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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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Arm-Training with T-WREX After Chronic Stroke: Preliminary Results of a Randomized Controlled Trial

Arm-Training with T-WREX After Chronic Stroke: Preliminary R...

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IEEE International Conference on Rehabilitation Robotics (ICORR)

作者： Sarah J. Housman Vu Le Tariq Rahman Robert J. Sanchez David J. Reinkensmeyer Sensory Motor Performance Program Rehabilitation Institute of Chicago Chicago IL USA Department of Mechanical & Aerospace Engineering University of California Irvine Irvine CA USA Computer Science and Mechanical Engineering Departments University of Delaware Newark DE USA

This study presents preliminary results of a randomized controlled trial comparing a novel passive arm orthosis training system, the Therapy Wilmington Robotic Exoskeleton (T-WREX), with conventional self-directed upper extremity exercises. Chronic stroke survivors (n = 23) with moderate to severe upper limb hemiparesis trained three times per week for eight weeks with minimal supervision from an occupational therapist. Both groups demonstrated significant improvements in arm movement ability according to the Fugl-Meyer (3.7 point mean improvement in T-WREX group, p = 0.001, and 2.7 point improvement in control group, p = 0.003). Individuals who completed T-WREX training also demonstrated significant gains in self-rated quality of arm movement on the Motor Activity Log (p=0.05), and showed a trend towards greater gains on all clinical measures, although this trend was not significant at the current study size. Post-treatment surveys revealed a subjective preference for T-WREX training over conventional gravity-supported exercises. These preliminary results suggest that the T-WREX is a safe device feasible for clinical use, and effective in enhancing upper extremity motor recovery and patient motivation. Next steps are discussed.

关键词： Medical treatment Extremities Rehabilitation robotics Control systems Aerospace engineering Gravity Robots Exoskeletons Current measurement Gain measurement

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AC 2007-1771: Mentoring new faculty: How much, how often, and how?

AC 2007-1771: Mentoring new faculty: How much, how often, an...

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114th Annual ASEE Conference and Exposition, 2007

作者： Jackson, Andrew Chin, Robert Coddington, Charles Petersen, Paul Hamid, Fonooni East Carolina University United States Department of Technology Systems College of Technology and Computer Science East Carolina University United States East Carolina University Indiana State University Graduate Faculties United States EDGJ Department of Technology Systems East Carolina University United States Faculty Senate East Carolina University United States Department of Technology East Carolina University College of Technology and Computer Science United States Cleveland State University Fenn College of Engineering United States Department of Technology Systems Science Occupational Safety Program East Carolina University Greenville NC United States Academic Practice Specialty Educational Standards Committee Task Force ASSE

The Department of Technology Systems (TSYS) at East Carolina University has implemented a new faculty mentoring process to enable junior faculty members to learn from senior faculty members as they prepare for a career in academia. Five tenured professors and associate professors in the TSYS department have recently established a new process to mentor faculty members within the department who have begun not yet completed their initial tenure process at a major university. This process includes a series of workshops regarding academic performance expectations during the early stages of an academic career. Our commitment to new faculty takes on several related, yet distinct features. Examples of these initiatives include: 1) reduced workloads for new faculty for the first two years to enable them to generate individual and collaborative research activities, funded grants, and publications, 2) periodic university-wide training to learn policies and procedures that affect day-to-day activities on a college campus, 3) periodic workshops hosted by senior faculty mentors, and 4) one-on-one discussions between senior faculty members and junior faculty members to encourage candid dialogue between professional colleagues. Another feature of the mentorship philosophy is a proposal to the dean of the college to offer newly hired faculty a contractual start date of July 1steach year instead of starting their contract one week prior to the start of fall classes, normally in late August. This additional period of time will be used to train new faculty in essential policies and procedures, to complete a variety of administrative tasks on campus, to get a head start on preparing for classes in the fall, and cleaning up those supplemental tasks that accompany every move to a new location. The goal of this early commitment to new faculty is to reduce the stress associated with preparing for a new course, in a new environment, with a new set of operating procedures. This will also enab

关键词： engineering education

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A weighted k-nearest neighbor method for gene ontology based protein function prediction

A weighted k-nearest neighbor method for gene ontology based...

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2nd International Multi-Symposiums on computer and Computational sciences 2007, IMSCCS'07

作者： Kharsikar, Saket Mugler, Dale Sheffer, Daniel Moore, Francisco Duan, Zhong-Hui Department of Biomedical Engineering University of Akron Akron OH 44236 United States Department of Theoretical and Applied Mathematics University of Akron Akron OH 44236 United States Integrated Bioscience PhD Program University of Akron Akron OH 44236 United States Department of Biology University of Akron Akron OH 44236 United States Department of Computer Science University of Akron Akron OH 44236 United States

ISBN: (纸本)0769530397

Numerous genome projects have produced a large and ever increasing amount of genomic sequence data. However, the biological functions of many proteins encoded by the sequences remain unknown. Protein function annotation and prediction become an essential and challenging task of post-genomic research. In this paper, we present an automated protein function prediction system based on a set of proteins of known biological functions. The functions of the proteins are characterized with gene ontology (GO) annotations. The prediction system uses a novel measure to calculate the pair-wise overall similarity between protein sequences. The protein function prediction is performed based on the GO annotations of similar sequences using a weighted k-nearest neighbor method. We show the prediction accuracies obtained using the model organism yeast (Sacchyromyces cerevisiae). The results indicate that the weighted k-nearest neighbor method significantly outperforms the regular k-nearest neighbor method for protein molecular function prediction. © 2007 IEEE.

关键词： Proteins

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Molecular dynamic simulation of heat pulse propagation in multiwall carbon nanotubes

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Physical Review B 2007年第15期76卷 155424-155424页

作者： Taejin Kim Mohamed A. Osman Cecilia D. Richards David F. Bahr Robert F. Richard Material Science Program Washington State University Pullman Washington 99164-4620 USA Department of Physics Washington State University Pullman Washington 99164-2814 USA School of Electrical Engineering and Computer Science Washington State University Pullman Washington 99164-2752 USA School of Mechanical and Materials Engineering Washington State University Pullman Washington 99164-2920 USA

The propagation of heat pulses in zigzag and armchair double wall nanotubes (DWNTs) has been investigated using molecular dynamics simulations. It is found that the leading heat wave packets in zigzag (9,0)∕(18,0) and armchair (5,5)∕(10,10) DWNTs move with the speed of longitudinal acoustic (LA) phonon modes. The intensities of the leading heat wave packets in outer and inner shells in DWNTs were found to be five to seven times larger than that of the corresponding single wall nanotubes (SWNTs). The heat energy carried by the leading heat wave packets in zigzag DWNT was about four and five times more than those in armchair DWNT shells. Within the leading LA wave packet, the strain in the inner shell of the DWNTs is stronger than the strain in the outer shell and considerably larger than strain in the corresponding SWNTs. The regions with the largest strain coincide with the regions of high kinetic temperatures within the LA mode wave packets. The higher energy of the LA mode waves in DWNT shells compared to SWNT is attributed to the presence of higher strain fields in DWNTs compared to individual SWNTs. The higher strain in the inner shell of DWNT compared to the outer shell accounts for the three to five times higher kinetic energy of leading wave packets in inner shells compared to those in outer shells. The induced strain fields in zigzag DWNT are distributed over a wider region compared to armchair DWNT, and the strains in inner and outer shells of zigzag DWNT are out phase by 180°.

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Towards better utilization of NEXRAD data in hydrology: An overview of hydro-NEXRAD

Towards better utilization of NEXRAD data in hydrology: An o...

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作者： Krajewski, Witold F. Kruger, Anton Lawrence, Ramon Smith, James A. Bradley, A. Allen Steiner, Matthias Baeck, Mary Lynn Ramamurthy, Mohan K. Weber, Jeffrey DelGreco, Stephen A. Seo, Bong-Chul Domaszczynski, Piotr Gunyon, Charles Goska, Radoslaw IIHR-Hydroscience and Engineering University of Iowa Iowa IA 52242 United States Civil and Environmental Engineering Princeton University Princeton NJ 08544 United States Unidata Program Center UCAR Boulder CO 80307 United States National Center for Atmospheric Research UCAR Boulder CO 80307 United States National Climatic Data Center Ashville NC 28801 United States Computer Science University of British Columbia Okanagan BC V1V 1V7 Canada

ISBN: (纸本)9780784409275

With a very modest investment in computer hardware and the open source local data manger (LDM) software from UCAR's Unidata program Center, an individual researcher can receive a variety of NEXRAD Level III gridded rainfall products, and the unprocessed Level II data in real-time from most NEXRAD radars. Additionally, the National Climatic Data Center has vast archives of these products and Level II data. Still, significant obstacles remain in order to unlock the full potential of the data. One set of obstacles is related to effective management of multi-terrabyte data sets: storing, compressing, and backing up. A second set of obstacles, for hydrologists and hydrometeorologists in particular, is that the NEXRAD Level III products are not well suited for application in hydrology. There is a strong need for the generation of high-quality products directly from the Level II data with well-documented steps that include quality control, removal of false echoes, rainfall estimation algorithms with variety of corrections, coordinate conversion and georeferencing, conversion to a convenient data format(s), and integration with GIS. For hydrologists it is imperative that these procedures are basin-centered as opposed to radar-centered. Thirdly, the amount of data present in a multi-year, multi-radar dataset is such that simple cataloging and indexing of the data is not sufficient. Rather, sophisticated metadata extraction and management techniques are required. The authors describe and discuss the Hydro-NEXRAD software system that addresses the above three challenges. With support from the National science Foundation through its ITR program, the authors are developing a basin-centered framework for addressing all these issues in a comprehensive manner, tailored specifically for use of NEXRAD data in hydrology and hydrometeorology. Through a flexible web interface users can search a large metadata database base, managed by a relational database, for subsets of interest. Well

关键词： Open systems

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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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Contribution of engineering management and systems engineering concepts to engineering design

Contribution of engineering management and systems engineeri...

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114th Annual ASEE Conference and Exposition, 2007

作者： Sireli, Yesim Conrad, James Kane, Martin Skinner, Frank University of North Carolina Charlotte United States Engineering Management Program University of North Carolina Charlotte United States ASEE IEEE Engineering Management Society Decision Sciences Institute United States ASEM Korea Republic of Marketing Science Institute United States Honor Society of Phi Kappa Phi United States IEEE Eta Kappa Nu United States Project Management Institute United States IEEE Computer Society Department of Civil and Environmental Engineering University of North-Carolina Charlotte United States Eno ASCE ITE Sigma Xi United States Chi Epsilon Industrial Solutions Department of Mechanical Engineering and Engineering Science University of North Carolina Charlotte United States Robo-Tech. Systems Inc. GE Advanced Products Corp.

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In vivo fiber tracking in the rat brain on a clinical 3T MRI system using a high strength insert gradient coil

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NeuroImage 2007年第3期35卷 1077-1085页

作者： Mayer, Dirk Zahr, Natalie M. Adalsteinsson, Elfar Rutt, Brian Sullivan, Edith V. Pfefferbaum, Adolf Department of Radiology Stanford University School of Medicine Stanford CA United States Department of Psychiatry and Behavioral Sciences Stanford University School of Medicine Stanford CA United States Harvard-MIT Division of Health Sciences and Technology MIT Cambridge MA United States Department of Electrical Engineering and Computer Science MIT Cambridge MA United States Imaging Research Laboratories Robarts Research Institute London Ont. Canada Neuroscience Program SRI International Menlo Park CA 333 Ravenswood Avenue United States

In vivo neuroimaging methods permit longitudinal quantitative examination of the dynamic course of neurodegenerative conditions in humans and animal models and enable assessment of therapeutic efforts in mitigating disease effects on brain systems. The study of conditions affecting white matter, such as multiple sclerosis, demyelinating conditions, and drug and alcohol dependence, can be accomplished with diffusion tensor imaging (DTI), a technique uniquely capable of probing the microstructural integrity of white matter fibers in the living brain. We used a 3T clinical MR scanner equipped with an insert gradient coil that yields an order of magnitude increase in performance over the whole-body hardware to acquire in vivo DTI images of rat brain. The resolution allowed for fiber tracking evaluation of fractional anisotropy (FA) and apparent diffusion coefficients in the genu and splenium of the corpus callosum. A comparison of short (46 min) and long (92 min) acquisition time DTI protocols indicated low but adequate signal-to-noise ratio (SNR = 6.2) of the shorter protocol to conduct quantitative fiber tracking enhanced by multiple acquisitions. As observed in human studies, FA in the rat splenium was higher than in the genu. Advantages of this technology include the use of similar user interface, pulse sequences, and field strength for preclinical animal and clinical human research, enhancing translational capabilities. An additional benefit of scanning at lower field strength, such as 3 T, is the reduction of artifacts due to main field inhomogeneity relative to higher field animal systems. © 2007 Elsevier Inc. All rights reserved.

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Linking protein mass with function via organismal massome networks

Linking protein mass with function via organismal massome ne...

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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Alterovitz, Gil Lyashenko, Eugenia Xiang, Michael 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 at Health Sciences and Technology Harvard Medical School 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 Department of Biomedical Informatics Columbia University New York NY United States

ISBN: (纸本)1424415098

With the human genome sequenced, attention has been shifting to proteins and their function. Several technologies including mass spectrometry and gel electrophoresis have traditionally been used to study proteins. These technologies rely on proteins' masses to characterize and/or identify them. Once identified, the discovered proteins' are often analyzed for their functional relevance. In this paper, we present an alternative approach to studying protein function directly, based on protein mass. By analyzing proteins with similar mass ranges (bins), we discovered that certain biological functions are associated with specific mass bins more frequently than would be expected by chance. Biological functional classes found in this manner could be seen across the three examined organisms: human, worm and fly. We found no sequence-based homology across significant mass-function proteins in the three different organisms. This investigation leads to useful property that the mass-based biological functional classes are preserved across the organisms. Thus, this paper describes a potential constraint for evolution of similar function based on mass constraints. Finally, this work yields a roadmap for experimental design for functional exploration of proteomes in mass-based technologies such as gel electrophoresis and mass spectrometry. ©2007 IEEE.

关键词： Proteins

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