Fourier spectrum based extraction of an equivalent trap state density in indium gallium zinc oxide transistors

Segregating the dynamics of gate bias induced threshold voltage shift, and in particular, charge trapping in thin film transistors (TFTs) based on time constants provides insight into the different mechanisms underlying TFTs instability. In this Letter we develop a representation of the time constants and model the magnitude of charge trapped in the form of an equivalent density of created trap states. This representation is extracted from the Fourier spectrum of the dynamics of charge trapping. Using amorphous In-Ga-Zn-O TFTs as an example, the charge trapping was modeled within an energy range of Delta E-t approximate to 0.3 eV and with a density of state distribution as D-t(Et-j) = D-t0 exp(-Delta E-t/kT) with D-t0 = 5.02 x 10(11) cm(-2) eV(-1). Such a model is useful for developing simulation tools for circuit design. (C) 2014 AIP Publishing LLC.

Efficient Adaptive Mesh Refinement for MoM-based Package-Board 3D Full-wave Extraction

The accurate solution of 3D full-wave Method of Moments (MoM) on an arbitrary mesh of a package-board structure does not guarantee accuracy, since the discretizations may not be fine enough to capture rapid spatial changes in the solution variable. At the same time, uniform over-meshing on the entire structure generates large number of solution variables and therefore requires an unnecessarily large matrix solution. In this work, a suitable refinement criterion for MoM based electromagnetic package-board extraction is proposed and the advantages of the adaptive strategy are demonstrated from both accuracy and speed perspectives.

Hardware Accelerator for 3D Method of Moments based Parasitic Extraction

A Field Programmable Gate Array (FPGA) based hardware accelerator for multi-conductor parasitic capacitance extraction, using Method of Moments (MoM), is presented in this paper. Due to the prohibitive cost of solving a dense algebraic system formed by MoM, linear complexity fast solver algorithms have been developed in the past to expedite the matrix-vector product computation in a Krylov sub-space based iterative solver framework. However, as the number of conductors in a system increases leading to a corresponding increase in the number of right-hand-side (RHS) vectors, the computational cost for multiple matrix-vector products present a time bottleneck, especially for ill-conditioned system matrices. In this work, an FPGA based hardware implementation is proposed to parallelize the iterative matrix solution for multiple RHS vectors in a low-rank compression based fast solver scheme. The method is applied to accelerate electrostatic parasitic capacitance extraction of multiple conductors in a Ball Grid Array (BGA) package. Speed-ups up to 13x over equivalent software implementation on an Intel Core i5 processor for dense matrix-vector products and 12x for QR compressed matrix-vector products is achieved using a Virtex-6 XC6VLX240T FPGA on Xilinx's ML605 board.

GPU-based normalized cuts for road extraction using satellite imagery

This paper presents a GPU implementation of normalized cuts for road extraction problem using panchromatic satellite imagery. The roads have been extracted in three stages namely pre-processing, image segmentation and post-processing. Initially, the image is pre-processed to improve the tolerance by reducing the clutter (that mostly represents the buildings, vegetation,. and fallow regions). The road regions are then extracted using the normalized cuts algorithm. Normalized cuts algorithm is a graph-based partitioning `approach whose focus lies in extracting the global impression (perceptual grouping) of an image rather than local features. For the segmented image, post-processing is carried out using morphological operations - erosion and dilation. Finally, the road extracted image is overlaid on the original image. Here, a GPGPU (General Purpose Graphical Processing Unit) approach has been adopted to implement the same algorithm on the GPU for fast processing. A performance comparison of this proposed GPU implementation of normalized cuts algorithm with the earlier algorithm (CPU implementation) is presented. From the results, we conclude that the computational improvement in terms of time as the size of image increases for the proposed GPU implementation of normalized cuts. Also, a qualitative and quantitative assessment of the segmentation results has been projected.

Lactoylglutathione lyase, a critical enzyme in methylglyoxal detoxification, contributes to survival of Salmonella in the nutrient rich environment

Glyoxalase I which is synonymously known as lactoylglutathione lyase is a critical enzyme in methylglyoxal (MG) detoxification. We assessed the STM3117 encoded lactoylglutathione lyase (Lgl) of Salmonella Typhimurium, which is known to function as a virulence factor, due in part to its ability to detoxify methylglyoxal. We found that STM3117 encoded Lgl isomerises the hemithioacetal adduct of MG and glutathione (GSH) into S-lactoylglutathione. Lgl was observed to be an outer membrane bound protein with maximum expression at the exponential growth phase. The deletion mutant of S. Typhimurium (lgl) exhibited a notable growth inhibition coupled with oxidative DNA damage and membrane disruptions, in accordance with the growth arrest phenomenon associated with typical glyoxalase I deletion. However, growth in glucose minimal medium did not result in any inhibition. Endogenous expression of recombinant Lgl in serovar Typhi led to an increased resistance and growth in presence of external MG. Being a metalloprotein, Lgl was found to get activated maximally by Co2+ ion followed by Ni2+, while Zn2+ did not activate the enzyme and this could be attributed to the geometry of the particular protein-metal complex attained in the catalytically active state. Our results offer an insight on the pivotal role of the virulence associated and horizontally acquired STM3117 gene in non-typhoidal serovars with direct correlation of its activity in lending survival advantage to Salmonella spp.

Adaptive Mesh Refinement for Fast Convergence of EFIE-Based 3-D Extraction

3-D full-wave method of moments (MoM) based electromagnetic analysis is a popular means toward accurate solution of Maxwell's equations. The time and memory bottlenecks associated with such a solution have been addressed over the last two decades by linear complexity fast solver algorithms. However, the accurate solution of 3-D full-wave MoM on an arbitrary mesh of a package-board structure does not guarantee accuracy, since the discretization may not be fine enough to capture spatial changes in the solution variable. At the same time, uniform over-meshing on the entire structure generates a large number of solution variables and therefore requires an unnecessarily large matrix solution. In this paper, different refinement criteria are studied in an adaptive mesh refinement platform. Consequently, the most suitable conductor mesh refinement criterion for MoM-based electromagnetic package-board extraction is identified and the advantages of this adaptive strategy are demonstrated from both accuracy and speed perspectives. The results are also compared with those of the recently reported integral equation-based h-refinement strategy. Finally, a new methodology to expedite each adaptive refinement pass is proposed.

CHEXVIS: a tool for molecular channel extraction and visualization

Background: Understanding channel structures that lead to active sites or traverse the molecule is important in the study of molecular functions such as ion, ligand, and small molecule transport. Efficient methods for extracting, storing, and analyzing protein channels are required to support such studies. Further, there is a need for an integrated framework that supports computation of the channels, interactive exploration of their structure, and detailed visual analysis of their properties. Results: We describe a method for molecular channel extraction based on the alpha complex representation. The method computes geometrically feasible channels, stores both the volume occupied by the channel and its centerline in a unified representation, and reports significant channels. The representation also supports efficient computation of channel profiles that help understand channel properties. We describe methods for effective visualization of the channels and their profiles. These methods and the visual analysis framework are implemented in a software tool, CHEXVIS. We apply the method on a number of known channel containing proteins to extract pore features. Results from these experiments on several proteins show that CHEXVIS performance is comparable to, and in some cases, better than existing channel extraction techniques. Using several case studies, we demonstrate how CHEXVIS can be used to study channels, extract their properties and gain insights into molecular function. Conclusion: CHEXVIS supports the visual exploration of multiple channels together with their geometric and physico-chemical properties thereby enabling the understanding of the basic biology of transport through protein channels. The CHEXVIS web-server is freely available at http://vgl.serc.iisc.ernet.in/chexvis/. The web-server is supported on all modern browsers with latest Java plug-in.

Accelerating method of moments based package-board 3D parasitic extraction using FPGA

In this article, a Field Programmable Gate Array (FPGA)-based hardware accelerator for 3D electromagnetic extraction, using Method of Moments (MoM) is presented. As the number of nets or ports in a system increases, leading to a corresponding increase in the number of right-hand-side (RHS) vectors, the computational cost for multiple matrix-vector products presents a time bottleneck in a linear-complexity fast solver framework. In this work, an FPGA-based hardware implementation is proposed toward a two-level parallelization scheme: (i) matrix level parallelization for single RHS and (ii) pipelining for multiple-RHS. The method is applied to accelerate electrostatic parasitic capacitance extraction of multiple nets in a Ball Grid Array (BGA) package. The acceleration is shown to be linearly scalable with FPGA resources and speed-ups over 10x against equivalent software implementation on a 2.4GHz Intel Core i5 processor is achieved using a Virtex-6 XC6VLX240T FPGA on Xilinx's ML605 board with the implemented design operating at 200MHz clock frequency. (c) 2016 Wiley Periodicals, Inc. Microwave Opt Technol Lett 58:776-783, 2016

Cumulative Impulse Strength for Epoch Extraction

Algorithms for extracting epochs or glottal closure instants (GCIs) from voiced speech typically fall into two categories: i) ones which operate on linear prediction residual (LPR) and ii) those which operate directly on the speech signal. While the former class of algorithms (such as YAGA and DPI) tend to be more accurate, the latter ones (such as ZFR and SEDREAMS) tend to be more noise-robust. In this letter, a temporal measure termed the cumulative impulse strength is proposed for locating the impulses in a quasi-periodic impulse-sequence embedded in noise. Subsequently, it is applied for detecting the GCIs from the inverted integrated LPR using a recursive algorithm. Experiments on two large corpora of speech with simultaneous electroglottographic recordings demonstrate that the proposed method is more robust to additive noise than the state-of-the-art algorithms, despite operating on the LPR.