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.

Practical deployment of the brushless doubly-fed machine in a medium scale wind turbine

The Brushless Doubly-Fed Machine (BDFM) is a brushless electrical generator which allows variable speed operation with a power converter rated at only a fraction of the machine rating. This paper details an example implementation of the BDFM in a medium-scale wind turbine. Details of a simplified design procedure based on electrical and magnetic loadings are given along with the results of tests on the manufactured machine. These show that a BDFM of the scale works as expected but that the 4/8 BDFM chosen was slower and thus larger than the turbine's original induction machine. The implementation of the turbine system is discussed, including the vector-based control scheme that ensures the BDFM operates at a demanded speed and the Maximum Power Point Tracking (MPPT) scheme that selects the rotor speed that extracts the most power from the incident wind conditions.

Operation of brushless doubly-fed machine for drive applications

This paper presents dynamic and steady-state performance of the Brushless Doubly-Fed Machine (BDFM) operating as a variable speed drive. A simple closed-loop control system is used which only requires a speed feedback. The controller is capable of stabilising the machine when changes in speed and torque are applied. The machine starts in cascade mode and then makes a transition to the synchronous mode to reach the desired speed. This will allow a uni-directional converter to be used. The experiments included in this paper were carried out on a 180 frame size BDFM.

The single-phase brushless doubly-fed machine as a generator for wind turbines

This paper proposes a single-phase variant of the Brushless Doubly-Fed Machine, the Single-Phase BDFM, SPB. Like the BDFM it is a variable speed generator which requires a converter rated at only a fraction of the machine rating, using structure with no brushes. Unlike the BDFM, most of its power is delivered directly into a single-phase grid connection. As such it is a potential replacement for PM generators in small-ish wind turbines, potentially with a much lower cost. In this paper we give details of its operation, with reference to results from the first prototype SPB. We also suggest how it may be controlled, again with experimental results. © 2011 IEEE.

A 4 GHz non-resonant clock driver with inductor-assisted energy return to power grid

Power consumption of a multi-GHz local clock driver is reduced by returning energy stored in the clock-tree load capacitance back to the on-chip power-distribution grid. We call this type of return energy recycling. To achieve a nearly square clock waveform, the energy is transferred in a non-resonant way using an on-chip inductor in a configuration resembling a full-bridge DC-DC converter. A zero-voltage switching technique is implemented in the clock driver to reduce dynamic power loss associated with the high switching frequencies. A prototype implemented in 90 nm CMOS shows a power savings of 35% at 4 GHz. The area needed for the inductor in this new clock driver is about 6% of a local clock region. © 2006 IEEE.

Optimal design of Functionally Graded Materials using a procedural model and Particle Swarm Optimization

A new method for the optimal design of Functionally Graded Materials (FGM) is proposed in this paper. Instead of using the widely used explicit functional models, a feature tree based procedural model is proposed to represent generic material heterogeneities. A procedural model of this sort allows more than one explicit function to be incorporated to describe versatile material gradations and the material composition at a given location is no longer computed by simple evaluation of an analytic function, but obtained by execution of customizable procedures. This enables generic and diverse types of material variations to be represented, and most importantly, by a reasonably small number of design variables. The descriptive flexibility in the material heterogeneity formulation as well as the low dimensionality of the design vectors help facilitate the optimal design of functionally graded materials. Using the nature-inspired Particle Swarm Optimization (PSO) method, functionally graded materials with generic distributions can be efficiently optimized. We demonstrate, for the first time, that a PSO based optimizer outperforms classical mathematical programming based methods, such as active set and trust region algorithms, in the optimal design of functionally graded materials. The underlying reason for this performance boost is also elucidated with the help of benchmarked examples. © 2011 Elsevier Ltd. All rights reserved.

Co-occurrence flow for pedestrian detection

The last few years have seen considerable progress in pedestrian detection. Recent work has established a combination of oriented gradients and optic flow as effective features although the detection rates are still unsatisfactory for practical use. This paper introduces a new type of motion feature, the co-occurrence flow (CoF). The advance is to capture relative movements of different parts of the entire body, unlike existing motion features which extract internal motion in a local fashion. Through evaluations on the TUD-Brussels pedestrian dataset, we show that our motion feature based on co-occurrence flow contributes to boost the performance of existing methods. © 2011 IEEE.

Increasing the open-circuit voltage of photoprotein-based photoelectrochemical cells by manipulation of the vacuum potential of the electrolytes.

The innately highly efficient light-powered separation of charge that underpins natural photosynthesis can be exploited for applications in photoelectrochemistry by coupling nanoscale protein photoreaction centers to man-made electrodes. Planar photoelectrochemical cells employing purple bacterial reaction centers have been constructed that produce a direct current under continuous illumination and an alternating current in response to discontinuous illumination. The present work explored the basis of the open-circuit voltage (V(OC)) produced by such cells with reaction center/antenna (RC-LH1) proteins as the photovoltaic component. It was established that an up to ~30-fold increase in V(OC) could be achieved by simple manipulation of the electrolyte connecting the protein to the counter electrode, with an approximately linear relationship being observed between the vacuum potential of the electrolyte and the resulting V(OC). We conclude that the V(OC) of such a cell is dependent on the potential difference between the electrolyte and the photo-oxidized bacteriochlorophylls in the reaction center. The steady-state short-circuit current (J(SC)) obtained under continuous illumination also varied with different electrolytes by a factor of ~6-fold. The findings demonstrate a simple way to boost the voltage output of such protein-based cells into the hundreds of millivolts range typical of dye-sensitized and polymer-blend solar cells, while maintaining or improving the J(SC). Possible strategies for further increasing the V(OC) of such protein-based photoelectrochemical cells through protein engineering are discussed.

Design of brushless doubly-fed machines based: On magnetic circuit modeling

This paper proposes a magnetic circuit model (MCM) for the design of a brushless doubly-fed machine (BDFM). The BDFM possesses advantages in terms of high reliability and reduced gearbox stages, and it requires a fractionally-rated power converter. This makes it suitable for utilization in offshore wind turbines. It is difficult for conventional design methods to calculate the flux in the stator because the two sets of stator windings, which have different pole number, form a complex flux pattern which is not easily determined using common analytical approaches. However, it is advantageous to predict the flux density in the teeth and air-gap at the initial design stage for sizing purposes without recourse finite element analysis. Therefore a magnetic circuit model is developed in this paper to calculate the flux density. A BDFM is used as a case study with FEA validation. © 1965-2012 IEEE.

Design and simulation of SMES system using YBCO tapes for direct drive wave energy converters

The ocean represents a huge energy reservoir since waves can be exploited to generate clean and renewable electricity; however, a hybrid energy storage system is needed to smooth the fluctuation. In this paper a hybrid energy storage system using a superconducting magnetic energy system (SMES) and Li-ion battery is proposed. The SMES is designed using Yttrium Barium Copper Oxide (YBCO) tapes, which store 60 kJ electrical energy. The magnet component of the SMES is designed using global optimization algorithm. Mechanical stress, coupled with electromagnetic field, is calculated using COMSOL and Matlab. A cooling system is presented and a suitable refrigerator is chosen to maintain a cold working temperature taking into account four heat sources. Then a microgrid system of direct drive linear wave energy converters is designed. The interface circuit connecting the generator and storage system is given. The result reveals that the fluctuated power from direct drive linear wave energy converters is smoothed by the hybrid energy storage system. The maximum power of the wave energy converter is 10 kW. © 2012 IEEE.

Energy recycling from multigigahertz clocks using fully integrated switching converters

Large digital chips use a significant amount of energy to broadcast a low-skew, multigigahertz clock to millions of latches located throughout the chip. Every clock cycle, the large aggregate capacitance of the clock network is charged from the supply and then discharged to ground. Instead of wasting this stored energy, it is possible to recycle the energy by controlling its delivery to another part of the chip using an on-chip dc-dc converter. The clock driver and switching converter circuits share many compatible characteristics that allow them to be merged into a single design and fully integrated on-chip. Our buck converter prototype, manufactured in 90-nm CMOS, provides a proof-of-concept that clock network energy can be recycled to other parts of the chip, thus lowering overall energy consumption. It also confirms that monolithic multigigahertz switching converters utilizing zero-voltage switching can be implemented in deep-submicrometer CMOS. With multigigahertz operation, fully integrated inductors and capacitors use a small amount of chip area with low losses. Combining the clock driver with the power converter can share the large MOSFET drivers necessary as well as being energy and space efficient. We present an analysis of the losses which we confirm by experimentally comparing the merged circuit with a conventional clock driver. © 2012 IEEE.

Use of a high-temperature superconducting coil for magnetic energy storage

A high temperature superconducting magnetic energy storage device (SMES) has been realised using a 350 m-long BSCCO tape wound as a pancake coil. The coil is mounted on a cryocooler allowing temperatures down to 17.2 K to be achieved. The temperature dependence of coil electrical resistance R(T) shows a superconducting transition at T 102.5 K. Measurements of the V(I) characteristics were performed at several temperatures between 17.2 K and 101.5 K to obtain the temperature dependence of the critical current (using a 1 νV/cm criterion). Critical currents were found to exceed 100 A for T < 30 K. An electronic DC-DC converter was built in order to control the energy flow in and out of the superconducting coil. The converter consists of a MOS transistor bridge switching at a 80 kHz frequency and controlled with standard Pulse Width Modulation (PWM) techniques. The system was tested using a 30 V squared wave power supply as bridge input voltage. The coil current, the bridge input and output voltages were recorded simultaneously. Using a 10 A setpoint current in the superconducting coil, the whole system (coil + DC-DC converter) can provide a stable output voltage showing uninterruptible power supply (UPS) capabilities over 1 s. © 2006 IOP Publishing Ltd.

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.

Exhaust gas ignition (EGI)-a new concept for rapid light-off of automotive exhaust catalyst

Increasing pressure on lowering vehicle exhaust emissions to meet stringent California and Federal 1993/1994 TLEV emission standards of 0.125 gpm NMOG, 3.4 gpm CO and 0.4 gpm NOx and future ULEV emission standards of 0.04 gpm NMOG, 1.7 gpm CO and 0.2 gpm NOx has focused specific attention on the cold start characteristics of the vehicle's emission system, especially the catalytic converter. From test data it is evident that the major portion of the total HC and CO emissions occur within the first two minutes of the driving cycle while the catalyst is heating up to operating temperature. The use of an electrically heated catalyst (EHC) has been proposed to alleviate this problem but the cost and weight penalties are high and the durability has yet to be fully demonstrated (1)*. This paper describes a method of reducing the light-off time of the catalytic converter to less than 20 seconds by means of an afterburner. The system uses exhaust gases from the engine calibrated to run rich and additional air injected into the exhaust gas stream to form a combustible mixture. The key feature concerns the method of making this combustible mixture ignitable within 2 seconds from starting the engine when the exhaust gases arriving at the afterburner are cold and essentially non-reacting. © Copyright 1992 Society of Automotive Engineers, Inc.

Single-sensor maximum power point tracking algorithms

Single-sensor maximum power point tracking algorithms for photovoltaic systems are presented. The algorithms have the features, characteristics and advantages of the widely used incremental conductance (INC) algorithm. However; unlike the INC algorithm which requires two sensors (the voltage sensor and the current sensor), the single-sensor algorithms are more desirable because they require only one sensor: the voltage sensor. The algorithms operate by maximising power at the DC-DC converter output, instead of the input. © 2013 The Institution of Engineering and Technology.