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21st International Symposium on High Performance computing Systems and Applications, HPCS 2007

作者： Ollivier-Gooch, Carl Diachin, Lori Freitag Shephard, Mark S. Tautges, Timothy Advanced Numerical Simulation Laboratory University of British Columbia Center for Applied Scientific Computing Lawrence Livermore National Laboratory Scientific Computing Research Center Rensselaer Polytechnic Institute Mathematics and Computer Science Division Argonne National Laboratory

ISBN: (纸本)0769528139

Software for numerical solution of partial differential equations requires accessing, manipulating, and often modifying information about the geometry of the computational domain, the mesh used for the simulation, and discrete data stored on that mesh. Typically, applications programmers would prefer to avoid the difficulty and complexity of creating their own modules for tasks like interacting with multiple geometric modelers, mesh adaptation, and optimization algorithms, rightly preferring instead to focus on the problem physics and on studying the physical results that the codeproduces. Ideally, these modules would be provided by experts in CAD modeling, meshing, and optimization, and written so that they can use the application's data regardless of the data structures used by the application. This paper describes a language- and data-structure-independent interface supporting query and modification of mesh data conforming to a general abstract data model. © 2007 IEEE.

关键词： Application programming interfaces (API)

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Improved evaluations of neutron-induced reactions on americium isotopes

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Nuclear Science and Engineering 2007年第1期155卷 84-95页

作者： Talou, P. Kawano, T. Young, P.G. Chadwick, M.B. MacFarlane, R.E. Los Alamos National Laboratory T-16 Nuclear Physics Group Los Alamos NM 87545 Los Alamos National Laboratory Advanced Simulation and Computing Program Los Alamos NM 87545 Commissariat à l'Energie Atomique-Cadarache St-Paul-lez-Durance 13108 Cedex France

The suite of neutron-induced reactions on 241Am, 242gAm, 242mAm, and 243Am has been evaluated for incident neutron energies above the unresolved resonance region and up to 20 MeV. Modern theoretical models and computational techniques were extensively used because of the rather limited experimental information. However, when available, experimental data were used to guide and benchmark the present evaluation work. All evaluation results were formatted and distributed as ENDF data files for possible inclusion in the ENDF/B-VII library.

关键词： Fission reactions

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A Language-Independent API for Unstructured Mesh Access and Manipulation

A Language-Independent API for Unstructured Mesh Access and ...

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IEEE International Symposium on High Performance computing Systems and Applications (HPCS)

作者： Carl Ollivier-Gooch Lori Freitag Diachin Mark S. Shephard Timothy Tautges Advanced Numerical Simulation Laboratory University of British Columbia Canada Lawrence Livermore National Laboratory Center for Applied Scientific Computing Scientific Computing Research Center Rensselaer Polytechnic Institute USA Argonne National Laboratory

Software for numerical solution of partial differential equations requires accessing, manipulating, and often modifying information about the geometry of the computational domain, the mesh used for the simulation, and discrete data stored on that mesh. Typically, applications programmers would prefer to avoid the difficulty and complexity of creating their own modules for tasks like interacting with multiple geometric modelers, mesh adaptation, and optimization algorithms, rightly preferring instead to focus on the problem physics and on studying the physical results that the code produces. Ideally, these modules would be provided by experts in CAD modeling, meshing, and optimization, and written so that they can use the application's data regardless of the data structures used by the application. This paper describes a language- and data-structure-independent interface supporting query and modification of mesh data conforming to a general abstract data model.

关键词： Solid modeling Partial differential equations Computational geometry Information geometry Computational modeling Application software Programming profession Adaptation model Physics Data structures

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Simultaneous estimation of optical flow and object state: A modified approach to optical flow calculation

Simultaneous estimation of optical flow and object state: A ...

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IEEE International Conference on Networking, Sensing and Control

作者： Pubudu N Pathirana Allan E.K. Lim John Carminati Malin Premaratne School of Engineering and Information Technology Deakin University Geelong Australia Advanced Computing and Simulation Laboratory (AXL) Department of Electrical and Computer Systems Monash University Clayton VIC Australia

Differential optical flow methods are widely used within the computer vision community. They are classified as being either local, as in the Lucas-Kanade method, or global, as in the Horn-Schunck technique. As the physical dynamics of an object is inherently coupled into the behavior of its image in the video stream, in this paper, we use such dynamic parameter information in calculating optical flow when tracking a moving object using a video stream. Indeed, we use a modified error function in the minimization that contains physical parameter information. Further, the refined estimates of optical flow is used for better estimation of the physical parameters of the object in the simultaneous estimation of optical flow and object state(SEOS).

关键词： Image motion analysis State estimation Optical sensors Optical filters Optical noise Parameter estimation Nonlinear optics Streaming media Optical fiber networks Computer vision

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simulation of a device concept for noninvasive sensing of blood glucose levels

Simulation of a device concept for noninvasive sensing of bl...

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International Conference on Information and Automation for Sustainability (ICIAfS)

作者： Chintha C. Handapangoda Malin Premaratne David M. Paganin Advanced Computing and Simulation Laboratory Department Electrical and Computer Systems Eng Monash University Clayton VIC Australia School of Physics Faculty of Science Monash University Clayton VIC Australia

ISBN: (纸本)9781424418992;9781424419005

This paper introduces a method of modeling noninvasive glucose sensing for patients who suffer from diabetes mellitus. The proposed technique involves simulation of light propagation through biological tissue with an embedded photonic crystal. The proposed detection technique is Raman spectroscopy and the use of the photonic crystal enables the enhancement of Raman scattering by engineering the photon density of states. Further enhancement can be achieved using noble metal clusters which result in surface enhanced Raman scattering and has the ability to provide enhancements of up to a million times.

关键词： Blood Sugar Photonic crystals Optical propagation Raman scattering Skin Maxwell equations Computational modeling Diabetes Australia

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Modeling of Light Propagation through Biological Tissues: A Novel Approach

Modeling of Light Propagation through Biological Tissues: A ...

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Frontiers in the Convergence of Bioscience and Information Technologies, FBIT

作者： Chintha C. Handapangoda Malin Premaratne Leslie Yeo James Friend Advanced Computing and Simulation Laboratory (AXL) Department of Electrical and Computer Systems Engineering Monash University Clayton VIC Australia Micro/Nanophysics Research Laboratory (MNRL) Department of Mechanical Engineering Monash University Clayton VIC Australia

An efficient numerical technique for modeling biological tissues using the radiative transfer equation is presented. Time dependence of the transient radiative transfer equation is approximated using Laguerre expansion. Azimuthal angle is discretized using the discrete ordinates method and the resulting set of ordinary differential equations is solved using the Runge-Kutta-Felhberg method.

关键词： Biological system modeling Optical propagation Biological tissues Equations Biology computing Laboratories Numerical models Azimuthal angle Optical scattering Cancer detection

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Gain modulation dynamics of a Raman amplified WDM system using time-division multiplexed pumps

Gain modulation dynamics of a Raman amplified WDM system usi...

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International Symposium on High Capacity Optical Networks and Enabling Technologies, HONET

作者： Vineetha Kalavally Malin Premaratne Tin Win Department of Electrical and Computer Systems Engineering School of Engineering Monash University Petaling Jaya Selangor Malaysia Department of Electrical and Computer Systems Engineering Advanced Computing and Simulation Laboratory Monash University Clayton Victoria Australia

ISBN: (纸本)9781424418282

The gain modulation characteristics of an 80 nm wide, counter-pumped distributed Raman amplified WDM system has been studied when the pumps are time division multiplexed. When many optical amplifiers are employed in multi-repeater transoceanic systems, the pump is intensity modulated to obtain information about the health of the repeaters. Gain modulation dynamics referring to dynamics of pump modulation transferred to the signal is studied to help make a reasonable choice of pump wavelength for modulation and to provide power compensation if necessary from the resulting power penalty. In this paper, we study using numerical modeling, the effect of time division multiplexed pumping on the gain modulation dynamics in a WDM system. It is found that modulation transfer response is flatter and stronger across the WDM channels when the Raman amplifier pumps are time division multiplexed. The resulting increase in power penalty is determined.

关键词： Gain Modulation Time division multiplexing Stimulated emission Wavelength division multiplexing Optical fiber amplifiers Intensity modulation

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The TSTT mesh interface

The TSTT mesh interface

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44th AIAA Aerospace Sciences Meeting 2006

作者： Ollivier-Gooch, Carl Chand, Kyle Dahlgren, Tamara Diachin, Lori Freitag Fix, Brian Kraftcheck, Jason Xiaolin, Li Seol, E. Seegyoung Shephard, Mark S. Tautges, Timothy Trease, Harold Advanced Numerical Simulation Laboratory University of British Columbia Center for Applied Scientific Computing Lawrence Livermore National Laboratory Dept. of Applied Mathematics and Statistics SUNY Stonybrook Parallel Computing Sciences Sandia National Laboratories Scientific Computation Research Center Rensselaer Polytechnic Institute Pacific Northwest National Laboratory

ISBN: (纸本)1563478072

PDE-based numerical simulation applications commonly use basic software infrastructure to manage mesh, geometry, and discretization data. The commonality of this infrastructure implies the software is theoretically amenable to re-use. However, the traditional reliance on library-based implementations of these functionalities hampers experimentation with different software instances that provide similar functionality. This is especially true for meshing and geometry libraries where applications often directly access the underlying data structures, which can be quite different from implementation to implementation. Thus, using different libraries interchangeably or interoperably for this functionality has proven difficult at best and has hampered the wide spread use of advanced meshing and geometry tools developed by the research community. To address these issues, the Terascale simulation Tools and Technologies center is working to develop standard interfaces to enable the creation of interoperable and interchangeable simulation tools. In this paper, we focus on a language-and data-structure-independent interface supporting query and modification of mesh data conforming to a general abstract data model. We describe the model and interface, and provide programming "best practices" recommendations based on early experience implementing and using the interface.

关键词： Software engineering

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A 55 TFLOPS simulation of amyloid-forming peptides from yeast prion Sup35 with the special-purpose computer system MDGRAPE-3

A 55 TFLOPS simulation of amyloid-forming peptides from yeas...

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2006 ACM/IEEE Conference on Supercomputing, SC'06

作者： Narumi, Tetsu Ohno, Yousuke Okimoto, Noriaki Koishi, Takahiro Suenaga, Atsushi Futatsugi, Noriyuki Yanai, Ryoko Himeno, Ryutaro Fujikawa, Shigenori Taiji, Makoto Ikei, Mitsuru Intel K.K. High Performance Molecular Simulation Team Genomic Sciences Center Innovative Nanopatterning Laboratory Topochemical Design Laboratory Frontier Research System Advanced Center for Computing and Communication Software and Solutions Group Parallel and Distributed Solutions Group

ISBN: (纸本)0769527000

We have achieved a sustained performance of 55 TFLOPS for molecular dynamics simulations of the amyloid fibril formation of peptides from the yeast Sup35 in an aqueous solution. For performing the calculations, we used the MDGRAPE-3 system - -a special-purpose computer system for molecular dynamics simulations. Its nominal peak performance was 415 TFLOPS for Coulomb force calculations;this is the highest-ever performance reported for classical molecular dynamics simulations. Amyloid fibril formation is known to be related to the occurrence of severe diseases such as Alzheimer's, Parkinson's, and Creutzfeldt-Jakob diseases. The Sup35 protein is a "yeast prion protein," which forms mini-crystals due to aggregation;it forms an effective platform for studying the formation process of amyloid fibrils. In these simulations, we first elucidate that the amyloid-forming peptides GNNQQNY aggregate at a higher frequency than non-amyloid-forming peptides SQNGNQQRG;further, the GNNQQNY peptides tend to form parallel two-stranded -sheets that would grow into a cross- amyloid nucleus. The results are consistent with those obtained experimentally. Furthermore, we could observe an early elongation of the amyloid nucleus. This result is expected to contribute toward a deeper understanding of the amyloid growth mechanism. © 2006 IEEE.

关键词： Peptides

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Challenges in Photonic System simulation

Challenges in Photonic System Simulation

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International Conference on Numerical simulation of Optoelectronic Devices, (NUSOD)

作者： Malin Premaratne Advanced Computing and Simulation Laboratory (AXL) Department of Electrical and Computer Systems Engineering Monash University Clayton VIC Australia

A comprehensive analysis on the requirements and challenges of next generation photonic system simulator technology for hybrid hierarchical optical networks is presented. Key challenges need to be met by simulator des... 详细信息

关键词： Optical fiber networks Optical design Traffic control Circuit simulation Computational modeling Telecommunication traffic Analytical models Electronics industry Optical sensors Image motion analysis

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