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11th International Conference on Miniaturized systems for Chemistry and Life sciences, uTAS 2007

作者： Choi, Young Hoon Song, Young Soo Kim, Do Hyun Department of Chemical and Biomolecular Engineering Center for Ultramicrochemical Process Systems Korea Advanced Institute of Science and Technology Korea Republic of

ISBN: (纸本)9780979806407

We report a novel method for active generation of drops in an aqueous two-phase system (ATPS). A small volume of fluid of one phase is separated from its laminar stream to be dispersed in the other phase by the perturbation of the liquid-liquid interface which is induced by electrohydrodynamic force. The number of drops generated is controlled by the change in the magnitude and duration of d.c. electric pulse. © 2007 CBMS.

关键词： Drops

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Multi-level coupling of dynamic data-driven experimentation with material identification

Multi-level coupling of dynamic data-driven experimentation ...

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7th International Conference on computational science (ICCS 2007)

作者： Michopoulos, John G. Furukawa, Tomonari Computational Multiphysics Systems Laboratory Center for Computational Material Science Special Projects Group United States ARC Centre of Excellence in Autonomous Systems School of Mechanical and Manufacturing Engineering J17 The University of New South Wales Sydney NSW 2052 Australia

ISBN: (纸本)9783540725831

We describe a dynamic data-driven methodology that is capable of simultaneously determining both the parameters of a constitutive model associated with the response of a composite material, and the optimum experimental design that leads to the corresponding material characterization. The optimum design of experiments may contain two parts. One involving the identification of the parameters that are tunable prior to performing the experiment such as specimen characteristics and a priori loading path. The other is involving the parameters characterizing the experiment during the experiment itself such as the directionality of the loading path for the case of multi-axial loading machine. A multi-level coupled design optimization methodology is developed and applied to demonstrate the concept. Essential to the process is the development of objective functions that express the quality of the experimental procedure in terms of the uniqueness and distinguishability associated with the inverse solution of the constitutive model determination. The examples provided are based on the determination of the linear constitutive response of a laminate composite material.

关键词： Data structures

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Microfluidic elisa system for the diagnosis of hepatitis b using microwells made of anodic aluminum oxide 11

Microfluidic elisa system for the diagnosis of hepatitis b u...

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11th International Conference on Miniaturized systems for Chemistry and Life sciences, uTAS 2007

作者： Yang, Kwang Suk Kim, Hye Jin Ahn, Jeong Keun Kim, Do Hyun Department of Chemical and Biomolecular Engineering Center for Ultramicrochemical Process Systems Korea Advanced Institute of Science and Technology Korea Republic of Department of Microbiology Chungnam National University Korea Republic of

ISBN: (纸本)9780979806407

An efficient microfluidic system for diagnosing disease marker molecules is reported. This system is constructed with the anodic aluminum oxide (AAO) as a porous substrate, which provides havens for target proteins and their antibodies from shear force of flow. AAO is embedded on microfluidic channels, where hepatitis B virus (HBV) antibody is immobilized in the surface-modified AAO pores. The performance using porous AAO in a PDMS microfluidic device is comparable to that of conventional ELISA system for the detection of hepatitis B surface antigen (HBsAg). © 2007 CBMS.

关键词： Microfluidics

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Surface solitons in three dimensions

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Physical Review E 2008年第3期78卷 036605-036605页

作者： Q. E. Hoq R. Carretero-González P. G. Kevrekidis B. A. Malomed D. J. Frantzeskakis Yu. V. Bludov V. V. Konotop Department of Mathematics Western New England College Springfield Massachusetts 01119 USA Nonlinear Dynamical Systems Group Department of Mathematics and Statistics and Computational Science Research Center San Diego State University San Diego California 92182-7720 USA Department of Mathematics and Statistics University of Massachusetts Amherst Massachusetts 01003-4515 USA Department of Physical Electronics Faculty of Engineering Tel Aviv University Tel Aviv 69978 Israel Department of Physics University of Athens Panepistimiopolis Zografos Athens 157 84 Greece Centro de Física Teórica e Computacional Universidade de Lisboa Complexo Interdisciplinar Avenida Professor Gama Pinto 2 Lisboa 1649-003 Portugal Departamento de Física Faculdade de Ciências Universidade de Lisboa Campo Grande Edifício C8 Piso 6 Lisboa 1749-016 Portugal

We study localized modes on the surface of a three-dimensional dynamical lattice. The stability of these structures on the surface is investigated and compared to that in the bulk of the lattice. Typically, the surface makes the stability region larger, an extreme example of that being the three-site “horseshoe”-shaped structure, which is always unstable in the bulk, while at the surface it is stable near the anticontinuum limit. We also examine effects of the surface on lattice vortices. For the vortex placed parallel to the surface, the increased stability-region feature is also observed, while the vortex cannot exist in a state normal to the surface. More sophisticated localized dynamical structures, such as five-site horseshoes and pyramids, are also considered.

关键词： Vortex flow

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Stream Data Management Based on Integration of a Stream processing Engine and Databases

Stream Data Management Based on Integration of a Stream Proc...

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IFIP International Conference on Network and Parallel Computing Workshops (NPC Workshops)

作者： Hiroyuki Kitagawa Yousuke Watanabe Graduate School of Systems and Information Engineering Center for Computational Sciences University of Tsukuba Japan Japan Science and Technology Agency Japan

Developments in network and sensor device technologies enable us to easily obtain real-world information, such as locations of moving objects, weather information, news, and stock prices. These data are continuously supplied, and they are regarded as data streams. Because of the dramatical increase of streaming data, their management and utilization has become more and more important. This paper describes a data stream management system named Harmonica. Harmonica employs an architecture combining our stream processing engine named stream-spinner and relational DBMSs. Based on the architecture, the system processes both continuous queries and traditional one-shot queries. Moreover, Harmonica supports continuous persistence requirements for streaming data as well as queries including selection, join, projection, and user-defined functions over data streams. Users can also specify continuous queries that integrate streaming data and persistent data stored in databases. Using the Harmonica API, users can develop a variety of applications coping with different continuous steaming data and data stored in databases. Our system can be deployed in network environments to achieve efficient and dependable distributed stream processing.

关键词： Engines Relational databases Remote monitoring Query processing Database languages Parallel processing Computer network management Conference management Technology management engineering management

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A master-worker type eigensolver for molecular orbital computations

A master-worker type eigensolver for molecular orbital compu...

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8th International Workshop on Applied Parallel Computing, PARA 2006

作者： Sakurai, Tetsuya Kodaki, Yoshihisa Tadano, Hiroto Umeda, Hiroaki Inadomi, Yuichi Watanabe, Toshio Nagashima, Umpei Department of Computer Science University of Tsukuba Tsukuba 305-8573 Japan Graduate School of Systems and Information Engineering University of Tsukuba Tsukuba 305-8573 Japan Core Research for Evolutional Science and Technology Japan Science and Technology Agency Japan Computational Science Research Division National Institute of Advanced Industrial Science and Technology Computing and Communications Center Kyushu University Fukuoka 812-8581 Japan

ISBN: (纸本)9783540757542

We consider a parallel method for solving generalized eigen-value problems that arise from molecular orbital computations. We use a moment-based method that finds several eigenvalues and their corresponding eigenvectors in a given domain, which is suitable for master-worker type parallel programming models. The computation of eigen-values using explicit moments is sometimes numerically unstable. We show that a Rayleigh-Ritz procedure can be used to avoid the use of explicit moments. As a test problem, we use the matrices that arise in the calculation of molecular orbitals. We report the performance of the application of the proposed method with several PC clusters connected through a hybrid MPI and GridRPC system. © Springer-Verlag Berlin Heidelberg 2007.

关键词： Computation theory

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OLAP Query processing for XML Data in RDBMS

OLAP Query Processing for XML Data in RDBMS

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IEEE International Workshop on Databases for Next Generation Researchers, SWOD

作者： Chantola Kit Toshiyuki Amagasa Hiroyuki Kitagawa Department of Computer Science Graduate School of Systems and Information Engineering Tsukuba Ibaraki Japan Center for Computational Sciences University of Tsukuba Tsukuba Ibaraki Japan

Extensible Markup Language (XML) has become an important format for data exchange and representation on the Web. In addition to conventional query processing, more complex analysis on XML data is considered to become important in order to discover valuable information. In this research, we attempt to investigate an XML-OLAP, by which we can perform multidimensional analysis on XML data taking XML's features into account. Users are allowed to specify XML data-cube by XPath, and perform analytical processing by XQuery with OLAP extension. The system is implemented on top of relational databases, and the given requests for data-cube specification and analysis are translated into SQL so that they can be processed using the underlying system. We show the feasibility of the proposed scheme by experimental evaluations.

关键词： Query processing XML Data analysis Relational databases Unified modeling language Multidimensional systems Information analysis Performance analysis Data mining Computer science

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Quantum diffusion dynamics in nonlinear systems: A modified kicked-rotor model

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Physical Review E 2007年第3期76卷 036217-036217页

作者： Jiangbin Gong Jiao Wang Department of Physics and Centre of Computational Science and Engineering National University of Singapore 117542 Singapore Temasek Laboratories and Beijing–Hong Kong–Singapore Joint Center for Nonlinear and Complex Systems (Singapore) National University of Singapore 117542 Singapore

Using a simple method analogous to a quantum rephasing technique, a simple modification to a paradigm of classical and quantum chaos is proposed. The interesting quantum maps thus obtained display remarkably rich quantum dynamics. Emphasis is placed on the destruction of dynamical localization without breaking periodicity, unbounded quantum anomalous diffusion in integrable systems, and transient dynamical localization. Experimental realizations of this work are also discussed.

关键词： CHAOS LOCALIZATION DELOCALIZATION SPECTRUM

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A robust two-step PCR method of template DNA production for high-throughput cell-free protein synthesis

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Journal of Structural and Functional Genomics 2007年第4期8卷 173-191页

作者： Yabuki, Takashi Motoda, Yoko Hanada, Kazuharu Nunokawa, Emi Saito, Miyuki Seki, Eiko Inoue, Makoto Kigawa, Takanori Yokoyama, Shigeyuki Protein Research Group RIKEN Genomic Sciences Center Tsurumi Yokohama 230-0045 1-7-22 Suehiro-cho Japan Department of Computational Intelligence and Systems Science Interdisciplinary Graduate School of Science and Engineering Tokyo Institute of Technology Midori-ku Yokohama 226-8502 4259 Nagatsuta-cho Japan Department of Biophysics and Biochemistry Graduate School of Science University of Tokyo Bunkyo-ku Tokyo 113-0033 7-3-1 Hongo Japan

A two-step PCR method has been developed for the robust, high-throughput production of linear templates ready for cell-free protein synthesis. The construct made from the cDNA expresses a target protein region with N- and/or C-terminal tags. The procedure consists only of mixing, dilution, and PCR steps, and is free from cloning and purification steps. In the first step of the two-step PCR, a target region within the coding sequence is amplified using two gene-specific forward and reverse primers, which contain the linker sequences and the terminal sequences of the target region. The second PCR concatenates the first PCR product with the N- and C-terminal double-stranded fragments, which contain the linker sequences as well as the sequences for the tag(s) and the initiation and termination, respectively, for T7 transcription and ribosomal translation, and amplifies it with the universal primer. Proteins can be fused with a variety of tags, such as natural poly-histidine, glutathione-S- transferase, maltose-binding protein, and/or streptavidin-binding peptide. The two-step PCR method was successfully applied to 42 human target protein regions with various GC contents (38-77%). The robustness of the two-step PCR method against possible fluctuations of experimental conditions in practical use was explored. The second PCR product was obtained at 60-120 μg/ml, and was used without purification as a template at a concentration of 2-4 μg/ml in an Escherichia coli coupled transcription-translation system. This combination of two-step PCR with cell-free protein synthesis is suitable for the rapid production of proteins in milligram quantities for genome-scale studies. © 2007 Springer science+Business Media B.V.

关键词： Cell-free protein synthesis Human proteins Linear template construction Tagged proteins Two-step PCR

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Inferring Markov chains: Bayesian estimation, model comparison, entropy rate, and out-of-class modeling

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Physical Review E 2007年第1期76卷 011106-011106页

作者： Christopher C. Strelioff James P. Crutchfield Alfred W. Hübler Center for Computational Science & Engineering and Physics Department University of California at Davis One Shields Avenue Davis California 95616 USA Center for Complex Systems Research and Physics Department University of Illinois at Urbana-Champaign 1110 West Green Street Urbana Illinois 61801 USA

Markov chains are a natural and well understood tool for describing one-dimensional patterns in time or space. We show how to infer kth order Markov chains, for arbitrary k, from finite data by applying Bayesian methods to both parameter estimation and model-order selection. Extending existing results for multinomial models of discrete data, we connect inference to statistical mechanics through information-theoretic (type theory) techniques. We establish a direct relationship between Bayesian evidence and the partition function which allows for straightforward calculation of the expectation and variance of the conditional relative entropy and the source entropy rate. Finally, we introduce a method that uses finite data-size scaling with model-order comparison to infer the structure of out-of-class processes.

关键词： STATISTICAL COMPLEXITY HOLLIDAY JUNCTIONS DYNAMICS INFORMATION INFERENCE INDUCTION ORDER

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