Parallel Devices Research Articles

Temperature-driven self-actuated microchamber sealing system for highly integrated microfluidic devices

We present here a novel microchamber sealing valve that is self-actuated by a pressure change during the temperature change in the thermal activation of reactions. Actuation of our valve requires only the use of the same heating device as employed for the reactions. A thermoplastic UV-curable polymer is used as a device material; the polymer allows realization of the temperature-driven valve actuation as well as the fabrication of multi-layered devices. The self-actuated valve achieves effective sealing of the microchamber for the polymerase chain reaction (PCR) even at 90 °C, which is essential for developing highly parallel PCR array devices without the need for complicated peripherals to control the valve operation.

Solution processable organic p–n junction bilayer vertical photodiodes

Organic p–n bilayer photodiodes were produced by solution casting poly(3-hexylthiophene) (P3HT) from chlorobenzene and phenyl-C61-butyric acid methyl ester (PCBM):poly(4-chlorostyrene) (PClS) blends from the nearly orthogonal solvent dichloromethane onto flexible indium tin oxide (ITO)/polyester as a substrate. This is the first demonstration of PCBM–inert polymer blends for such a device. The electron mobility of a 90% PCBM–10% PClS blend was 3.5×10−3cm2/Vs in a field-effect transistor. The diodes showed a rectification ratio of 2.0×103 at ±2.0V with a forward bias current density as high as 340μA/cm2 at 2.0V in the dark. Irradiation with various light sources (0.013–291mW/cm2) under ambient atmosphere generated a linear increase in photocurrent. Photodiodes with thinner active layers showed larger photocurrent and relative photoresponse, probably because of lower series resistance and lower recombination probability. The reverse bias response was less dependent on device area than the forward bias response. Photocurrents from multiple devices in parallel were additive as expected. The results demonstrate a simple fabrication route to light detectors compatible with solution processes and flexible substrates.

Code reordering using local random extraction and insertion (LREI) operator for GPGPU-based track-before-detect systems

Track-before-detect (TBD) algorithms are used for tracking systems, where the object's signal is below the noise floor (low-SNR objects). A lot of computations and memory transfers for real-time signal processing are necessary. GPGPU in parallel processing devices for TBD algorithms is well suited. Finding optimal or suboptimal code, due to lack of documentation for low-level programming of GPGPUs is not possible. High-level code optimization is necessary and the evolutionary approach, based on the single parent and single child is considered, that is local search approach. Brute force search technique is not feasible, because there are N! code variants, where N is the number of motion vectors components. The proposed evolutionary operator--LREI (local random extraction and insertion) allows source code reordering for the reduction of computation time due to better organization of memory transfer and the texture cache content. The starting point, based on the sorting and the minimal execution time metric is proposed. The unbiased random and biased sorting techniques are compared using experimental approach. Tests shows significant improvements of the computation speed, about 8 % over the conventional code for CUDA code. The time period of optimization for the sample code is about 1 h (1,000 iterations) for the considered recursive spatio-temporal TBD algorithm.

Efficient Sparse Matrix Algorithm to Speed Up the Calculation of the Ladder Term in Coupled Cluster Programs.

A new algorithm is presented for the calculation of the ladder-type term of the coupled cluster singles and doubles (CCSD) equations using two-electron integrals in atomic orbital (AO) basis. The method is based on an orbital grouping scheme, which results in an optimal partitioning of the AO integral matrix into sparse and dense blocks allowing efficient matrix multiplication. Carefully chosen numerical tests have been performed to analyze the performance of all aspects of the new algorithm. It is shown that the suggested scheme allows an efficient utilization of modern highly parallel architectures and devices in CCSD calculations. Details of the implementation in the development version of CFOUR quantum chemical program package are also presented.

Maximizing Parallel Testing in an FM Receiver

High volume production environments create great challenges for production testing and verification of Radio Frequency (RF) devices. In this environment, much emphasis is put on parallel testing, or the ability to test multiple devices at the same time using a single tester. In order for this parallelism to become a reality, there is a need for production RF tests to be simplified and reduced to requiring only the simplest test stimulus and analysis. In this paper, we present a new method of measuring the performance of a Frequency Modulation (FM) receiver that requires only a continuous wave signal input in order to eliminate the more costly Signal-to-Noise Ratio test. Using this new technique we will then demonstrate how simplifying this test and adding frequency diversity enables testing of up to 8 devices in parallel using a single tester.

A high density of vertically-oriented graphenes for use in electric double layer capacitors

The growth, capacitance and frequency response of vertically-oriented graphenes grown by radio frequency plasma-enhanced chemical vapor deposition on nickel substrates and used as electrodes in electric double layer capacitors (EDLCs) are presented. The graphenes grown on the grain boundary of substrates show a faster growth rate, but less ordered structure than in the center of the nickel grain. At a few nanometers away from the grain boundaries the graphenes grow vertically at the rate of 70–80nm per minute. The film height increased linearly with growth time from 700nm (10min sample) to 3.1μm (40min sample). Raman spectra show that the intensity ratio of the D band to G band gradually decreased with growth time to a value of 0.5, indicating that the crystalline order of the graphene increases with height. The specific capacitance of symmetric, parallel plate EDLC devices fabricated with these films was found to increase in a linear fashion with growth time up to values greater than 120μF/cm2 at 1kHz. An impedance phase angle of −45° was reached at 30kHz. Specific capacitance normalized to growth height suggests that mechanisms other than double layer charge storage on planar surface area were operative.

Platform independent, efficient implementation of the Ising Model on parallel acceleration devices

In this paper we present a versatile and scalable simulation code for the two- and three dimensional Ising model which can be used across different parallel acceleration frameworks (CUDA, OpenCL, OpenMP, MPI).

Non-deterministic cellular automata and languages

We summarize results on non-deterministic cellular language acceptors. The non-determinism is regarded as limited resource. For parallel devices, it is natural to bound the non-determinism in time and/or space. Depending on the length of the input, the number of allowed non-deterministic state transitions as well as the number of non-deterministic cells at all is limited. We centre our attention to real-time, linear-time, and unrestricted-time computations and discuss the computational power of these machines. Speed-up results and the possibility to reduce the non-determinism as well as closure properties of languages acceptable with a constant number of non-deterministic transitions are presented. By considering the relations with context-free languages, several relations between the devices in question are implied. We do not prove these results but we merely draw attention to the big picture and some of the main ideas involved, and open problems for further research.

Design and fabrication of densely integrated silicon quantum dots using a VLSI compatible hydrogen silsesquioxane electron beam lithography process

► Fabricated smallest high density Si double quantum dot transistors using HSQ resist. ► E-Beam lithography gave reproducible device dimensions down to 25 nm. ► Eighty percent of the fabricated devices had dimensional variations of less than 5 nm. ► Our fabrication process can realise up to 144 scalable devices in parallel. ► This approach is compatible with very large scale integration. Hydrogen silsesquioxane (HSQ) is a high resolution negative-tone electron beam resist allowing for direct transfer of nanostructures into silicon-on-insulator. Using this resist for electron beam lithography, we fabricate high density lithographically defined Silicon double quantum dot (QD) transistors. We show that our approach is compatible with very large scale integration, allowing for parallel fabrication of up to 144 scalable devices. HSQ process optimisation allowed for realisation of reproducible QD dimensions of 50 nm and tunnel junction down to 25 nm. We observed that 80% of the fabricated devices had dimensional variations of less than 5 nm. These are the smallest high density double QD transistors achieved to date. Single electron simulations combined with preliminary electrical characterisations justify the reliability of our device and process.

A multilevel fault model for integrated parallel fault‐tolerant systems

SUMMARYThe appearance of multithreaded, multicore, and manycore systems has led to a performance leap. Such systems are denoted as integrated, when there are electrical and physical dependencies between different functional units, that is, multiple cores integrated on a single die. Typically, such systems have a common, shared interface to the outside world, bearing the potential of a single point of failure. In this work, several questions concerning fault propagation shall be tackled. First, if one component within a core fails, how likely is a faulty behavior of other components on the same or other cores? Second, what is the overall reliability of such a system? It is important to answer these questions prior to an implementation, because the total costs of a reliable product shall be as small as possible. Our approach combines different abstraction levels in one multilevel fault model. The first stage is the physical level, covering the physical effects of a fault. Validation on this level can be omitted, if the modeling is precise enough. The second stage is a component and routing model where current is represented as logic value. The last level is the behavioral modeling of components by finite state machines. Because of the different number and nature of existing parallel systems, a theoretical approach is followed. The model can cover the whole range of parallel devices from field programmable gate arrays to multicore CPUs and manycore graphics processing units. Therefore, it can help to improve the reliability of current and future parallel fault‐tolerant systems by identifying the underlying bottlenecks. The function of the model is exemplarily shown by applying it to a field programmable gate array, identifying switchboxes as the main reliability bottleneck. Copyright © 2012 John Wiley & Sons, Ltd.

BarraCUDA - a fast short read sequence aligner using graphics processing units

BackgroundWith 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.FindingsUsing 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.ConclusionsBarraCUDA 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

Productivity of GPUs under different programming paradigms

SUMMARYGraphical processing units have been gaining rising attention because of their high performance processing capabilities for many scientific and engineering applications. However, programming such highly parallel devices requires adequate programming tools. Many such programming tools have emerged and hold the promise for high levels of performance. Some of such tools may require specialized parallel programming skills, while others attempt to target the domain scientist. The costs versus the benefits out of such tools are often unclear. In this work we examine the use of several of these programming tools such as Compute Unified Device Architecture, Open Compute Language, Portland Group Inc., and MATLAB in developing kernels from the (NAS) NASA Advanced Supercomputing parallel benchmarking suite. The resulting performance as well as the needed programmers' efforts were quantified and used to characterize the productivity of graphical processing units using these different programming paradigms. Copyright © 2011 John Wiley & Sons, Ltd.

Enhanced single-photon emission from a diamond–silver aperture

We have developed a scalable method for coupling single color centers in diamond to plasmonic resonators and demonstrated Purcell enhancement of the single photon emission rate of nitrogen-vacancy (NV) centers. Our structures consist of single nitrogen-vacancy (NV) center-containing diamond nanoposts embedded in a thin silver film. We have utilized the strong plasmon resonances in the diamond-silver apertures to enhance the spontaneous emission of the enclosed dipole. The devices were realized by a combination of ion implantation and top-down nanofabrication techniques, which have enabled deterministic coupling between single NV centers and the plasmonic modes for multiple devices in parallel. The plasmon-enhanced NV centers exhibited over six-fold improvements in spontaneous emission rate in comparison to bare nanoposts and up to a factor of 3.6 in radiative lifetime reduction over bulk samples, with comparable increases in photon counts. The hybrid diamond-plasmon system presented here could provide a stable platform for the implementation of diamond-based quantum information processing and magnetometry schemes.

Title: Using Alignment and 2D Network Simulations to Study Charge Transport Through Doped ZnO Nanowire Thin Film Electrodes

AbstractFactors affecting charge transport through ZnO nanowire mat films were studied by aligning ZnO nanowires on substrates and coupling experimental measurements with 2D nanowire network simulations. Gallium doped ZnO nanowires were aligned on thermally oxidized silicon wafer by shearing a nanowire dispersion in ethanol. Sheet resistances of nanowire thin films that had current flowing parallel to nanowire alignment direction were compared to thin films that had current flowing perpendicular to nanowire alignment direction. Perpendicular devices showed ∼5 fold greater sheet resistance than parallel devices supporting the hypothesis that aligning nanowires would increase conductivity of ZnO nanowire electrodes. 2‐D nanowire network simulations of thin films showed that the device sheet resistance was dominated by inter‐wire contact resistance. For a given resistivity of ZnO nanowires, the thin film electrodes would have the lowest possible sheet resistance if the inter‐wire contact resistance was one order of magnitude lower than the single nanowire resistance. Simulations suggest that the conductivity of such thin film devices could be further enhanced by using longer nanowires.

Novel Electronic Devices in Macroporous Silicon: Design of FET Transistors for Power Applications

In this paper, we study the application of macroporous silicon (MpSi) to the fabrication of transistors: Four different FET transistor structures are proposed using MpSi as the base material. These devices have been studied by simulation, and their characteristics are shown herein. The proposed structures include JFET, MOSFET, and trio de-like devices; in this study, we have considered both vertical and horizontal structures. For the vertical case, the proposed devices use the MpSi tubes to create the channel, filling them with a semiconductor and using the bulk silicon as a cylindrical gate all around. In contrast, for the horizontal transistors, the MpSi structure is used as the channel medium, while the conductor-filled pores serve as the controlling gate, thus obtaining a trio de-like device. The use of MpSi allows one to obtain large transistor arrays of extremely high density, thus obtaining a large amount of parallel devices in a moderate-to-small device area. Even more, pore engineering introduces a degree of freedom in the design of the transistor characteristics. We show that the proposed devices have a low threshold voltage and can support large currents. Finally, the behavior of these structures is studied for different geometries.

“DNA-Dressed NAnopore” for complementary sequence detection

Single molecule electrical sensing with nanopores is a rapidly developing field with potential revolutionary effects on bioanalytics and diagnostics. The recent success of this technology is in the simplicity of its working principle, which exploits the conductance modulations induced by the electrophoretic translocation of molecules through a nanometric channel. Initially proposed as fast and powerful tools for molecular stochastic sensing, nanopores find now application in a range of different domains, thanks to the possibility of finely tuning their surface properties, thus introducing artificial binding and recognition sites. Here we show the results of DNA translocation and hybridization experiments at the single molecule level by a novel class of selective biosensor devices that we call “DNA-Dressed NAnopore” (DNA2), based on solid state nanopore with large initial dimensions, resized and activated by functionalization with DNA molecules. The presented data demonstrate the ability of the DNA2 to selectively detect complementary target sequences, that is to distinguish between molecules depending on their affinity to the functionalization. The DNA2 can thus constitute the basis for the design of integrable parallel devices for mutation DNA analysis, diagnostics and bioanalytic investigations.

Accelerating the Fourier split operator method via graphics processing units

Current generations of graphics processing units have turned into highly parallel devices with general computing capabilities. Thus, graphics processing units may be utilized, for example, to solve time dependent partial differential equations by the Fourier split operator method. In this contribution, we demonstrate that graphics processing units are capable to calculate fast Fourier transforms much more efficiently than traditional central processing units. Thus, graphics processing units render efficient implementations of the Fourier split operator method possible. Performance gains of more than an order of magnitude as compared to implementations for traditional central processing units are reached in the solution of the time dependent Schrödinger equation and the time dependent Dirac equation.

Special Section Guest Editorial: Integrated Optics

The first demonstration of the laser in May 19601 opened the way to the development of lightwave technology. Almost 20 years later, the production of very-low-loss optical fibers2 made guided-wave optical communication systems a reality. One of the problems associated with the development of longhaul systems was obviously related to the introduction in the transmission line of a number of repeaters, able to recondition and to reamplify the optical signal. The solution offered by conventional optics was unsatisfactory, due to the size and electrical power consumption, as well as to the critical effects of temperature variations, mechanical vibrations, and the presence of moisture. Similar problems existed for signal distribution to end users, which required a very large number of splitters and switches. The alternative first suggested by S. E. Miller, a researcher at Bell Laboratories, was to miniaturize the repeater, integrate all the components onto a single chip, and interconnect them via optical waveguides: the concept of integrated optics was born.3 Technology of materials and devices has progressed a great deal since then, and terminology has also slightly changed: it is now common to speak about integrated optoelectronics or integrated photonics rather than integrated optics. The basic aim, however, has not changed with time: to integrate as many optical and electronic functions as possible into a chip as small as possible. One of the most complex photonic integrated circuits (PICs) reported to date is an InP monolithic tunable optical router with 8 input and 8 output ports, capable of 40 Gb/s operation per port.4 The size of this PIC is 4.25 × 14.5 mm, and it includes more than 200 functional elements integrated on-chip. In recent years, besides the telecommunications applications, a continuously growing interest has been focused on the field of integrated optical sensors, especially for biomedical sensing. Hot topics in this area concern, for instance: (i) the integration of surface plasmon resonance (SPR) sensors in a waveguide configuration (waveguide-based SPR sensors can accommodate several sensing elements on a single platform, thus allowing us the development of highly integrated, multichannel, and robust sensing devices); see, for instance, Ref. 5; (ii) the integration of high-Q microresonators with optofluidics for ultrasensitive spectroscopic measurements (which could enable miniaturized, low-cost, fully automated, and massively parallel devices for lab-on-a-chip applications); see, for instance, Ref. 6; and (iii) the combination of ultrahigh-Q whispering gallery mode microresonators with optical waveguides for the implementation of very sensitive biosensors; see, for instance, Ref. 7. Several books8–13 and a huge number of papers on this subject have been published in the 40 years since the seminal paper by P. K. Tien in 1971, which described not only the physics of guided waves in thin films and the prismcoupling method, but also some very early nonlinear optical phenomena in integrated optics.14 An early 2011 search of the SPIE Digital Library on the term “integrated optics” within Abstract/Title/Keyword produced about 2000 papers; of those, more than 10% were published in Optical Engineering. A similar search on the ISI Web of Knowledge produced 3810 journal articles and 3655 proceedings papers. The histogram in Fig. 1 shows the publication rate in the last 20 years; it appears evident that the number of publications on integrated optics stayed high and almost constant, on the order of 500 per year, in the last 7 to 8 years, thus testifying to the continuous importance of this RD the paper by Tervonen et al. presents a comprehensive review of this process, while Hassanzadeh and Mittler discuss the optimization of a two-step ion exchange (K+ –Na+ followed by an Ag+ – Na+ ) for producing low-loss waveguides with high surface refractive indices. In some glasses, however, ion exchange is not effective, and other waveguide fabrication techniques

Flexible ZnO–Cellulose Nanocomposite for Multisource Energy Conversion

Materials with the ability to harness multiple sources of energy from the ambient environment could lead to new types of energy-harvesting systems. It is demonstrated that nanocomposite films consisting of zinc oxide nanostructures embedded in a common paper matrix can be directly used as energy-conversion devices to transform mechanical and thermal energies to electric power. These mechanically robust and flexible devices can be fabricated over large areas and are capable of producing an output voltage and power up to 80 mV and 50 nW cm(-2) , respectively. Furthermore, it is shown that by integrating a certain number of devices (in series and parallel) the output voltage and the concomitant output power can be significantly increased. Also, the output voltage and power can be enhanced by scaling the size of the device. This multisource energy-harvesting system based on ZnO nanostructures embedded in a flexible paper matrix provides a simplified and cost-effective platform for capturing trace amounts of energy for practical applications.

Scaling deterministic lateral displacement arrays for high throughput and dilution-free enrichment of leukocytes

A disposable device for fractionation of blood into its components that is simple to operate and provides throughput of greater than 1 mL min−1 is highly sought after in medical diagnostics and therapies. This paper describes a device with parallel deterministic lateral displacement devices for enrichment of leukocytes from blood. We show capture of 98% and approximately ten-fold enrichment of leukocytes in whole blood. We demonstrate scaling up through the integration of six parallel devices to achieve a flow rate of 115 µL of undiluted blood per minute per atmosphere of applied pressure.