http://hdl.handle.net/10027/1241 Mon, 20 May 2013 03:04:11 GMT 2013-05-20T03:04:11Z http://hdl.handle.net/10027/8610 High Performance Multiple Sequence Alignment System for Pyrosequencing Reads from Multiple Reference Genomes Saeed, Fahad; Perez-Rathke, Alan; Gwarnicki, Jaroslaw; Berger-Wolf, Tanya; Khokhar, Ashfaq Genome resequencing with short reads generated from pyrosequencing generally relies on mapping the short reads against a single reference genome. However, mapping of reads from multiple reference genomes is not possible using a pairwise mapping algorithm. In order to align the reads w.r.t each other and the reference genomes, existing multiple sequence alignment(MSA) methods cannot be used because they do not take into account the position of these short reads with respect to the genome, and are highly inefficient for large number of sequences. In this paper, we develop a highly scalable parallel algorithm based on domain decomposition, referred to as PPyro- Align, to align such large number of reads from single or multiple reference genomes. The proposed alignment algorithm accurately aligns the erroneous reads, and has been implemented on a cluster of workstations using MPI library. Experimental results for different problem sizes are analyzed in terms of execution time, quality of the alignments, and the ability of the algorithm to handle reads from multiple haplotypes. We report high quality multiple alignment of up to 0.5 million reads. The algorithm is shown to be highly scalable and exhibits superlinear speedups with increasing number of processors. NOTICE: this is the author’s version of a work that was accepted for publication in Journal of Parallel and Distributed Computing. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Journal of Parallel and Distributed Computing, Vol 72, Issue 1, (JAN 2012). DOI: 10.1016/j.jpdc.2011.08.001 Sun, 01 Jan 2012 06:00:00 GMT http://hdl.handle.net/10027/8610 2012-01-01T06:00:00Z http://hdl.handle.net/10027/8527 Piezoelectricity in wurtzite polar semiconductor nanowires: A theoretical study Sen, B.; Stroscio, M.; Dutta, M. By considering acoustic phonon mode displacements in nanowires, the piezoelectrically induced electric polarization vector and the associated potential are calculated. For the case of charge-free semiconductor nanowires, the piezo energies generated by strains applied in different directions are compared. For the directions considered, it is found that the maximum piezo energy in these nanowires is generated for strain applied in the vertical direction (i.e., along z-axis). Moreover, for these nanowires, energy generation in AlN and ZnO are found to be superior to GaN, just as expected based on past treatments of nanowires using phonons of bulk structures. (C) 2011 American Institute of Physics.[doi:10.1063/1.3603036] Copyright (2011) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in J. Appl. Phys. 110, 024506 (2011) and may be found at http://jap.aip.org/resource/1/japiau/v110/i2/p024506_s1?view=fulltext Fri, 15 Jul 2011 05:00:00 GMT http://hdl.handle.net/10027/8527 2011-07-15T05:00:00Z http://hdl.handle.net/10027/8519 Modeling and Simulation of Long‐Wave Infrared InAs/GaSb Strained Layer Superlattice Photodiodes with Different Passivants Banerjee, Koushik; Huang, Jun; Ghosh, Siddhartha Current-voltage characteristics of long-wave infrared (LWIR) InAs/GaSb strained layer superlattice photodiodes (cut-off wavelength ~10 μm), passivated with different surface passivants, have been modeled and simulated using ATLAS software from SILVACO. The simulated results are fitted to previous experimental results obtained on unpassivated devices and those passivated by silicon-dioxide (SiO2), silicon nitride (SixNy) and zinc sulfide (ZnS). Surface parameters in terms of surface recombination velocity, shunt resistance and interface trap density are extracted for different passivants. The performance of silicon-dioxide passivated diode is solely dominated by a shunt leakage path with a shunt resistance value of 0.56 Ω-cm2. Extracted electron and hole surface recombination velocities have values of 105 cm/s and 107 cm/s for unpassivated, 103 cm/s and 105 cm/s for SixNy passivated and 102 cm/s and 103 cm/s for ZnS passivated devices. Interface trap density follows a similar trend with values of 1015 cm-2, 8.5×1014 cm-2 and 1010 cm-2 for unpassivated, SixNy passivated and ZnS passivated devices respectively. The suitability and limitations of the simulation tool are discussed. NOTICE: this is the author’s version of a work that was accepted for publication in Infrared Physics and Technology. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Infrared Physics and Technology, Vol 54, Issue 6 , (NOV 2011) http://dx.doi.org/10.1016/j.infrared.2011.08.003 Tue, 01 Nov 2011 05:00:00 GMT http://hdl.handle.net/10027/8519 2011-11-01T05:00:00Z http://hdl.handle.net/10027/8470 Outage Analysis of Block-Fading Gaussian Interference Channels Weng, Yang; Tuninetti, Daniela This paper considers the asymptotic behavior of the outage probability of a two-source block-fading single-antenna Gaussian interference channel in the high-SNR regime by means of the diversity-multiplexing tradeoff. A general setting where the user rates and the average channel gains are not restricted to be symmetric is investigated. This asymmetric scenario allows to analyze networks with “mixed” interference, i.e., when different sources are at different distance from their intended destination, that are not possible under the commonly used symmetric assumption. Inner and outer bounds for the diversity are derived. The outer bound is based on the recent “to within one bit” capacity result of Etkin et al. for the unfaded Gaussian channel and is a re-derivation of a known bound for which an error is pointed out. The inner bound is based on the Han and Kobayashi achievable region both without rate splitting and with a rate spitting inspired by the “to within one bit” capacity result. An analytical comparison of the diversity upper and lower bounds for a general channel seems difficult; by numerical evaluations, the two bounds are shown to coincide for a fairly large set of channel parameters. (c) 2011 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works. DOI: 10.1109/TIT.2011.2161957 Sat, 01 Oct 2011 05:00:00 GMT http://hdl.handle.net/10027/8470 2011-10-01T05:00:00Z