance comparable to that achieved in a fast reactor. Using multiple batch fuel management, competitive or improved end-of-cycle burn-up appears achievable. The void coefficient (VC), moderator temperature coefficient (MTC) and Doppler coefficient remained negative. The quantity of soluble boron required for a fixed fuel cycle length was comparable to that for enriched uranium fuel, and acceptable amounts can be added without causing a positive VC or MTC. This analysis is limited by the consideration of a single fuel assembly, and it will be necessary to perform a full core coupled neutronic-thermal-hydraulic analysis to determine if the design in its current form is feasible. In particular, the potential for positive VCs if the core is highly or locally voided is a cause for concern. However, these results provide a compelling case for further work on concept feasibility and fuel management, which is in progress. © 2011 Elsevier Ltd. All rights reserved.

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.

Fast L0-based sparse signal recovery

This paper develops an algorithm for finding sparse signals from limited observations of a linear system. We assume an adaptive Gaussian model for sparse signals. This model results in a least square problem with an iteratively reweighted L2 penalty that approximates the L0-norm. We propose a fast algorithm to solve the problem within a continuation framework. In our examples, we show that the correct sparsity map and sparsity level are gradually learnt during the iterations even when the number of observations is reduced, or when observation noise is present. In addition, with the help of sophisticated interscale signal models, the algorithm is able to recover signals to a better accuracy and with reduced number of observations than typical L1-norm and reweighted L1 norm methods. ©2010 IEEE.

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.

The performance of closed reactor grade plutonium-thorium fuel cycles in reduced-moderation pressurised water reactors

The production of long-lived transuranic (TRU) waste is a major disadvantage of fission-based nuclear power. Previous work has indicated that TRU waste can be virtually eliminated in a pressurised water reactor (PWR) fuelled with a mixture of thorium and TRU waste, when all actinides are returned to the reactor after reprocessing. However, the optimal configuration for a fuel assembly operating this fuel cycle is likely to differ from the current configuration. In this paper, the differences in performance obtained in a reduced-moderation PWR operating this fuel cycle were investigated using WIMS. The chosen configuration allowed an increase of at least 20% in attainable burn-up for a given TRU enrichment. This will be especially important if the practical limit on TRU enrichment is low. The moderator reactivity coefficients limit the enrichment possible in the reactor, and this limit is particularly severe if a negative void coefficient is required for a fully voided core. Several strategies have been identified to mitigate this. Specifically, the control system should be designed to avoid a detrimental effect on moderator reactivity coefficients. The economic viability of this concept is likely to be dependent on the achievable thermal-hydraulic operating conditions. © 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.

Accelerator-induced transients in Accelerator Driven Subcritical Reactors

Achieving higher particles energies and beam powers have long been the main focus of research in accelerator technology. Since Accelerator Driven Subcritical Reactors (ADSRs) have become the subject of increasing interest, accelerator reliability and modes of operation have become important matters that require further research and development in order to accommodate the engineering and economic needs of ADSRs. This paper focuses on neutronic and thermo-mechanical analyses of accelerator-induced transients in an ADSR. Such transients fall into three main categories: beam interruptions (trips), pulsed-beam operation, and beam overpower. The concept of a multiple-target ADSR is shown to increase system reliability and to mitigate the negative effects of beam interruptions, such as thermal cyclic fatigue in the fuel cladding and the huge financial cost of total power loss. This work also demonstrates the effectiveness of the temperature-to-reactivity feedback mechanisms in ADSRs. A comparison of shutdown mechanisms using control rods and beam cut-off highlights the intrinsic safety features of ADSRs. It is evident that the presence of control rods is crucial in an industrial-scale ADSR. This paper also proposes a method to monitor core reactivity online using the repetitive pattern of beam current fluctuations in a pulsed-beam operation mode. Results were produced using PTS-ADS, a computer code developed specifically to study the dynamic neutronic and thermal responses to beam transients in subcritical reactor systems. © 2012 Elsevier B.V.

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.