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5th International Symposium on High Dielectric Constant Materials and Gate Stacks - 212th ECS Meeting

作者： Umezawa, N. Shiraishi, K. Miyazaki, S. Uedono, A. Akasaka, Y. Inumiya, S. Oshiyama, A. Hasunuma, R. Yamabe, K. Momida, H. Ohno, T. Ohmori, K. Chikyow, T. Nara, Y. Yamada, K. Advanced Electronic Materials Center National Institute for Materials Science Tsukuba 305-0044 Japan California NanoSystems Institute University of California Santa Barbara Santa Barbara 93106 United States Graduate School of Pure and Applied Sciences Univ. of Tsukuba Tsukuba 305-8571 Japan Graduate School of Advanced Sciences of Matter Hiroshima University Hiroshima 739-8530 Japan Leading Edge Process Development Center Tokyo Electron Ltd. Yamanashi 407-0912 Japan Semiconductor Leading Edge Technology Inc. Tsukuba 305-8569 Japan Semiconductor Company Toshiba Corporation Yokohama 235-8522 Japan Computational Materials Science Center National Institute for Materials Science Tsukuha 305-0047 Japan Nanotechnology Research Laboratories Waseda University Tokyo 169-0041 Japan

ISBN: (纸本)9781566775700

Ionicity has been raised as an important factor in discussing defect formation in Hf-based oxides. It has been elucidated from our first-principles calculations, that the stability of defects is dominated by Coulomb interactions between charged defects and surrounding ions. For instance, the formation energy of positively charged oxygen vacancies (Vo+2) is markedly decreased when they are coupled with substitutional N atoms at O sites, as the nominal charges of N3- are negatively greater than those of the oxygen ions O2-. Our computational results have further revealed that the ionic character of Hf causes generation of a low-lying Si dangling bond level in Si doped HfSiOx. These results suggest that one must take into account the ionicity of the Hf-based compounds, which possess totally different properties from the conventional gate insulator SiO2 in terms of defect formation. © The Electrochemical Society.

关键词： Calculations

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Ab Initio MO Studies of the Weak Interaction in Cu-Histamine-Tyrosine Complex as an Model of Pseudoazurin M16Y Mutant

Ab Initio MO Studies of the Weak Interaction in Cu-Histamine...

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2007年全国核反应会暨生物物理与核物理学科交叉前沿研讨会

作者： Umpei Nagashima Toshio Watanabe Takamitsu Kohzuma Yoshiko Uchida Osamu Yamauchi Research Institute for Computational Science National Institute of Advanced Industrial Science and Technology 1-1-1 Umezono Tsukuba Ibaraki 305-8568 Japan Research Institute for Computational Science National Institute of Advanced Industrial Science and Technology 1-1-1 Umezono Tsukuba Ibaraki 305-8568 Japan Institute of Applied Beam Science Ibaraki University 2-1-1 Bunkyo Mito Ibaraki 310-8512 Japan Institute of Applied Beam Science Ibaraki University 2-1-1 Bunkyo Mito Ibaraki 310-8512 Japan Faculty of Engineering Kansai University 2-1-1 Ryozenji-cho Takatsuki Osaka 569-1095 Japan

Noncovalent weak interactions play important roles in biological *** bonding and aromatic ring stacking interactions are well established weak interaction in the structure and function of proteins and nucleic ***,the biological significance of a weak interaction between metal ion coordinated imidazole ring and the phenyl ring of a phenylalanine residue has been found in plastocyanin from fern *** reported the spectroscopic and electrochemical studies of the M16F mutant of a blue copper protein,

关键词： Ab Initio MO Studies of the Weak Interaction in Cu-Histamine-Tyrosine Complex as an Model of Pseudoazurin M16Y Mutant Model

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Theory of large-scale electronic structure calculation and nanoscale mechanical property in fracture behavior of silicon

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MRS Online Proceedings Library 2006年第1期880卷 1-6页

作者： Takeo Hoshi Ryu Takayama Yusuke Iguchi Takeo Fujiwara Department of Applied Physics University of Tokyo Hongo Bunkyo-ku Tokyo Japan Core Research for Evolutional Science and Technology (CREST-JST) Japan Science and Technology Agency Honcho Kawaguchi-shi Saitama Japan Research and Development for Applying Advanced Computational Science and Technology (ACT-JST) Japan Science and Technology Agency USA

Several theories and program codes were developed for large-scale atomistic simulations with fully quantum mechanical description of electron systems. The fundamental concepts are generalized Wannier state and Krylov subspace. Test calculations were carried out with upto 106 atoms using a standard workstation. How electronic state is described in large-scale calculation was demonstrated on Si(001)-(2×1) surface. As a practical application, cleavage fracture of silicon was simulated with 10-nm-scale samples for investigating its nanoscale mechanical behavior. Discussions are focused on the unstable (001) cleavage mode and the stable (experimentally observed) (111)-(2×1) cleavage mode. As well as elementary surface reconstruction, step formation and bending in cleavage path were observed. These results were compared with experiments, such as scanning tunneling microscope (STM).

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Event ontology: A pathway-centric ontology for biological processes

Event ontology: A pathway-centric ontology for biological pr...

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11th Pacific Symposium on Biocomputing 2006, PSB 2006

作者： Kushida, Tatsuya Takagi, Toshihisa Fukuda, Ken Ichiro Institute for Bioinformatics Research and Development Japan Science and Technology Agency 2-42 Aomi Koutou-ku Tokyo 135-0064 Japan School of Frontier Sciences University of Tokyo 5-1-5 Kashiwanoha Kashiwa-shi Chiba 277-8562 Japan Computational Biology Research Center AIST Bio-IT Research Building National Institute of Advanced Industrial Science and Technology 2-42 Aomi Koutou-ku Tokyo 135-0064 Japan

ISBN: (纸本)9812564632

Event ontology is a new biomedical ontology developed to annotate pathway components in a pathway database It organizes the concepts and terms of sub-pathways, pathways, biological phenomena, experimental conditions, medications, and external stimuli appearing in biological pathways (e.g. signal transduction, disease-, metabolic-, molecular interaction-, genetic interaction pathways, etc.). Concepts in the Event ontology are extracted manually from scientific literature. Each term has links to external databases such as Gene Ontology, Reactome, KEGG, BioCyc, and PubMed.

关键词： Gene Ontology

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Linear algebraic calculation of the Green’s function for large-scale electronic structure theory

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Physical Review B 2006年第16期73卷 165108-165108页

作者： R. Takayama T. Hoshi T. Sogabe S.-L. Zhang T. Fujiwara Research and Development for Applying Advanced Computational Science and Technology (ACT-JST) Japan Science and Technology Agency 4-1-8 Honcho Kawaguchi-shi Saitama 332-0012 Japan Department of Applied Physics University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan Core Research for Evolutional Science and Technology (CREST-JST) Japan Science and Technology Agency 4-1-8 Honcho Kawaguchi-shi Saitama 332-0012 Japan

A linear algebraic method named the shifted conjugate-orthogonal conjugate-gradient method is introduced for large-scale electronic structure calculation. The method gives an iterative solver algorithm of the Green’s function and the density matrix without calculating eigenstates. The problem is reduced to independent linear equations at many energy points and the calculation is actually carried out only for a single energy point. The method is robust against the round-off error and the calculation can reach the machine accuracy. With the observation of residual vectors, the accuracy can be controlled, microscopically, independently for each element of the Green’s function, and dynamically, at each step in dynamical simulations. The method is applied to both a semiconductor and a metal.

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Effects of electrode contact on transport properties of carbon nanotubes

Effects of electrode contact on transport properties of carb...

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2006 6th IEEE Conference on Nanotechnology, IEEE-NANO 2006

作者： Kobayashi, Nobuhiko Ozaki, Taisuke Hirose, Kenji Institute of Applied Physics University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8573 Japan CREST-JST Research Institute for Computational Sciences National Institute of Advanced Industrial Science and Technology 1-1-1 Umezono Tsukuba Ibaraki 305-8568 Japan Fundamental and Environmental Research Laboratories NEC Corporation 34 Miyukigaoka Tsukuba Ibaraki 305-8501 Japan

ISBN: (纸本)1424400783

We report ab initio calculation of transport properties of a semiconducting carbon nanotube connected to aluminum metallic electrodes to analyze the effects of metallic electrode contacts on transport properties. Electrons are transmitted in the nanotube in the band-gap energy region due to the hybridization of the metallic states of the electrodes. © 2006 IEEE.

关键词： Carbon nanotubes

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Visualization of boundaries in volumetric data sets using LH histograms

Visualization of boundaries in volumetric data sets using LH...

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作者： Šereda, Petr Bartrolí, Anna Vilanova Serlie, Iwo W.O. Gerritsen, Frans A. Eindhoven University of Technology Department of Biomedical Engineering Image Analysis Group WH 3.2a Postbus 513 5600 MB Eindhoven Netherlands Delft University of Technology Department of Applied Physics Pattern Recognition Group Lorenzweg 1 2628 CJ Delft Netherlands PHILIPS Medical Systems Nederland BV Research and Advanced Development P.O. Box. 10000 5680 DA Best Netherlands Biomedical Engineering Department Eindhoven University of Technology Biomedical Image Analysis Section Biomedical Engineering Department Eindhoven University of Technology Quantitative Imaging Group Department of Imaging Science and Technology Delft University of Technology Biomedical Engineering Department Technische Universiteit Eindhoven Research and Advanced Development Business Group Medical IT Philips Medical Systems Best Netherlands

A crucial step in volume rendering is the design of transfer functions that will highlight those aspects of the volume data that are of interest to the user. For many applications, Boundaries carry most of the relevant information. Reliable detection of Boundaries is often hampered by limitations of the imaging process, such as blurring and noise. We present a method to identify the materials that form the boundaries. These materials are then used in a new domain that facilitates interactive and semiautomatic design of appropriate transfer functions. We also show how the obtained boundary information can be used in region-growing-based segmentation. © 2006 IEEE.

关键词： Volumetric analysis

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Gene expression profiles of hepatic cell-type specific marker genes in progression of liver fibrosis

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World Journal of Gastroenterology 2006年第40期12卷 6473-6499页

作者： Yoshiyuki Takahara Mitsuo Takahashi Hiroki Wagatsuma Fumihiko Yokoya Qing-Wei Zhang Mutsuyo Yamaguchi Hiroyuki Aburatani Norifumi Kawada Exploratory and Applied Pharmaceutical Research Department Pharmaceutical Company Ajinomoto Co. Inc Kawasaki 210-8681 Japan Biochemical Information project BiolT Business Development Group Fujitsu Limited Tokyo Japan Center for Collaborative Research Research Center for Advanced Science and Technology the University of Tokyo Tokyo Japan Department of Hepatology Graduate School of Medicine Osaka City University Osaka Japan

AIM: To determine the gene expression profile data for the whole liver during development of dimethylni-trosamine (DMN)-induced hepatic ***: Marker genes were identified for different types of hepatic cells, including hepatic stellate cells (HSCs), Kupffer cells (including other inflammatory cells), and hepatocytes, using independent temporal DNA microarray data obtained from isolated hepatic cells. RESULTS: The cell-type analysis of gene expression gave several key results and led to formation of three hypotheses: (1) changes in the expression of HSC-specific marker genes during fibrosis were similar to gene expression data in in vitro cultured HSCs, suggesting a major role of the self-activating characteristics of HSCs in formation of fibrosis; (2) expression of mast cell-specific marker genes reached a peak during liver fibrosis, suggesting a possible role of mast cells in formation of fibrosis; and (3) abnormal expression of hepatocyte-specific marker genes was found across several metabolic pathways during fibrosis, including sulfur-containing amino acid metabolism, fatty acid metabolism, and drug metabolism, suggesting a mechanistic relationship between these abnormalities and symptoms of liver fibrosis. CONCLUSION: Analysis of marker genes for specific hepatic cell types can identify the key aspects of fibro-genesis. Sequential activation of inflammatory cells and the self-supporting properties of HSCs play an important role in development of fibrosis.

关键词： Liver fibrosis Gene expression Microarray Dimethylnitrosamine Marker genes Hepatic stellate cell Kupffer cell Hepatocytes Metabolic pathway

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Effects of Electrode Contact on Transport Properties of Carbon Nanotubes

Effects of Electrode Contact on Transport Properties of Carb...

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IEEE Conference on Nanotechnology

作者： N. Kobayashi T. Ozaki K. Hirose Institute of Applied Physics University of Tsukuba Tsukuba Ibaraki Japan Research Institute of Computational Sciences National Institute of Advanced Industrial Science and Technology Tsukuba Ibaraki Japan Fundamental and Environmental Research Laboratories NEC Corporation Limited Tsukuba Ibaraki Japan

关键词： Electrodes Carbon nanotubes Semiconductivity Nanoscale devices Chromium Aluminum Physics computing Computer industry Metals industry National electric code

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IMPOSING ESSENTIAL AND NATURAL BOUNDARY CONDITIONS ON GEOMETRIC BOUNDARIES FOR X-FEM

IMPOSING ESSENTIAL AND NATURAL BOUNDARY CONDITIONS ON GEOMET...

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The Fourth China-Japan-Korea Joint symposium on Optimization of Structural and Mechanical Systems

作者： Geol Choi Akira Tezuka Byung Man Kwak Ph.D.candidate Dept.of Engineering Mechanics Korea Advanced Institute of Science and Technology 305-701 Daejeon Korea Group Leader Process-oriented Computational Applied Mechanics Group Advanced Manufacturing Research Institute AIST Tsukuba East Tsukuba 305-8564 Japan Professor Dept. of Engineering Mechanics Korea Advanced Institute of Science and Technology 305-701.Deajeon Korea

How to impose essential and natural boundary conditions has been the key issue of mesh-free methods because the nodes are not located along a boundary in arbitrary geometry in general unlike conventional finite element method(FEM). The extended finite element method(X-FEM), one of the mesh-free methods is suitable to deal with geometric discontinuity inside an element in fixed mesh such as crack or hole, but has the same problem. In this paper we introduce a method of constructing nodal constraint equations and distributing loading into element nodes for essential or natural boundary conditions imposed along boundaries in the X-FEM problems.

关键词： Mesh-free methods, Extended finite element method(X-FEM), Essential and natural boundary conditions

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