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International Conference on Intelligent Systems, Modelling and Simulation (ISMS)

作者： Arcot Rajasekar Reagan Moore Mike Wan Wayne Schroeder Adil Hasan Data Intensive Cyber Environments Center University of North Carolina Chapel Hill Chapel Hill NC USA Institute of Neural Computing University of California San Diego San Diego CA USA School of English University of Liverpool Liverpool UK

ISBN: (纸本)9781424459841;9780769539737

Large scientific projects need collaborative data sharing environments. For projects like the Ocean Observations Initiative (OOI), the Temporal Dynamics of Learning center (TDLC) and Large-scale Synoptic Survey Telescope (LSST) the amount of data collected will be on the order of Petabytes, stored across distributed heterogeneous resources under multiple administrative organizations. Policy-oriented data management is essential in such collaborations. The integrated Rule-Oriented data System (iRODS) is a peer-to-peer, federated server-client architecture that uses a distributed rule engine for data management to apply policies encoded as rules. The rules are triggered on data management events (ingestion, access, modifications, annotations, format conversion, etc) as well as periodically (to check integrity of the data collections, intelligent data archiving and placement, load balancing, etc). Rules are applied by system administrators (e.g. for resource creation, user management, etc.) and by individual users, groups and data providers to tailor the sharing and access of data for their own needs. In this paper, we will discuss the architecture of the iRODS middleware system and discuss some of the applications of the software.

关键词： Large-scale systems Collaboration Oceans Telescopes data systems Peer to peer computing Engines Load management Resource management Computer architecture

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Selecting Differentially Expressed Proteomic Markers from Mass Spectrometry data

Selecting Differentially Expressed Proteomic Markers from Ma...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Xuena Wang Wei Zhu J. Glimm Juan Li State University of New York Stony Brook NY USA Brookhaven National Laboratory Center for Data Intensive Computing Upton NY USA With Department of Psychiatry-Center for Brain Health School of Medicine New York University New York NY USA

High-throughput mass spectrometry and statistical analysis methodologies are promising technologies to aid the medical diagnostics field by detecting the cancer-related proteomic markers. We propose statistical methods to cull the potential markers by ranking them in relations to their power of separability distinguishing cancerous patients from normal persons or among different cancer stages. To assess the training variability, resampling via bootstrap strategy is adopted to select stable markers which show the potential of a large probability to classify specific groups. Selected marker pattern is validated by a combined classifier. Methods are demonstrated by a colon cancer dataset screened by SELDI technology

关键词： Proteomics Mass spectroscopy Statistical analysis Proteins Oncological surgery Medical diagnostic imaging Medical diagnosis Diseases Cancer detection Probability

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Tracked flame simulation for a type Ia supernova

Tracked flame simulation for a type Ia supernova

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3rd M.I.T. Conference on Computational Fluid and Solid Mechanics

作者： Zhang, Yongmin Glimm, James Dutta, Srabasti Department of Applied Mathematics and Statistics University at Stony Brook Stony Brook NY 11794 United States Center for Data Intensive Computing Brookhaven National Laboratory Upton NY 11793 United States

In this paper, we present a numerical model for a Type Ia supernova explosion. Our method is based on explicit tracking of the flame front, which is critically important to the accurate modeling of turbulent thermonuc... 详细信息

ISBN: (纸本)0080444814

关键词： Combustion

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Jet simulation in a diesel engine

Jet simulation in a diesel engine

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3rd M.I.T. Conference on Computational Fluid and Solid Mechanics

作者： Glimm, James Kim, M.N. Li, X.-L. Samulyak, R. Xu, Z.-L. Department of Applied Mathematics and Statistics University at Stony Brook Stony Brook NY 11794 United States Brookhaven National Laboratory Center for Data Intensive Computing Upton NY 11793 United States

ISBN: (纸本)0080444814

In this paper, we report a numerical study of the jet breakup and spray formation in a diesel engine by the Front Tracking method. We model a mixed vapor-liquid region through a heterogeneous model with dynamic vapor bubble insertion. On the liquid/vapor interface, a phase transition problem is solved numerically. © 2005 Elsevier Ltd.

关键词： Diesel engines

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Selecting differentially expressed proteomic markers from mass spectrometry data

Selecting differentially expressed proteomic markers from ma...

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2005 27th Annual International Conference of the Engineering in Medicine and Biology Society, IEEE-EMBS 2005

作者： Wang, Xuena Zhu, Wei Glimm, James Li, Juan State University of New York Stony Brook NY 11794 United States State University of New York Stony Brook NY 11794 Center for Data Intensive Computing Brookhaven National Laboratory Upton NY 11973 Department of Psychiatry Center for Brain Health New York University School of Medicine New York NY 10016

ISBN: (纸本)0780387406

关键词： Biomarkers

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Radiation-coupled front-tracking simulations for laser-driven shock experiments

Radiation-coupled front-tracking simulations for laser-drive...

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作者： Zhang, Yongmin Drake, R. Paul Glimm, James Grove, John W. Sharp, David H. Department of Applied Mathematics and Statistics University at Stony Brook Stony Brook NY 11974-3600 United States University of Michigan 2455 Hayward St. Ann Arbor MI 48105 United States Center for Data Intensive Computing Brookhaven National Laboratory Upton NY 11793-6000 United States Continuum Dynamics Group Computer and Computational Science Division Los Alamos National Laboratory Los Alamos NM 87545 United States Complex Systems Group Theoretical Division Los Alamos National Laboratory Los Alamos NM 87545 United States

The purpose of this paper is to develop a numerical algorithm to track the preheat interface motion driven by radiation transfer in high-intensity laser experiments. Our front-tracking algorithm is coupled to a radiation process through an inter-package coupling by connecting the output from a radhydro code HYADES to the input of FronTier code of front tracking. Our coupled algorithm is validated by comparing simulation results from both codes in both low and high radiation cases. Significant interface motion and deformation of the harmonic perturbation due to radiation preheat are observed in high radiation heat case. © 2005 Elsevier Ltd. All rights reserved.

关键词： Algorithms

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Structural and electronic properties of Si3P4

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Physical Review B 2004年第5期69卷 054112-054112页

作者： M. Huang Y. P. Feng A. T. L. Lim J. C. Zheng Center for Data Intensive Computing Brookhaven National Laboratory Upton New York 11973 USA

Structural and electronic properties of Si3P4 were investigated using first-principles total-energy method based on density-functional theory and the local-density approximation (LDA). It was found that pseudocubic-Si3P4 is energetically favored relative to other phases of Si3P4 considered in this study. All phases of Si3P4 have low bulk moduli, with the γ phase being the hardest (110 GPa). Furthermore, band-structure and density-of-states calculations reveal that α, β1, pseudocubic, and graphitic phases of Si3P4 are semiconducting while β2, cubic, and γ phases are metallic within LDA. Correction of LDA energy band gap by a more accurate method will likely result in Si3P4 being a narrow gap semiconductor. The structural and electronic properties of Si3P4 are compared with those of similar compounds, i.e., C3N4, Si3N4, Ge3N4, and C3P4.

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Ferromagnetism and stability of half-metallic MnSb and MnBi in the strained zinc-blende structure: Predictions from full potential and pseudopotential calculations

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Physical Review B 2004年第14期69卷 144415-144415页

作者： Jin-Cheng Zheng James W. Davenport Center for Data Intensive Computing Brookhaven National Laboratory Upton New York 11973 USA

We use first principles calculations to study the energy and magnetic moment of MnSb and MnBi in the (equilibrium) nickel arsenide, zinc-blende, and tetragonally distorted zinc-blende structures. We find that the zinc-blende structure is mechanically unstable, i.e., the energy is a relative maximum for c/a=1 at fixed volume. We studied the tetragonal structures by fixing the in-plane lattice constant to be equal to that of typical semiconductors (such as GaAs) which might serve as substrates for epitaxial growth and then minimizing the energy as a function of c/a. Over a wide range of a, including that of GaAs, we find half-metallic ferromagnets. We suggest that these structures are much more likely to be achieved as thin films than the cubic zinc-blende phases.

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Enhanced Front Tracking Method for the Computation of Discontinuous Structures in Fluid Dynamics

Enhanced Front Tracking Method for the Computation of Discon...

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The Sixth World Congress on Computational Mechanics in Conjunction with the Second Asian-Pacific Congress on Computational Mechanics

作者： James Glimm Department of Applied Mathematics and Statistics Stony Brook University Stony Brook NY 11794-3600 USA Center for Data Intensive Computing Brookhaven National Laboratory Upton NY 11793-6000 USA

The front tracking method is a high resolution method to study continuum mechanics with discontinuous interfaces. In this paper we discuss three important developments of this method. The first development deals with the robust and high quality computation of dynamically moving front. We introduced a locally grid-based method which uses Lagrangian propagation and redistribution, but applies Eulerian reconstruction for the bifurcation of topology. This method maintains high quality surface mesh and confines geometrical diffusion only in the regions where topological bifurcations are needed). Secondly, we have made important changes to the coupling of finite difference interior solver and the front propagation. Global conservation is achieved by using dynamic flux in the finite difference stencil near the interface. The third enhancement is to add the Colella-Burger adaptive mesh refinement method to the FronTier code. This is accomplished by merging the Fron Tier code with the Overture code (Livermore) through the use of a common data model called the TSTT interface. We will demonstrate these features through application of the front tracking method to the computation of fluid interface instabilities.

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Conservative front tracking with improved accuracy

Conservative front tracking with improved accuracy

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作者： Glimm, James Xiaolin, L.I. Liu, Yingjie Zhiliang, X.U. Zhao, Ning Department of Applied Mathematics SUNY at Stony Brook Stony Brook NY 11794-3600 Center for Data Intensive Computing Brookhaven National Laboratory Upton NY 11793-5000 Department of Aerodynamics Nanjing Univ. Aero. and Astronaut. Nanjing 210016 China

We propose a fully conservative front tracking algorithm for systems of nonlinear conservation laws. The algorithm improves by one order in its convergence rate over most finite difference schemes. Near tracked discontinuities in the solution, the proposed algorithm has script O sign(Δx) errors, improving over script O sign(1) errors commonly found near a discontinuity. Numerical experiments which confirm these assertions are presented.

关键词： Nonlinear systems

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