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Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

Human genomics 2016年第1期10 Suppl 1卷 12页

作者： A. K. Srivastava Y. Wang R. Huang C. Skinner T. Thompson L. Pollard T. Wood F. Luo R. Stevenson R. Polimanti J. Gelernter X. Lin I. Y. Lim Y. Wu A. L. Teh L. Chen I. M. Aris S. E. Soh M. T. Tint J. L. MacIsaac F. Yap K. Kwek S. M. Saw M. S. Kobor M. J. Meaney K. M. Godfrey Y. S. Chong J. D. Holbrook Y. S. Lee P. D. Gluckman N. Karnani A. Kapoor D. Lee A. Chakravarti C. Maercker F. Graf M. Boutros G. Stamoulis F. Santoni P. Makrythanasis A. Letourneau M. Guipponi N. Panousis M. Garieri P. Ribaux E. Falconnet C. Borel S. E. Antonarakis S. Kumar J. Curran J. Blangero S. Chatterjee J. Akiyama D. Auer C. Berrios L. Pennacchio T. R. Donti G. Cappuccio M. Miller P. Atwal A. Kennedy A. Cardon C. Bacino L. Emrick J. Hertecant F. Baumer B. Porter M. Bainbridge P. Bonnen B. Graham R. Sutton Q. Sun S. Elsea Z. Hu P. Wang Y. Zhu J. Zhao M. Xiong David A. Bennett A. Hidalgo-Miranda S. Romero-Cordoba S. Rodriguez-Cuevas R. Rebollar-Vega E. Tagliabue M. Iorio E. D’Ippolito S. Baroni B. Kaczkowski Y. Tanaka H. Kawaji A. Sandelin R. Andersson M. Itoh T. Lassmann Y. Hayashizaki P. Carninci A. R. R. Forrest C. A. Semple E. A. Rosenthal B. Shirts L. Amendola C. Gallego M. Horike-Pyne A. Burt P. Robertson P. Beyers C. Nefcy D. Veenstra F. Hisama R. Bennett M. Dorschner D. Nickerson J. Smith K. Patterson D. Crosslin R. Nassir N. Zubair T. Harrison U. Peters G. Jarvik F. Menghi K. Inaki X. Woo P. Kumar K. Grzeda A. Malhotra H. Kim D. Ucar P. Shreckengast K. Karuturi J. Keck J. Chuang E. T. Liu B. Ji A. Tyler G. Ananda G. Carter H. Nikbakht M. Montagne M. Zeinieh A. Harutyunyan M. Mcconechy N. Jabado P. Lavigne J. Majewski J. B. Goldstein M. Overman G. Varadhachary R. Shroff R. Wolff M. Javle A. Futreal D. Fogelman L. Bravo W. Fajardo H. Gomez C. Castaneda C. Rolfo J. A. Pinto K. C. Akdemir L. Chin S. Patterson C. Statz S. Mockus S. N. Nikolaev X. I. Bonilla L. Parmentier B. King F. Bezrukov G. Kaya V. Zoete V. Seplyarskiy H. Sharpe T. McKee K. Popadin N. Basset-Seguin R. Ben Chaabene M. Andrianova C. Verdan K. Grosdemange O. Sumara M. E JCSRI Greenwood Genetic Center Greenwood USA School of Computing Clemson University Clemson USA Biochemical Genetics Laboratory Greenwood Genetic Center Greenwood USA Department Psychiatry Yale Sch Med and VA CT Healthcare Center West Haven USA Department Genetics Yale Sch Med and VA CT Healthcare Center West Haven USA Department Neurobiology Yale Sch Med and VA CT Healthcare Center West Haven USA Singapore Institute for Clinical Sciences Singapore Singapore National University of Singapore Singapore Singapore University of British Columbia Vancouver Canada KK Women’s and Children’s Hospital Singapore Singapore University of Southampton and University Hospital Southampton NHS Foundation Trust Southampton UK University of Auckland Auckland New Zealand McKusick-Nathans Institute of Genetic Medicine Johns Hopkins University School of Medicine Baltimore USA Esslingen University of Applied Sciences Esslingen Germany German Cancer Research Center Heidelberg Germany Department of Genetic Medicine and Development University of Geneva Medical School Geneva Switzerland Geneva University Hospitals-HUG Service of Genetic Medicine Geneva Switzerland GE3 Institute of Genetics and Genomics of Geneva University of Geneva Medical School Geneva Switzerland South Texas Diabetes and Obesity Institute School of Medicine University of Texas Rio-Grande Valley Edinburg USA South Texas Diabetes and Obesity Institute School of Medicine University of Texas Rio-Grande Valley Brownsville USA Institute of Genetic Medicine Johns Hopkins University Baltimore USA Genomics Division Lawrence Berkeley National Laboratory Berkeley USA Molecular and Human Genetics Baylor College of Medicine Houston USA Department of Translational Medical Sciences Federico II University Naples Italy Metabolon Inc Durham USA Section of Pediatric Neurology and Neuroscience Baylor College of Medicine Houston USA Tawam Hospital Abu Dhabi United Arab Emirates Stanford Medical School Stanford USA Sch

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s

关键词： Pulmonary Arterial Hypertension Oral Squamous Cell Carcinoma Deep Neural Network Autosomal Recessive Polycystic Kidney Disease Whole Genome Bisulfite Sequencing

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Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data

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BMC Biophysics 2011年第1期4卷 1-12页

作者： Morita, Mizuki Katta, AVSK M. Ahmad, Shandar Mori, Takaharu Sugita, Yuji Mizuguchi, Kenji Department of Fundamental Research National Institute of Biomedical Innovation Ibaraki Osaka 7-6-8 Saito Asagi Japan Institute of Bioinformatics Research and Development Japan Science and Technology Agency Chiyoda-ku Tokyo 5-3 Yonbancho Japan RIKEN Quantitative Biology Center Kobe Hyogo 7-1-26 Minatojima-minamimachi Chuo-ku Japan RIKEN Advanced Science Institute Saitama 2-1 Hirosawa Wako-shi Japan RIKEN Advanced Institute for Computational Science Kobe Hyogo 7-1-26 Minatojima-minamimachi Chuo-ku Japan

Background: Protein-lipid interactions play essential roles in the conformational stability and biological functions of membrane proteins. However, few of the previous computational studies have taken into account the atomic details of protein-lipid interactions ***: To gain an insight into the molecular mechanisms of the recognition of lipid molecules by membrane proteins, we investigated amino acid propensities in membrane proteins for interacting with the head and tail groups of lipid molecules. We observed a common pattern of lipid tail-amino acid interactions in two different data sources, crystal structures and molecular dynamics simulations. These interactions are largely explained by general lipophilicity, whereas the preferences for lipid head groups vary among individual proteins. We also found that membrane and water-soluble proteins utilize essentially an identical set of amino acids for interacting with lipid head and tail ***: We showed that the lipophilicity of amino acid residues determines the amino acid preferences for lipid tail groups in both membrane and water-soluble proteins, suggesting that tightly-bound lipid molecules and lipids in the annular shell interact with membrane proteins in a similar manner. In contrast, interactions between lipid head groups and amino acids showed a more variable pattern, apparently constrained by each protein's specific molecular function. © 2011 Morita et al;licensee BioMed Central Ltd.

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Paper supplement: Study on the pan carbon-fiber-innovation for modeling a successful R&D management - An excited-oscillation management model

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Synthesiology 2011年第2期4卷 111-114页

作者： Nakamura, Osamu Ohana, Tsuguyori Tazawa, Masato Yokota, Shinji Shinoda, Wataru Nakamura, Osamu Itoh, Junji Evaluation Division AIST Tsukuba central 2 Umezono1-1-1 Tsukuba 305-8568 Japan Advanced Manufacturing Research Institute AIST Tsukuba central 2 Higashi 1-1-1 Tsukuba 305-8565 Japan Materials Research Institute for Sustainable Development AIST Anagahora 2266-98 Shimoshidami Moriyama-ku Nagoya 463-8560 Japan Research and Innovation Promotion Office AIST Kasumigaseki 1-3-1 Chiyoda-ku 100-8921 Japan Research Institute for Computational Sciences AIST Tsukuba Central 2 Umezono1-1-1 Tsukuba 305-8568 Japan Science and Technology Promotion Division Nagasaki Prefectural Govenment Edo-cho 2-13 Nagasaki 850-8570 Japan AIST Board of Trustees AIST Tsukuba Central 2 Umezono1-1-1 Tsukuba 305-8568 Japan

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The Broad Institute-Six Years Later

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CHEMISTRY & BIOLOGY 2010年第4期17卷 311-312页

作者： McCarthy, Alice Main Text “In June 2003 the scientific and medical communities at MIT Harvard University and its affiliated hospitals and the Whitehead Institute banded together as collaborating partners to form the Eli and Edythe L. Broad Institute based in Cambridge MA. The Broad Institute established with initial funding from a $100 million philanthropic donation from the Los Angeles-based Broad family was primarily viewed as a marriage between the Whitehead Institute's Center for Genome Research (WICGR) and the Harvard Institute of Chemistry and Cell Biology (ICCB). Eli Broad founder and chairman of AIG SunAmerica Inc. explained “the purpose of the Broad Institute is to create a new type of research institute to build on the accomplishments of the human genome project and to move to clinical applications to both prevent and cure diseases.” Every Thursday morning we meet with perhaps 20 faculty members and 100 other researchers to discuss what we're all doing and should be doing next. -David Altschuler This paragraph was written five years ago when the Broad Institute was in its very earliest days as a life science research community (McCarthy 2005). Since that time “the Broad” as it's known has kept true to Eli Broad's vision having attracted a talented group of researchers faculty trainees and professional staff. This 1600 person research community known internally as “Broadies” includes faculty staff and students from throughout the MIT and Harvard biomedical research communities and beyond with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. “What is special about the Broad is that we have people from Harvard MIT and the Harvard hospitals come together and work on problems of shared interest that could not be solved in their own individuals labs” explains David Altshuler M.D. Ph.D. Deputy Director and one of the Broad's six core faculty members. “These problems require expertise beyond any one principal investigator and in

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Study on the PAN carbon-fiber-innovation for modeling a successful R&D management

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Synthesiology 2009年第2期2卷 154-164页

作者： Nakamura, Osamu Ohana, Tsuguyori Tazawa, Masato Yokota, Shinji Shinoda, Wataru Itoh, Junji Evaluation Division AIST Tsukuba Central 2 Tsukuba 305-8568 Japan Advanced Manufacturing Research Institute AIST Tsukuba Central 5 Tsukuba 305-8565 Japan Materials Research Institute for Sustainable Development AIST Anagahora 2266-98 Shimoshidami Moriyama-ku Nagoya 463-8560 Japan Research and Innovation Promotion Office AIST Kasumigaseki 1-3-1 Chiyoda-ku 100-8921 Japan Research Institute for Computational Sciences AIST Tsukuba Central 2 Tsukuba 305-8568 Japan Science and Technology Promotion Bureau Nagasaki Prefectural Government 2-13 Edo-machi Nagasaki 850-8570 Japan AIST Board of Trustees AIST Tsukuba Central 2 Tsukuba 305-8568 Japan

We have investigated the processes of invention of PAN (Polyacrylonitrile) carbon fiber and its technology transfer to private companies. From this investigation and analysis, we have found a new R&D management model, named "excited-oscillation model". This model suggests that both the top-down management and the personal motivation should be in phase and synergetic with each other. In this paper, the results and concept of the above model are described in detail.

关键词： Innovation model Management PAN-based carbon fiber technology transfer

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Chemical controllability of charge states of nitrogen-related defects in HfOxNy: First-principles calculations

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Physical Review B 2008年第16期77卷 165130-165130页

作者： N. Umezawa K. Shiraishi Y. Akasaka A. Oshiyama S. Inumiya S. Miyazaki K. Ohmori T. Chikyow T. Ohno K. Yamabe Y. Nara K. Yamada Advanced Electronic Materials Center National Institute for Materials Science Tsukuba 305-0044 Japan Graduate School of Pure and Applied Sciences University of Tsukuba Tsukuba 305-8571 Japan Leading Edge Process Development Center Tokyo Electron Ltd. Yamanashi 407-0912 Japan Department of Applied Physics University of Tokyo Tokyo 113-8656 Japan Semiconductor Company Toshiba Corporation Yokohama 235-8522 Japan Graduate School of Advanced Sciences of Matter Hiroshima University Hiroshima 739-8530 Japan Nanotechnology Research Laboratories Waseda University Tokyo 169-0041 Japan Computational Materials Science Center National Institute for Materials Science Tsukuba 305-0047 Japan Semiconductor Leading Edge Technology Inc. Tsukuba 305-8569 Japan

Relative stabilities of nitrogen-related defects in HfOxNy have been extensively studied in terms of formation energies by using first-principles calculations. We have found that the two oxygen vacancies coupled with two substitutional nitrogen atoms at oxygen sites is the predominant defect in a low oxygen chemical potential (μO) with doubly positive [(NO)2(VO)2]+2 and neutral [(NO)2(VO)2]0 forms for the p-type and n-type silicon substrates, respectively. On the other hand, the negatively charged substitutional nitrogen [(NO)2]−2 predominates in a higher μO condition. A neutral defect, [(NO)2VO]0, is found to be stabilized in the midregion of μO, which indicates that the oxygen partial pressure is an important factor to control fixed charges that cause malfunction in HfOxNy-based devices. An electron counting concept is shown to be valid to predict the stable forms of the defects.

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Vacancy-type defects in MOSFETs with high-k gate dielectrics probed by monoenergetic positron beams

Vacancy-type defects in MOSFETs with high-k gate dielectrics...

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

作者： Uedono, A. Hasunuma, R. Shiraishi, K. Yamabe, K. Inumiya, S. Akasaka, Y. Kamiyama, S. Matsuki, T. Aoyama, T. Nara, Y. Miyazaki, S. Watanabe, H. Umezawa, N. Chikyow, T. Ishibashi, S. Ohdaira, T. Suzuki, R. Yamada, K. Graduate School of Pure and Applied Science University of Tsukuba Tsukuba Ibaraki 305-8573 Japan Semiconductor Leading Edge Technologies Inc Tsukuba Ibaraki 305-8569 Japan Graduate School of Advanced Sciences of Matter Hiroshima University Kagamiyama Higashi-Hiroshima 739-8530 Japan Graduate School of Engineering Osaka University Suita Osaka 565-0871 Japan Advanced Electronic Materials Center National Institute for Materials Science Tsukuba Ibaraki 305-0044 Japan Research Institute for Computational Sciences National Institute of Advanced Industrial Science and Technology Tsukuba Ibaraki 305-8568 Japan Research Institute of Instrumentation Frontier National Institute of Advanced Industrial Science and Technology Tsukuba Ibaraki 305-8568 Japan Nano Technology Research Laboratory Waseda University Shinjuku Tokyo 16-0041 Japan Process and Manufacturing Engineering Center Toshiba Co. Isogo-Ku Yokohama 235-8522 Japan Leading Edge Process Development Center Tokyo Electron LTD. 650 Mitsuzawa Hosaka-cho Nirasaki City Yamanashi 407-0192 Japan

ISBN: (纸本)9781566775700

Vacancy-type defects in MOSFET structures fabricated with high-k (HfSiON) gate dielectrics were studied by monogenetic positron beams An expansion of open volumes in HfSiON fabricated on Si substrates using atomic layer deposition technique was observed with increasing nitrogen concentration This fact was discussed in terms of a role of nitrogen in Hf-related oxide using results obtained by first-principles calculation and XPS. MOSFETs fabricated by F +-channel implantation technique were also characterized. The major defect species which causes the F& shift of MOSFETs was identified as vacancy-fluorine complexes (such as V3F2) locate in channel regions of Si substrates. The preset work suggests that positron annihilation can be used to detect microscopic defects in MOSFETs, and it is a useful tool for determining process parameters for MOSFET fabrications with high-k gate dielectrics. © The Electrochemical Society.

关键词： Fabrication

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Role of the ionicity in defect formation in Hf-based dielectrics

Role of the ionicity in defect formation in Hf-based dielect...

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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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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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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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