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Tight binding modelling of electronic structure of GaPN/GaP, InAsN/InAs and GaAsN/GaAs heterostructures

physica status solidi c 2008年第2期5卷

作者： Özden Akıncı H. Hakan Gürel Hilmi Ünlü İstanbul Technical University Informatics Institute Computational Science and Engineering Division Maslak 34469 İstanbul Turkey İstanbul Technical University Faculty of Science and Letters Department of Physics Maslak 34469 İstanbul Turkey

We present a second nearest neighbor semi-empirical sp 3 s * tight binding model to calculate the electronic band structure of nitride/arsenide or phosphide heterostructures. The sp 3 s * model Hamiltonian includes the spin-orbit coupling of p-states, second nearest neighbor (2NN) atomic interactions. Atomic energy levels and bond lengths of ternary semi- conductors are taken as nonlinear function of alloy com- position. The model findings for InAsN/InAs, GaPN/GaP and GaAsN/GaAs structures are in excellent agreement with experiment for the band gaps at Γ, L and X symmetry points. It is found that the bulk band structure properties and lattice mismatch strain have significant effects on band offsets and GaPN/GaP, InAsN/InAs and GaAsN/GaAs heterostructures are type II for small composition (0.0 < x < 0.50) and become type I for large composition 0.50 < x < 1.0. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

关键词： 71.20.Nr 71.55.Eq 73.21.Cd 73.21.Fg 73.40.Kp 73.43.Cd

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Multi-step inverse analysis for rebar corrosion using genetic algorithm and boundary element method

Zairyo to Kankyo/ Corrosion Engineering

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Zairyo to Kankyo/ Corrosion engineering 2008年第6期57卷 282-287页

作者： Minagawa, Koichi Hayabusa, Keisuke Suga, Kazuhiro Ridha, M. Amaya, Kenji Aoki, Shigeru Intelligent Material and Mechanics System Toyo University 2100 Kujirai Kawagoe 350-8585 Japan Ebara Research. Co. LTD. 4-2-1 HonfuJisawa Fujisawa 251-0875 Japan CCMR Toyo University 2-36-5 Hakusan Bunkyoku Tokyo 112-0001 Japan Department of Mechanical and Environmental Informatics Tokyo Institute of Technology 2-12-1 O-okayama Meguro-ku Tokyo 152-8552 Japan Department of Computational Engineering and Science Toyo University 2100 Kujirai Kawagoe 350-8585 Japan

This research proposes an effective inverse analysis technique for solving an inverse problem to detect corrosion in reinforced concrete non-destructively from potentials on a concrete surface. The technique can detect the number, the shape and the location of corrosion without particular assumption with GA (genetic algorithm), and increases accuracy of solution gradually if necessary. The following three strategies achieve the proposed technique: (1) Control of analysis precision, i.e. coarseness of BEM (boundary element method) meshes, depending on required precision of solution. (2) Use of the net elements for BEM for decreasing the number of elements for steels. (3) Analysis with higher precision only within detected corrosion area on lower precise analysis. We performed a numerical simulation to solve an inverse problem for detecting steel corrosion in concrete with the proposed technique. The result showed that the proposed method could detect corrosion with high accuracy. The calculation time of the proposed method was about 1/100 in comparison with that of the previously proposed method.

关键词： Boundary element method

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Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

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Molecular Systems Biology 2008年第1期4卷 198-198页

作者： Kunin, Victor Raes, Jeroen Harris, J. Kirk Spear, John R. Walker, Jeffrey J. Ivanova, Natalia Von Mering, Christian Bebout, Brad M. Pace, Norman R. Bork, Peer Hugenholtz, Philip Microbial Ecology Program DOE Joint Genome Institute Walnut Creek CA United States Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany Department of Pediatrics University of Colorado Denver Aurora CO United States Division of Environmental Science and Engineering Colorado School of Mines Golden CO United States Department of Molecular Cellular and Developmental Biology University of Colorado Boulder CO United States Genome Biology Program DOE Joint Genome Institute Walnut Creek CA United States Institute of Molecular Biology Swiss Institute of Bioinformatics University of Zurich Zurich Switzerland Microbial Ecology/Biogeochemistry Research Laboratory Exobiology Branch NASA Ames Research Center Moffett Field CA United States Microbial Ecology Program DOE Joint Genome Institute Walnut Creek CA 94598 2800 Mitchell Drive United States

To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter-scale genetic gradients that were consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near-identical and acid-shifted isoelectric point profiles due to a molecular convergence of amino-acid usage, indicating that hypersalinity enforces an overriding selective pressure on the mat community. © 2008 EMBO and Nature Publishing Group All rights reserved.

关键词： Fine-scale Hypersalinity Metagenomics Microbial ecology Salt-in

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General Nonlinear Equilibrium Equation Solution of the Straight Wire Strand

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AIP Conference Proceedings 2007年第1期936卷 174-177页

作者： C. Erdönmez C. E. İmrak aIstanbul Technical University Institute of Informatics Computational Science and Engineering Program 34469 Maslak Istanbul Turkey bIstanbul Technical University Faculty of Mechanical Engineering 34394 Gumussuyu Istanbul Turkey

The most analyses of wire ropes are based on the well known classical treatise on elasticity by Love in 1944. A general theory of thin rods are included and investigated extensively. General equilibrium equations of a thin rod on arc length are derived and presented. The analytical and numerical solutions of wire ropes are based on the equilibrium equations as the starting point for the solutions in most of the papers. Helical rod model is first introduced by Phillips and Costello based on the equilibrium equations given by Love. General nonlinear equilibrium equation solution of the straight wire strand is given in this study and showed that it is harmonious with the results presented by Costello.

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Semiempirical Tight Binding Modeling of Electronic Band Structure of III‐V Nitride Heterostructures

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AIP Conference Proceedings 2007年第1期893卷 171-172页

作者： H. Hakan Gürel Özden Akinci Hilmi Ünlü Computational Science and Engineering Division Informatics Institute Istanbul Technical University Maslak 34469 Istanbul Turkey Department of Physics Faculty of Science and Letters Istanbul Technical University Maslak 34469 Istanbul Turkey

In this work, we discuss the composition and strain effects on the electronic band structure modeling of III‐V nitrides heterostructures using the second nearest neighbor sp3s* semi‐empirical tight binding theory. The model Hamiltonian includes the second nearest neighbor (2nn) interactions, the spin‐orbit splitting and the nonlinear variations of the atomic energy levels and the bond length with ternary mole fraction. There is an excellent agreement between the model predictions and experiment for the principal band gaps at Γ, L and X symmetry points of Brillouin zone for AlN, GaN, InN and GaAs binaries and AlGaN, InGaN and GaAsN ternaries. The model predicts that the composition effects on the valence band offsets is small and linear but the conduction band offsets is nonlinear function of composition and large for large strain due to large deformation potential.

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Decision fusion of circulating markers for breast cancer detection in premenopausal women

Decision fusion of circulating markers for breast cancer det...

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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Jesneck, Jonathan L. Mukherjee, Sayan Nolte, Loren W. Lokshin, Anna E. Marks, Jeffrey R. Lo, Joseph Department of Biomedical Engineering Department of Statistical Science Computational Biology and Bioinformatics Program Duke Advanced Imaging Labs. Institute for Genome Sciences and Policy Department of Computer Science Duke University Department of Electrical and Computer Engineering Division of Hematology/Oncology University of Pittsburgh School of Medicine University of Pittsburgh Cancer Institute Pittsburgh PA 15213 United States Department of Experimental Surgery Duke University Medical Center Medical Physics Graduate Program Duke University Durham NC 27708 United States

ISBN: (纸本)1424415098

Current mammographic screeningfor breast cancer is less effective for younger women. To complement mammography for premenopausal women, we investigated the feasibility screening test using 98 blood serum proteins. Because the data set was very noisy and contained only weak features, we used a classifier designed for noisy data: decision fusion. Decision fusion outperformed both a support vector machine (SVM) and linear regression with forward stepwise feature selection on all three two-class classification tasks: normal tissue vs. cancer, normal tissue vs. benign lesions, and benign lesions vs. cancer. Decision fusion detected cancer moderately well (AUC=0.84 on normal vs. cancer), demonstrating promise as a screening tool. Decision fusion also detected benign lesions similarly well (AUC=0.83 on normal vs. benign lesions) and was the only classifier to achieve any success in separating benign from malignant lesions (AUC=0.64 on benign vs. cancer). The classification results suggest that the assayed proteins are more indicative of a secondary effect, such as immune response, rather than specific for breast cancer. In conclusion, the decision fusion classifier demonstrated some promise in detecting breast lesions and outperformed other classifiers, especially for the very noisy classification problem of distinguishing benign from malignant lesions. ©2007 IEEE.

关键词： Tissue

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A new implementation method of the reverse engineering algorithm to elucidate gene functional dependencies

IEEJ Transactions on Electronics, Information and Systems

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IEEJ Transactions on Electronics, Information and Systems 2007年第10期127卷 1712-1718+32页

作者： Inaoka, Hidenori Fukuoka, Yutaka Ueno, Akinori Kohane, Isaac S. Institute of Biomaterials and Biomedical Engineering Tokyo Medical and Dental University 2-3-10 Kanda-Surugadai Chiyoda-ku Tokyo 101-0062 Japan School of Biomedical Science Tokyo Medical and Dental University 1-5-45 Yushima Bunkyo-ku Tokyo 113-8510 Japan Graduate School of Science and Engineering Tokyo Denki University Ishizaka Hatoyama-Cho Hiki-Gun Saitama 350-0394 Japan Informatics Program Childrens's Hospital Harvard Medical School Boston MA United States

Various clustering methods are applied to characterizing gene expression data from DNA microarrays. However, to elucidate functional dependencies of genes analysis of their associations is important. The REVerse engineering ALgorithm (REVEAL) was developed for analyzing the functional dependencies. Although the algorithm has been tested using binary models of genetic networks, it remains unclear how the method or similar technology will operate with systems of continuous variables. In this study, first, the REVEAL was examined using noisy, continuous data and the results suggested that its application to such data required considerable refinement of the algorithm. Then a new implementation method of REVEAL was proposed. This implementation method was tested through numerical experiments. The results of the simulations demonstrated the potential of the proposed method for extracting gene associations.

关键词： Reverse engineering

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A systematic approach to quantifying evolutionary functional trends across the universal tree of life

A systematic approach to quantifying evolutionary functional...

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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Alterovitz, Gil Muso, Taro Malalur, Paresh 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 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

ISBN: (纸本)1424415098

The accumulation of genomic and proteomic data of many organisms presents an opportunity to analyze entire phylogenetic trees in a systematic, quantified manner. The universal tree of life, constructed by genomic data, provides an evolutionary context for proteomic data of individual organisms. Using proteomic information mapped to biological functions, we survey the tree of life for evolutionary trends, where trends are low p-value linear regressions of relative protein diversity against an evolutionary timeline. These trends provide quantified perspectives across evolution that would be otherwise difficult to discern from the large amount of available bioinformatic data. We analyzed 22,762 functions across 167 proteomes for approximately 3.8 million information content calculations. Of particular interest is the rise of protein-protein interactions along the path of mammalian evolution. Of general interest are the numerous uncovered trends that open the door to future queries of focused scope. ©2007 IEEE.

关键词： Information theory

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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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Page Segmentation Competition

Page Segmentation Competition

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International Conference on Document Analysis and Recognition

作者： A. Antonacopoulos B. Gatos D. Bridson Pattern Recognition and Image Analysis (PRImA) Research Lab School of Computing Science and Engineering University of Sanford Manchester UK Computational Intelligence Laboratory Institute of Informatics and Telecommunications National Center for Scientific Research Demokritos Athens Greece

This paper continues the authors' attempt to address the need for objective comparative evaluation of layout analysis methods in realistic circumstances. It describes the Page Segmentation Competition (modus operandi, dataset and evaluation criteria) held in the context of ICDAR2007 and presents the results of the evaluation of three candidate methods. The main objective of the competition was to compare the performance of such methods using scanned documents from commonly-occurring publications. The results indicate that although methods continue to mature, there is still a considerable need to develop robust methods that deal with everyday documents.

关键词： Image analysis Performance analysis Image segmentation Text analysis Optical character recognition software Information analysis Pattern recognition Telecommunication computing computational intelligence informatics

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