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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...

引用

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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An Adaptive Quality of Service Based Scheduling Algorithm for Wide Area Large Scale Problems

An Adaptive Quality of Service Based Scheduling Algorithm fo...

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IEEE International Symposium on Network computing and Applications

作者： W. Lozano W. Rivera Parallel and Distributed Computing Laboratory Electrical and Computer Engineering Department University of Puerto Rico MayagÜez Puerto Rico

This paper explores the problem of dynamically scheduling large scale applications over wide area networks and then proposes an adaptive scheduling algorithm to provide quality of service. Our adaptive algorithm takes into account unexpected events and priority fluctuations and gives high priority to jobs with low probability of failure. Experimental results show that the new approach outperforms traditional scheduling approaches in grid computing environments

关键词： Quality of service Scheduling algorithm Large-scale systems Dynamic scheduling Wide area networks Adaptive scheduling Adaptive algorithm Fluctuations Processor scheduling Grid computing

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Using Grid computing to Enable distributed Radar Data Retrieval and Processing

Using Grid Computing to Enable Distributed Radar Data Retrie...

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IEEE International Conference on parallel and distributed computing, Applications and Technologies (PDCAT)

作者： Diego Arias Wilson Rivera Parallel and Distributed Computing Laboratory Electrical and Computer Engineering Department University of Puerto Rico MayagÜez Puerto Rico

We describe a tool that implements a set of services to manipulate and store data from a radar network in a transparent way to end users. A major requirement of this system is data availability and reliability. Consequently, we have implemented a redundancy schema based on the information dispersal algorithm (IDA). Preliminary results show that the IDA based replication provides better reliability and less storage spending than traditional replication

关键词： Grid computing Radar Information retrieval Atmosphere Earth distributed computing Computer networks Concurrent computing Reliability engineering Availability

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An Interface Theory Based Approach to Verification of Web Services

An Interface Theory Based Approach to Verification of Web Se...

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IEEE Annual International Computer Software and Applications Conference (COMPSAC)

作者： Zhenbang Chen Ji Wang Wei Dong Zhichang Qi W.l. Yeung National Laboratory for Parallel and Distributed Processing Changsha China Department of Computing and Decision Sciences Lingnan University Hong Kong China

The verification of Web services becomes a challenge in software verification. This paper presents a framework for verification of Web service interfaces at various abstraction levels. Its foundation is the interface theory for Web services, in which transaction features are incorporated. Within the framework, one may check non mutual invocation, compatibility and refinement of Web services at signature, conversation and protocol levels. At protocol level, we present a model checking approach to verifying the protocol properties in action set computation tree logic (ASCTL). The paper also discusses the integration of our framework into the Web service development

关键词： Web services Protocols Laboratories distributed processing Supply chain management Automata distributed computing Research and development Computer applications Computer interfaces

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Verifying Choreographic Descriptions of Web Services Based on CSP

Verifying Choreographic Descriptions of Web Services Based o...

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IEEE Services computing Workshops, SCW

作者： W. L. Yeung Ji Wang Wei Dong Department of Computing and Decision Sciences Lingnan University Hong Kong China National Laboratory for Parallel and Distributed Processing Changsha Hunan China

The emerging service-oriented architectures based on Web services is fostering a new generation of intra- and inter-organizational cross-platform Web-based business applications. With the new architectures comes a new set of standards (e.g. XML, SOAP, WSDL, UDDI) for enabling self-describing interoperable Web services, as well as for modeling and implementing workflow or process-oriented Web applications. The latter kind of standards include the Web Service Business Process Execution language (BPEL) and the Web Service Choreography Description Language (WS-CDL). While BPEL supports the modeling and implementation of a particular (composite) Web service, WS-CDL can be seen as a behavioral modeling language for the collaboration between multiple parties (Web services) within the same business process. In this paper, we outline how communicating sequential processes (CSP) can be used as a formal basis for checking the behavioral consistency among the participants of a business process with respect to a choreography. The use of a model checking tool for automating the consistency checking is also discussed

关键词： Web services Process design Service oriented architecture Unified modeling language Concurrent computing distributed computing Laboratories distributed processing XML Simple object access protocol

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Towards an agent oriented programming language with caste and scenario mechanisms

Towards an agent oriented programming language with caste an...

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4th International Conference on Autonomous Agents and Multi agent Systems, AAMAS 05

作者： Wang, Ji Shen, Rui Zhu, Hong National Laboratory for Parallel and Distributed Processing Changsha 410073 China Department of Computing Oxford Brookes University Oxford OX33 1HX United Kingdom

The paper presents an agent-oriented programming language SLABSp. It provides caste and scenario mechanisms in a coherent way to support the caste-centric methodology of agent-oriented software development. It uses caste as a modular facility to organize agents into castes and to represent their structure and behavior characteristics. SLABSp also uses scenarios to define agents' behaviors in the context of environment situations. In the paper, the implementation of the language is briefly described. An example of the program is given to illustrate its programming style. Copyright 2005 ACM.

关键词： Computer programming languages

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Security mechanisms for legacy code applications in GT3 environment

Security mechanisms for legacy code applications in GT3 envi...

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Euromicro Conference on parallel, distributed and Network-Based Processing

作者： G. Terstyanszky T. Delaitre A. Goyeneche T. Kiss K. Sajadah S.C. Winter P. Kacsuk Centre of Parallel Computing Universitv of Westminster London Centre of Parallel Computing Cavendish School of Computer Science University of Westminster London UK MTA SZTAKI Laboratory of Parallel and Distributed Systems Budapest Hungary

There are many legacy code applications that cannot be run in grid environment without significant modifications. To avoid reengineering of legacy code, we developed the grid execution management for legacy code architecture (GEMLCA) that enables deployment of legacy code applications as grid services. GEMLCA is an OGSI grid service layer that supports submitting jobs, getting their results and status back. Security requirements are essential to any grid application to preserve the confidentiality and integrity of data. To meet these requirements the GT3 security model was implemented in GEMLCA. The paper introduces GEMLCA and how grid security infrastructure (GSI) components have been added to GEMLCA in order to enable secure execution of jobs in grid. The paper also presents how a legacy code traffic simulator was transformed into a grid service using GEMLCA and gives some simulation results.

关键词： Java Data security Computational modeling Wrapping Application software Testing Grid computing Computer architecture Concurrent computing distributed computing

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Decision tree construction for data mining on grid computing environments

Decision tree construction for data mining on grid computing...

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19th International Conference on Advanced Information Networking and Applications, AINA 2005

作者： Yang, Chao-Tung Tsai, Shu-Tzu Li, Kuan-Ching High-Performance Computing Laboratory Department of Computer Science and Information Engineering Tunghai University Taichung City 40704 Taiwan Parallel and Distributed Processing Center Department of Computer Science and Information Management Providence University Taichung County 43301 Taiwan

ISBN: (纸本)0769522491

In this paper, we present our Grid-based decision tree architecture, with the intention of applying it to both parallel and sequential algorithms. Also, we show that, based on the scope and model of data mining applied in the Grid environment as well as user equivalent perspective, Grid roles can be categorized into three types. It is our goal, through these definitions, to help software developers define clear system processes and differentiate the application scope for software applications. To, fulfill our architecture, we first apply an existing parallel decision tree algorithm (the SPRINT algorithm) to the Grid environment. The performance and differences in many other areas are compared using datasets of different sizes. The experimental results will be used for future reference and further development. © 2005 IEEE.

关键词： Data mining

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The collaborative P-GRADE Grid Portal

引用

5th International Conference on Computational Science - ICCS 2005

作者： Lewis, Gareth J. Sipos, Gergely Urmetzer, Florian Alexandrov, Vassil N. Kacsuk, Peter Advanced Computing and Emerging Technologies Centre School of Systems Engineering University of Reading WhiteKnights Reading RG6 6AY United Kingdom MTA SZTAKI Laboratory of Parallel and Distributed Systems H-1518 Budapest Hungary

ISBN: (纸本)9783540260448

Grid portals are increasingly used to provide uniform access to the grid infrastructure. This paper describes how the P-GRADE Grid Portal could be used in a collaborative manner to facilitate group work and support the notion of Virtual Organisations. We describe the development issues involved in the construction of a collaborative portal, including ensuring a consistent view between participants of a collaborative workflow and management of proxy credentials to allow separate nodes of the workflow to be submitted to different grids. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Computational methods

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An enhanced parallel loop self-scheduling scheme for cluster environments

An enhanced parallel loop self-scheduling scheme for cluster...

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19th International Conference on Advanced Information Networking and Applications, AINA 2005

作者： Yang, Chao-Tung Cheng, Kuan-Wei Li, Kuan-Ching High-Performance Computing Laboratory Department of Computer Science and Information Engineering Tunghai University Taichung City 40704 Taiwan Parallel and Distributed Processing Center Department of Computer Science and Information Management Providence University Taichung County 43301 Taiwan

ISBN: (纸本)0769522491

In this paper, a parallel loop self-scheduling scheme for heterogeneous PC cluster systems is proposed. Though the proposed scheme does allow users to choose parameters before the execution initialization phase, there are still weaknesses that motivate us to go further with new improvements in that scheme. For instance, a decision on a fixed and monotonous parameter can easily lead to invalid schedule by using previous input information. Thus, it is proposed in this paper a new scheme, where the scheduling parameter can be adjusted dynamically and fit into most widely available computer systems, in order to provide higher overall performance. © 2005 IEEE.

关键词： Scheduling

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