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Lattice Boltzmann algorithms for fluid turbulence

Lattice Boltzmann algorithms for fluid turbulence

department of Defense - HPCMP Users Group Conference 2007;High Performance Computing Modernization program: A Bridge to Future Defense, DoD HPCMP UGC

作者： Vahala, George Yepez, Jeffrey Soe, Min Vahala, Linda Ziegeler, Sean Department of Physics College of William and Mary Williamsburg VA United States Hanscom Field MA United States Department of Mathematics and Science Rogers State University Claremore OK United States Department of Electrical and Computer Engineering Old Dominion University Norfolk VA United States High Performance Computing Modernization Program Mississippi State University MS United States

ISBN: (纸本)0769530885

Lattice Boltzmann algorihms are a mesoscopic representation of nonlinear continuum physics (like Navier-Stokes, magnetohydrodynamics (MHD), Gross-Pitaevskii equations) which are ideal for parallel supercomputers because they transform the difficult nonlinear convective macroscopic derivatives into purely local moments of distribution functions. The macroscopic nonlinearities are recovered by relaxation distribution functions in the collision operator whose dependence on the macroscopic velocity is algebraically nonlinear and thus purely local. Unlike standard computational fluid dynamics codes, there is no loss in parallelization in handling arbitrary geometric boundaries, e.g., using bounce-back rules from kinetic theory. By encoding detailed balance into the collision operator through the introduction of discrete H-function, the lattice Boltzmann algorithm can be made unconditionally stable for arbitrary high Reynolds numbers. It is shown that this approach is a special case of a quantum lattice Boltzmann algorithm that entangles local qubits through unitary collision operators and which is ideally parallelized on quantum computer architectures. Here we consider turbulence simulations using 2,048 PEs on a 1,6003-spatial grid. A connection is found between the rate of change of enstrophy and the onset of laminar-to-turbulent flows. © 2007 IEEE.

关键词： Magnetohydrodynamics

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Using pitch, amplitude modulation, and spatial cues for separation of harmonic instruments from stereo music recordings

Eurasip Journal on Advances in Signal Processing

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Eurasip Journal on Advances in Signal Processing 2007年 2007卷

作者： Woodruff, John Pardo, Bryan Music Technology Program School of Music Northwestern University Evanston IL 60208 United States Department of Electrical Engineering and Computer Science Northwestern University Evanston IL 60208 United States

Recent work in blind source separation applied to anechoic mixtures of speech allows for improved reconstruction of sources that rarely overlap in a time-frequency representation. While the assumption that speech mixtures do not overlap significantly in time-frequency is reasonable, music mixtures rarely meet this constraint, requiring new approaches. We introduce a method that uses spatial cues from anechoic, stereo music recordings and assumptions regarding the structure of musical source signals to effectively separate mixtures of tonal music. We discuss existing techniques to create partial source signal estimates from regions of the mixture where source signals do not overlap significantly. We use these partial signals within a new demixing framework, in which we estimate harmonic masks for each source, allowing the determination of the number of active sources in important time-frequency frames of the mixture. We then propose a method for distributing energy from time-frequency frames of the mixture to multiple source signals. This allows dealing with mixtures that contain time-frequency frames in which multiple harmonic sources are active without requiring knowledge of source characteristics. Copyright © 2007 Hindawi Publishing Corporation. All rights reserved.

关键词： Harmonic generation

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New Insights in the Modification of the Work Function of Cathode Materials due to Thin Surface Coatings using Ab-initio Modelling

New Insights in the Modification of the Work Function of Cat...

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International Conference on Vacuum Electronics

作者： Vasilios Vlahos Dane D. Morgan John H. Booske University of Wisconsin Madison Madison WI USA 1415 Engineering Dr. Madison WI Department of Materials Science and Engineering University of Wisconsin Madison Madison WI USA Department of Materials Science and Engineering Department of Electrical and Computer Engineering University of Wisconsin-Madison Madison USA Interdisciplinary Materials Science Program

The changes in the work function upon adsorption of coating layers on materials utilized in both field and thermionic emission applications have been investigated computationally within the framework of Density Functional Theory (DFT) [1] as implemented by the Vienna Ab-initio Simulation Package (VASP) [2]. This approach provides valuable information for understanding the origin of the improvement in the emitted current density by monitoring changes in the electronic structure of a material system upon adsorption of surface species. The presence of surface coatings induces changes in the charge density in the surface and sub-surface regions of the substrate, significantly influencing the value of the work function. The origin of the enhanced emission properties of Cesium-Iodide (Csl) coated Carbon-based field emission cathodes [3] as well as Barium-Oxide (Ba-O) Tungsten thermionic cathode systems has been investigated. The former is a promising cathode material system capable of operating under low global electric fields, demonstrating operation lifetimes in excess of one million pulses, and characterized by good shot-to-shot-reproducibility, low levels of outgassing, and no evident plasma formation upon appropriate conditioning.

关键词： Cathodes Coatings Thermionic emission Density functional theory Computational modeling Electronic packaging thermal management Current density Monitoring Tungsten Plasma applications

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Intraoperative optical biopsy of breast cancer

Intraoperative optical biopsy of breast cancer

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Frontiers in Optics, FiO 2007

作者： Zysk, Adam M. Boppart, Stephen A. Department of Electrical and Computer Engineering 405 North Mathews Avenue Urbana IL 61801 United States Departments of Bioengineering and Internal Medicine 405 North Mathews Avenue Urbana IL 61801 United States Mills Breast Cancer Institute Carle Foundation Hospital Beckman Institute for Advanced Science Technology University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana IL 61801 United States

Optical coherence tomography (OCT) of breast tissue yields high-resolution optical biopsies that can be used to identify cancerous regions. We present intraoperative OCT studies of surgical margin scanning and biopsy ... 详细信息

ISBN: (纸本)1557528462

关键词： Optical tomography

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A systematic approach to quantifying evolutionary functional trends across the universal tree of life

A systematic approach to quantifying evolutionary functional...

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7th IEEE International Conference on Bioinformatics and bioengineering, BIBE

作者： Alterovitz, Gil Muso, Taro Malalur, Paresh Ramoni, Marco F. Division of Health Sciences and Technology Harvard Medical School Massachusetts Institute of Technology Boston MA United States Children's Hospital Informatics Program Boston MA United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA United States Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA United States

ISBN: (纸本)1424415098

The accumulation of genomic and proteomic data of many organisms presents an opportunity to analyze entire phylogenetic trees in a systematic, quantified manner. The universal tree of life, constructed by genomic data, provides an evolutionary context for proteomic data of individual organisms. Using proteomic information mapped to biological functions, we survey the tree of life for evolutionary trends, where trends are low p-value linear regressions of relative protein diversity against an evolutionary timeline. These trends provide quantified perspectives across evolution that would be otherwise difficult to discern from the large amount of available bioinformatic data. We analyzed 22,762 functions across 167 proteomes for approximately 3.8 million information content calculations. Of particular interest is the rise of protein-protein interactions along the path of mammalian evolution. Of general interest are the numerous uncovered trends that open the door to future queries of focused scope. ©2007 IEEE.

关键词： Information theory

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Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis (vol 69, pg 298, 2007)

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CHEMICAL BIOLOGY & DRUG DESIGN 2007年第6期69卷 455-455页

作者： Chellappan, S. Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute 9600 Gudelsky Drive Rockville MD 20850 USA Chemical Biology Program Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA Department of Chemistry Massachusetts Institute of Technology Cambridge MA 02139 USA Biological Engineering Division Department of Electrical Engineering & Computer Science Massachusetts Institute of Technology Cambridge MA 02139 USA *Correspondence: Michael K. Gilson *Correspondence: * Michael K. Gilson gilson@umbi.umd.edu http://gilsonlab.umbi.umd.edu[?][?]These authors contributed equally to this study.

There is a clinical need for HIV protease inhibitors that can evade resistance mutations. One possible approach to designing such inhibitors relies upon the crystallographic observation that the substrates of HIV protease occupy a rather constant region within the binding site. In particular, it has been hypothesized that inhibitors which lie within this region will tend to resist clinically relevant mutations. The present study offers the first prospective evaluation of this hypothesis, via computational design of inhibitors predicted to conform to the substrate envelope, followed by synthesis and evaluation against wild-type and mutant proteases, as well as structural studies of complexes of the designed inhibitors with HIV protease. The results support the utility of the substrate envelope hypothesis as a guide to the design of robust protease inhibitors.

关键词： AIDS crystal drug design inhibitor protease

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Automatic Classification of Whistles Produced by Indo-Pacific Humpback Dolphins (Sousa chinensis)

Automatic Classification of Whistles Produced by Indo-Pacifi...

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Oceans 2007 - Europe, vol.3

作者： Suranga Chandima Nanayakkara Mandar Chitre S. H. Ong Elizabeth Taylor Marine Mammal Research Laboratory Tropical Marine Science Institute National University of Singapore Singapore Acoustic Research Laboratory Tropical Marine Science Institute National University of Singapore Singapore Department of Electrical and Computer Engineering Division of Bioengineering National University of Singapore Singapore

ISBN: (纸本)9781424406340

A fast, robust technique is needed to facilitate studies of vocalisations by dolphins and other marine mammals such as whales in which large quantities of acoustic data are commonly generated. It is sometimes necessary to be able to describe whistle contours quantitatively, rather than simply looking at descriptors such as start frequency, maximum frequency, number of inflection points, etc. This is important when whistles are to be compared using an automated classification system, and is an essential component of a real-time, automated classification system for use with a raw data stream. In this paper we describe a rapid and robust high order polynomial curve fitting technique which extracts features in preparation for automated classification. We applied this method to classify natural vocalizations of Indo-Pacific humpback dolphins (Sousa chinensis). We believe the method will be widely applicable to bioacoustic studies involving FM acoustic signals in both underwater and in-air environments.

关键词： Feature extraction Whistle classification

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An information theoretic framework for ontology-based bioinformatics

An information theoretic framework for ontology-based bioinf...

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2007 Information Theory and Applications Workshop, ITA

作者： Alterovitz, Gil Xiang, Michael Ramoni, Marco F. Division of Health Sciences and Technology Harvard Medical School Massachusetts Institute of Technology Boston MA United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA United States Children's Hospital Informatics Program Boston MA United States Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA United States Department of Biology Massachusetts Institute of Technology Cambridge MA United States

ISBN: (纸本)9780615153148

With myriad information being generated from high-throughput experiments such as microarrays and sequencing technologies, an ever-increasing amount of data is being recorded and analyzed with the help of hierarchical ontologies, such as the Gene Ontology (GO). We have developed a novel framework-based on the well established foundations of information theory - that allows for the evaluation of new types of hypotheses. The framework, encapsulated in Open Biomedical Ontology-Based Exploration and Search (OBOES), has already been applied in the investigation of different kinds of questions. The resulting framework enables the new field of information theoretic ontology-based analysis. We have applied this framework to create methods to re-engineer ontologies, explore fundamental questions on the evolution of biological complexity, determine optimal ontology terms for bioinformatics analysis, and quantify the usefulness of biofluids as proxies for tissues/diseases. In each case, we found that our methods provide novel, significant findings. An open source Java implementation of OBOES is available at: http://***. net.

关键词： Information theory

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Towards building an experiential music visualizer

Towards building an experiential music visualizer

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International Conference on Information, Communications and Signal Processing

作者： Suranga Chandima Nanayakkara Elizabeth Taylor Lonce Wyse S.H. Ong Marine Mammal Research Laboratory Tropical Marine Science Institute National University of Singapore Singapore Communications and New Media Programme Faculty of Arts and Social Sciences National University of Singapore Singapore Department of Electrical and Computer Engineering Division of Bioengineering National University of Singapore Singapore

ISBN: (纸本)9781424409822

There have been many attempts to represent music using a wide variety of different music visualisation schemes. In this paper, we propose a novel system architecture which combines Max/MSPtrade with Flashtrade that can be used to build real-time music visualisations rapidly. In addition, we have used this proposed architecture to develop a music visualisation scheme that uses individual notes from a MIDI keyboard or from a standard MIDI file and creates novel displays that reflect pitch, note duration, characteristics such as how hard a key is struck, and which instruments are playing at any one time. The proposed music visualization scheme is a first step towards developing a music visualization that alone can provide a sense of musical experience to the user.

关键词： Visualization Music Instruments Art Data mining Real time systems Streaming media Displays Laboratories Biomedical engineering

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Intraoperative needle-based refractive index measurement of Ex Vivo human breast tissue

Intraoperative needle-based refractive index measurement of ...

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Frontiers in Optics, FiO 2007

作者： Zysk, Adam M. Marks, Daniel L. Nguyen, Freddy T. Kotynek, Jan G. Bellafiore, Frank J. Johnson, Patricia A. Rowland, Kendrith M. Boppart, Stephen A. Department of Electrical and Computer Engineering Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana IL 61801 United States Department of Chemistry Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana IL 61801 United States Departments of Bioengineering and Internal Medicine Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana IL 61801 United States Mills Breast Cancer Institute Carle Foundation Hospital Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana IL 61801 United States

Refractive index measurements offer high contrast between normal fatty tissue and diagnostically significant structures. We have developed a needle-based device capable of measuring internal tissue properties. We pres... 详细信息

ISBN: (纸本)1557528462

关键词： Needles

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