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Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

Science Bulletin 2016年第15期61卷 1176-1186页

作者： Yong Wang Zhao-Ming Gao Jiang-Tao Li Salim Bougouffa Ren Mao Tian Vladimir B. Bajic Pei-Yuan Qian Sanya Institute of Deep Sea Science and Engineering ChineseAcademy of Sciences Sanya 572000 China Division of Life Science Hong Kong University of Science and Technology Clear Water Bay Hong Kong China State Key Laboratory of Marine Geology Tongji UniversityShanghai 200092 China Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Jeddah 23955-6900 Saudi Arabia

Aerophobetes （or CD12） is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bac- terium TCSI from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS 1 and some thermophilic bac- terial phyla. The genome of TCS1 （at least 1.27 Mbp） contains a full set of genes encoding core metabolic path- ways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved inthe sediment under the microbial mat. Aerophobetes bac- terium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood-Ljung- dahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood-Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aero- phobetes bacterium TCS 1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal trans- duction and cell motility. The metabolic activities of TCS 1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCSI might be a facultative bacterium in anaerobic saline sedi- ments near cold seeps.

关键词： Deep-sea sediment Aerophobetes Metagenome Sugar fermentation Cold seep

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Tuberculosis infection and lung adenocarcinoma: Mendelian randomization and pathway analysis of genome-wide association study data from never-smoking Asian women

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Genomics 2020年第2期112卷 1223-1232页

作者： Jason Y Y Wong Han Zhang Chao A Hsiung Kouya Shiraishi Kai Yu Keitaro Matsuo Maria Pik Wong Yun-Chul Hong Jiucun Wang Wei Jie Seow Zhaoming Wang Minsun Song Hee Nam Kim I-Shou Chang Nilanjan Chatterjee Wei Hu Chen Wu Tetsuya Mitsudomi Wei Zheng Jin Hee Kim Adeline Seow Neil E Caporaso Min-Ho Shin Lap Ping Chung She-Juan An Ping Wang Yang Yang Hong Zheng Yasushi Yatabe Xu-Chao Zhang Young Tae Kim Qiuyin Cai Zhihua Yin Young-Chul Kim Bryan A Bassig Jiang Chang James Chung Man Ho Bu-Tian Ji Yataro Daigo Hidemi Ito Yukihide Momozawa Kyota Ashikawa Yoichiro Kamatani Takayuki Honda H Dean Hosgood Hiromi Sakamoto Hideo Kunitoh Koji Tsuta Shun-Ichi Watanabe Michiaki Kubo Yohei Miyagi Haruhiko Nakayama Shingo Matsumoto Masahiro Tsuboi Koichi Goto Jianxin Shi Lei Song Xing Hua Atsushi Takahashi Akiteru Goto Yoshihiro Minamiya Kimihiro Shimizu Kazumi Tanaka Fusheng Wei Fumihiko Matsuda Jian Su Yeul Hong Kim In-Jae Oh Fengju Song Wu-Chou Su Yu-Min Chen Gee-Chen Chang Kuan-Yu Chen Ming-Shyan Huang Li-Hsin Chien Yong-Bing Xiang Jae Yong Park Sun-Seog Kweon Chien-Jen Chen Kyoung-Mu Lee Batel Blechter Haixin Li Yu-Tang Gao Biyun Qian Daru Lu Jianjun Liu Hyo-Sung Jeon Chin-Fu Hsiao Jae Sook Sung Ying-Huang Tsai Yoo Jin Jung Huan Guo Zhibin Hu Wen-Chang Wang Charles C Chung Laurie Burdett Meredith Yeager Amy Hutchinson Sonja I Berndt Wei Wu Herbert Pang Yuqing Li Jin Eun Choi Kyong Hwa Park Sook Whan Sung Li Liu C H Kang Meng Zhu Chung-Hsing Chen Tsung-Ying Yang Jun Xu Peng Guan Wen Tan Chih-Liang Wang Michael Hsin Ko-Yung Sit James Ho Ying Chen Yi Young Choi Jen-Yu Hung Jun Suk Kim Ho Il Yoon Chien-Chung Lin In Kyu Park Ping Xu Yuzhuo Wang Qincheng He Reury-Perng Perng Chih-Yi Chen Roel Vermeulen Junjie Wu Wei-Yen Lim Kun-Chieh Chen Yao-Jen Li Jihua Li Hongyan Chen Chong-Jen Yu Li Jin Tzu-Yu Chen Shih-Sheng Jiang Jie Liu Taiki Yamaji Belynda Hicks Kathleen Wyatt Shengchao A Li Juncheng Dai Hongxia Ma Guangfu Jin Bao Song Zhehai Wang Sensen Cheng Xuelian Li Yangwu Ren Ping Cui Motoki Iwasaki Taichi Shimazu Shoichiro Tsugane Junjie Division of Cancer Epidemiology and Genetics National Cancer Institute Bethesda MD USA. Electronic address: jason.wong@nih.gov. Division of Cancer Epidemiology and Genetics National Cancer Institute Bethesda MD USA. Institute of Population Health Sciences National Health Research Institutes Zhunan Taiwan. Division of Genome Biology National Cancer Center Research Institute Tokyo Japan. Division of Cancer Epidemiology and Prevention Aichi Cancer Center Research Institute Nagoya Japan Department of Cancer Epidemiology Nagoya University Graduate School of Medicine Nagoya Japan. Department of Pathology Queen Mary Hospital The University of Hong Kong Hong Kong. Department of Preventive Medicine Seoul National University College of Medicine Seoul Republic of Korea. Ministry of Education Key Laboratory of Contemporary Anthropology School of Life Sciences Fudan University Shanghai China State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai China. Saw Swee Hock School of Public Health National University of Singapore Singapore. Cancer Genomics Research Laboratory Leidos Biomedical Research Inc Gaithersburg MD USA Department of Computational Biology St. Jude Children's Research Hospital Memphis TN USA. Division of Cancer Epidemiology and Genetics National Cancer Institute Bethesda MD USA Department of Statistics Sookmyung Women's University Seoul Republic of Korea. Department of Preventive Medicine Chonnam National University Medical School Gwangju Republic of Korea. National Institute of Cancer Research National Health Research Institutes Zhunan Taiwan. Bloomberg School of Public Health Johns Hopkins University Baltimore MD USA. Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology Cancer Institute and Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China. Division of Thoracic Surgery Kinki University School of Medicine Sayama Japan. Division of

We investigated whether genetic susceptibility to tuberculosis (TB) influences lung adenocarcinoma development among never-smokers using TB genome-wide association study (GWAS) results within the Female Lung Cancer Consortium in Asia. Pathway analysis with the adaptive rank truncated product method was used to assess the association between a TB-related gene-set and lung adenocarcinoma using GWAS data from 5512 lung adenocarcinoma cases and 6277 controls. The gene-set consisted of 31 genes containing known/suggestive associations with genetic variants from previous TB-GWAS. Subsequently, we followed-up with Mendelian Randomization to evaluate the association between TB and lung adenocarcinoma using three genome-wide significant variants from previous TB-GWAS in East Asians. The TB-related gene-set was associated with lung adenocarcinoma (p = 0.016). Additionally, the Mendelian Randomization showed an association between TB and lung adenocarcinoma (OR = 1.31, 95% CI: 1.03, 1.66, p = 0.027). Our findings support TB as a causal risk factor for lung cancer development among never-smoking Asian women.

关键词： Lung adenocarcinoma Lung cancer Mendelian randomization Pathway analysis Tuberculosis

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Inside Cover Image, Volume 234, Number 11, November 2019

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Journal of Cellular Physiology 2019年第11期234卷

作者： William J. Wulftange Michelle A. Rose Marcial Garmendia-Cedillos Davi da Silva Joanna E. Poprawski Dhruv Srinivasachar Taylor Sullivan Langston Lim Valery V. Bliskovsky Matthew D. Hall Thomas J. Pohida Robert W. Robey Nicole Y. Morgan Michael M. Gottesman Trans-NIH Shared Resources on Biomedical Engineering and Physical Sciences (BEPS) National Institutes of Biomedical Imaging and Bioengineering (NIBIB) National Institutes of Health Bethesda Maryland Laboratory of Cell Biology Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda Maryland Division of Computational Bioscience Center for Information Technology National Institutes of Health Bethesda Maryland Confocal Microscopy Core Facility Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda Maryland CCR Genomics Core National Cancer Institute National Institutes of Health Bethesda Maryland National Center for Advancing Translational Sciences National Institutes of Health Bethesda Maryland

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Author Correction: RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

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Nature communications 2021年第1期12卷 3128页

作者： Alessandro Bonetti Federico Agostini Ana Maria Suzuki Kosuke Hashimoto Giovanni Pascarella Juliette Gimenez Leonie Roos Alex J Nash Marco Ghilotti Christopher J F Cameron Matthew Valentine Yulia A Medvedeva Shuhei Noguchi Eneritz Agirre Kaori Kashi Joachim Luginbühl Riccardo Cazzoli Saumya Agrawal Nicholas M Luscombe Mathieu Blanchette Takeya Kasukawa Michiel de Hoon Erik Arner Boris Lenhard Charles Plessy Gonçalo Castelo-Branco Valerio Orlando Piero Carninci RIKEN Center for Integrative Medical Sciences Yokohama Kanagawa 230-0045 Japan. alessandro.bonetti@riken.jp. Laboratory of Molecular Neurobiology Department Medical Biochemistry and Biophysics Karolinska Institutet Stockholm Sweden. alessandro.bonetti@riken.jp. The Francis Crick Institute 1 Midland Road London NW1 1AT UK. RIKEN Center for Integrative Medical Sciences Yokohama Kanagawa 230-0045 Japan. Department of Medicine (H7) Karolinska Institutet Stockholm 141 86 Sweden. Epigenetics and Genome Reprogramming Laboratory IRCCS Fondazione Santa Lucia Rome Italy. Faculty of Medicine Imperial College London Institute of Clinical Sciences London W12 0NN UK. MRC London Institute of Medical Sciences London W12 0NN UK. School of Computer Science McGill University Montréal QC Canada. Department of Biochemistry and Goodman Cancer Research Centre McGill University Montréal QC Canada. Institute of Bioengineering Research Centre of Biotechnology Russian Academy of Science 117312 Moscow Russia. Department of Computational Biology Vavilov Institute of General Genetics Russian Academy of Science 119991 Moscow Russia. Department of Biological and Medical Physics Moscow Institute of Physics and Technology 141701 Dolgoprudny Moscow Region Russia. Laboratory of Molecular Neurobiology Department Medical Biochemistry and Biophysics Karolinska Institutet Stockholm Sweden. Department of Experimental Oncology IEO European Institute of Oncology IRCCS Milan Italy. UCL Genetics Institute University College London London WC1E 6BT UK. Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha Onna-son Kunigami-gun Okinawa 904-0495 Japan. Sars International Centre for Marine Molecular Biology University of Bergen 5008 Bergen Norway. Epigenetics and Genome Reprogramming Laboratory IRCCS Fondazione Santa Lucia Rome Italy. valerio.orlando@kaust.edu.sa. KAUST Environmental Epigenetics Program King Abdullah University of Science and Technology (KAUS

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Where Does AlphaGo Go: From Church-Turing Thesis to AlphaGo Thesis and Beyond

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IEEE/CAA Journal of Automatica Sinica 2016年第2期3卷 113-120页

作者： Fei-Yue Wang Jun Jason Zhang Xinhu Zheng Xiao Wang Yong Yuan Xiaoxiao Dai Jie Zhang Liuqing Yang IEEE the State Key Laboratory of Management and Control for Complex Systems Institute of Automation Chinese Academy of Sciences (SKL-MCCS CASIA) Research Center of Computational Experiments and Parallel Systems The National University of Defense Technology the Department of Electrical and Computer Engineering Ritchie School of Engineering and Computer Science University of Denver the Department of Computer Science and Engineering University of Minnesota the Qingdao Academy of Intelligent Industries (QAII) Qingdao Shandong China and SKL-MCCS CASIA the Department of Electrical and Computer Engineering Colorado State University

An investigation on the impact and significance of the AlphaGo vs. Lee Sedol Go match is conducted, and concludes with a conjecture of the AlphaGo Thesis and its extension in accordance with the Church-Turing Thesis in the history of computing. It is postulated that the architecture and method utilized by the AlphaGo program provide an engineering solution for tackling issues in complexity and intelligence. Specifically, the AlphaGo Thesis implies that any effective procedure for hard decision problems such as NP-hard can be implemented with AlphaGo-like approach. Deep rule-based networks are proposed in attempt to establish an understandable structure for deep neural networks in deep learning. The success of AlphaGo and corresponding thesis ensure the technical soundness of the parallel intelligence approach for intelligent control and management of complex systems and knowledge automation. © 2014 Chinese Association of Automation.

关键词： Religious buildings

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Quantum simulators: Architectures and opportunities

arXiv

引用

arXiv 2019年

作者： Altman, Ehud Brown, Kenneth R. Carleo, Giuseppe Carr, Lincoln D. Demler, Eugene Chin, Cheng DeMarco, Brian Economou, Sophia E. Eriksson, Mark A. Fu, Kai-Mei C. Greiner, Markus Hazzard, Kaden R.A. Hulet, Randall G. Kollár, Alicia J. Lev, Benjamin L. Lukin, Mikhail D. Ma, Ruichao Mi, Xiao Misra, Shashank Monroe, Christopher Murch, Kater Nazario, Zaira Ni, Kang-Kuen Potter, Andrew C. Roushan, Pedram Saffman, Mark Schleier-Smith, Monika Siddiqi, Irfan Simmonds, Raymond Singh, Meenakshi Spielman, I.B. Temme, Kristan Weiss, David S. Vučković, Jelena Vuletić, Vladan Ye, Jun Zwierlein, Martin Department of Physics University of California BerkeleyCA94720 United States Department of Electrical and Computer Engineering Department of Physics Department of Chemistry Duke University DurhamNC27708 United States Center for Computational Quantum Physics Flatiron Institute New YorkNY10010 United States Department of Physics Colorado School of Mines GoldenCO80401 United States Department of Physics Harvard University CambridgeMA02138 United States Department of Physics Chicago University ChicagoIL60637 United States Department of Physics and IQUIST University of Illinois Urbana-ChampaignIL61801 United States Department of Physics Virgina Tech BlacksburgVA24061 United States Department of Physics University of Wisconsin-Madison MadisonWI53706 United States Department of Electrical and Computer Engineering Department of Physics University of Washington SeattleWA98195 United States Department of Physics and Astronomy Rice University HoustonTX77005 United States Joint Quantum Institute Department of Physics University of Maryland College ParkMD20742 United States IonQ Inc. College ParkMD20740 United States Department of Physics Department of Applied Physics Stanford University StanfordCA94305 United States Department of Physics and Astronomy Purdue University West LafayetteIN47907 United States Google Inc. Santa BarbaraCA93101 United States Sandia National Laboratory AlbuquerqueNM87123 United States Department of Physics Washington University St. LouisMO63130 United States IBM T.J. Watson Research Center Yorktown HeightsNY10598 United States Department of Chemistry and Chemical Biology Harvard University CambridgeMA02138 United States Department of Physics The University of Texas at Austin AustinTX78712 United States National Institute of Standards and Technology BoulderCO80305 United States Department of Physics Pennsylvania State University University ParkPA16802 United States Department of Electri

Quantum simulators are a promising technology on the spectrum of quantum devices from specialized quantum experiments to universal quantum computers. These quantum devices utilize entanglement and many-particle behaviors to explore and solve hard scientific, engineering, and computational problems. Rapid development over the last two decades has produced more than 300 quantum simulators in operation worldwide using a wide variety of experimental platforms. Recent advances in several physical architectures promise a golden age of quantum simulators ranging from highly optimized special purpose simulators to flexible programmable devices. These developments have enabled a convergence of ideas drawn from fundamental physics, computer science, and device engineering. They have strong potential to address problems of societal importance, ranging from understanding vital chemical processes, to enabling the design of new materials with enhanced performance, to solving complex computational problems. It is the position of the community, as represented by participants of the NSF workshop on "Programmable Quantum Simulators," that investment in a national quantum simulator program is a high priority in order to accelerate the progress in this field and to result in the first practical applications of quantum machines. Such a program should address two areas of emphasis: (1) support for creating quantum simulator prototypes usable by the broader scientific community, complementary to the present universal quantum computer effort in industry;and (2) support for fundamental research carried out by a blend of multi-investigator, multi-disciplinary collaborations with resources for quantum simulator software, hardware, and education. Copyright © 2019, The Authors. All rights reserved.

关键词： Blending

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Author Correction: A robust benchmark for detection of germline large deletions and insertions

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Nature biotechnology 2020年第11期38卷 1357页

作者： Justin M Zook Nancy F Hansen Nathan D Olson Lesley Chapman James C Mullikin Chunlin Xiao Stephen Sherry Sergey Koren Adam M Phillippy Paul C Boutros Sayed Mohammad E Sahraeian Vincent Huang Alexandre Rouette Noah Alexander Christopher E Mason Iman Hajirasouliha Camir Ricketts Joyce Lee Rick Tearle Ian T Fiddes Alvaro Martinez Barrio Jeremiah Wala Andrew Carroll Noushin Ghaffari Oscar L Rodriguez Ali Bashir Shaun Jackman John J Farrell Aaron M Wenger Can Alkan Arda Soylev Michael C Schatz Shilpa Garg George Church Tobias Marschall Ken Chen Xian Fan Adam C English Jeffrey A Rosenfeld Weichen Zhou Ryan E Mills Jay M Sage Jennifer R Davis Michael D Kaiser John S Oliver Anthony P Catalano Mark J P Chaisson Noah Spies Fritz J Sedlazeck Marc Salit Material Measurement Laboratory National Institute of Standards and Technology Gaithersburg MD USA. jzook@nist.gov. National Human Genome Research Institute National Institutes of Health Rockville MD USA. Material Measurement Laboratory National Institute of Standards and Technology Gaithersburg MD USA. National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda MD USA. Department of Human Genetics University of California Los Angeles Los Angeles CA USA. Roche Sequencing Solutions Belmont CA USA. Ontario Institute for Cancer Research Toronto Ontario Canada. Charles-Bruneau Cancer Centre Division of Hematology-Oncology CHU Sainte-Justine Montreal Quebec Canada. Molecular Biology Institute University of California Los Angeles Los Angeles CA USA. Department of Physiology and Biophysics Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA. The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA. The WorldQuant Initiative for Quantitative Prediction Weill Cornell Medicine New York NY USA. The Feil Family Brain and Mind Research Institute Weill Cornell Medicine New York NY USA. Bionano Genomics Inc. San Diego CA USA. Davies Research Centre School of Animal and Veterinary Sciences University of Adelaide Roseworthy SA Australia. 10× Genomics Pleasanton CA USA. Broad Institute of Harvard and MIT Cambridge MA USA. Google Mountain View CA USA. Department of Computer Science Roy G. Perry College of Engineering Prairie View A&M University Prairie View TX USA. Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York NY USA. BC Cancer Genome Sciences Centre Vancouver British Columbia Canada. Biomedical Genetics Department of Medicine Boston University Medical School Boston MA USA. Pacific Biosciences Menlo Park CA USA. Department of Computer Engin

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Causes of blindness and vision impairment in 2020 and trends over 30 years, and prevalence of avoidable blindness in relation to VISION 2020: the Right to Sight: an analysis for the Global Burden of Disease Study (vol 2, pg 144, 2021)

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LANCET GLOBAL HEALTH 2021年第4期9卷 E408-E408页

作者： Steinmetz, Jaimie D. Vision and Eye Research Institute Anglia Ruskin University Cambridge United Kingdom Biomedical Informatics Seoul National University Hospital Seoul South Korea Institute for Health Metrics and Evaluation University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States Institute of Health Services Research Yonsei University Seoul South Korea Department of Ophthalmology University of Washington Seattle WA United States Department of Mathematics Imperial College London London United Kingdom WHO Collaborating Centre for Public Health Education and Training Imperial College London London United Kingdom Department of Primary Care and Public Health Imperial College London London United Kingdom School of Population and Global Health University of Melbourne Carlton VIC Australia School of Optometry and Vision Science UNSW Sydney NSW Australia Brien Holden Vision Institute Sydney Australia Department of Ophthalmology University of Adelaide Adelaide SA Australia Department of Parasitology and Mycology Jahrom University of Medical Sciences Jahrom Iran Department of Clinical Sciences University of Sharjah Sharjah United Arab Emirates Ophthalmic Research Center Shahid Beheshti University of Medical Sciences Tehran Iran Department of Ophthalmology Shahid Beheshti University of Medical Sciences Tehran Iran Research Institute for Endocrine Sciences Shahid Beheshti University of Medical Sciences Tehran Iran Ophthalmic Epidemiology Research Center Shahid Beheshti University of Medical Sciences Tehran Iran Health Services Management Department Qazvin University of Medical Sciences Qazvin Iran Department of Systems Populations and Leadership University of Michigan Ann Arbor MI United States Department of Medicine Sofia Ismail Memorial Medical Centre Bogura Bangladesh The Fred Hollows Foundation Sydney NSW Australia Berhan Public Health & Eye Care Consultancy Addis A

Hospital El Salvador: a novel paradigm of intensive care in response to COVID-19 in central America. Lancet Glob Health 2021;9: e241?42?In this Comment, the conflict of interest statement should have included the following: ?By virtue of their roles within a public hospital or the Ministry of Health, MB, LC, WH, and XS are government employees. The findings and conclusions in the Comment are only those of the authors.? This correction has been made as of Feb 26, 2021.

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Author Correction: The power of genetic diversity in genome-wide association studies of lipids

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Nature 2023年第7965期618卷 E19-E20页

作者： Sarah E Graham Shoa L Clarke Kuan-Han H Wu Stavroula Kanoni Greg J M Zajac Shweta Ramdas Ida Surakka Ioanna Ntalla Sailaja Vedantam Thomas W Winkler Adam E Locke Eirini Marouli Mi Yeong Hwang Sohee Han Akira Narita Ananyo Choudhury Amy R Bentley Kenneth Ekoru Anurag Verma Bhavi Trivedi Hilary C Martin Karen A Hunt Qin Hui Derek Klarin Xiang Zhu Gudmar Thorleifsson Anna Helgadottir Daniel F Gudbjartsson Hilma Holm Isleifur Olafsson Masato Akiyama Saori Sakaue Chikashi Terao Masahiro Kanai Wei Zhou Ben M Brumpton Humaira Rasheed Sanni E Ruotsalainen Aki S Havulinna Yogasudha Veturi QiPing Feng Elisabeth A Rosenthal Todd Lingren Jennifer Allen Pacheco Sarah A Pendergrass Jeffrey Haessler Franco Giulianini Yuki Bradford Jason E Miller Archie Campbell Kuang Lin Iona Y Millwood George Hindy Asif Rasheed Jessica D Faul Wei Zhao David R Weir Constance Turman Hongyan Huang Mariaelisa Graff Anubha Mahajan Michael R Brown Weihua Zhang Ketian Yu Ellen M Schmidt Anita Pandit Stefan Gustafsson Xianyong Yin Jian'an Luan Jing-Hua Zhao Fumihiko Matsuda Hye-Mi Jang Kyungheon Yoon Carolina Medina-Gomez Achilleas Pitsillides Jouke Jan Hottenga Gonneke Willemsen Andrew R Wood Yingji Ji Zishan Gao Simon Haworth Ruth E Mitchell Jin Fang Chai Mette Aadahl Jie Yao Ani Manichaikul Helen R Warren Julia Ramirez Jette Bork-Jensen Line L Kårhus Anuj Goel Maria Sabater-Lleal Raymond Noordam Carlo Sidore Edoardo Fiorillo Aaron F McDaid Pedro Marques-Vidal Matthias Wielscher Stella Trompet Naveed Sattar Line T Møllehave Betina H Thuesen Matthias Munz Lingyao Zeng Jianfeng Huang Bin Yang Alaitz Poveda Azra Kurbasic Claudia Lamina Lukas Forer Markus Scholz Tessel E Galesloot Jonathan P Bradfield E Warwick Daw Joseph M Zmuda Jonathan S Mitchell Christian Fuchsberger Henry Christensen Jennifer A Brody Mary F Feitosa Mary K Wojczynski Michael Preuss Massimo Mangino Paraskevi Christofidou Niek Verweij Jan W Benjamins Jorgen Engmann Rachel L Kember Roderick C Slieker Ken Sin Lo Nuno R Zilhao Phuong Le Marcus E Kleber Graciela E Delgado Shaofeng Huo Dai Department of Internal Medicine Division of Cardiology University of Michigan Ann Arbor MI USA. VA Palo Alto Health Care System Palo Alto CA USA. Department of Medicine Division of Cardiovascular Medicine Stanford University School of Medicine Stanford CA USA. Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI USA. William Harvey Research Institute Barts and the London School of Medicine and Dentistry Queen Mary University of London London UK. Department of Biostatistics and Center for Statistics Genetics University of Michigan Ann Arbor MI USA. Department of Genetics Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Clinical Pharmacology William Harvey Research Institute Barts and The London School of Medicine and Dentistry Queen Mary University of London London UK. Endocrinology Boston Children's Hospital Boston MA USA. Medical and Population Genetics Broad Institute Cambridge MA USA. Department of Genetic Epidemiology University of Regensburg Regensburg Germany. McDonnell Genome Institute and Department of Medicine Washington University St Louis MO USA. Department of Precision Medicine Division of Genome Science National Institute of Health Cheongju-si South Korea. Tohoku Medical Megabank Organization Tohoku University Sendai Japan. Sydney Brenner Institute for Molecular Bioscience Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa. Center for Research on Genomics and Global Health National Human Genome Research Institute National Institutes of Health Bethesda MD USA. Blizard Institute Barts and the London School of Medicine and Dentistry Queen Mary University of London London UK. Wellcome Sanger Institute Hinxton UK. Department of Epidemiology Emory University Rollins School of Public Health Atlanta GA USA. Atlanta VA Health Care System Decatur GA USA. Malcolm Randall VA Medical Center Gainesville FL USA. Division of Vascular Sur

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QMCPACK: An open source ab initio Quantum Monte Carlo package for the electronic structure of atoms, molecules, and solids

arXiv

引用

arXiv 2018年

作者： Kim, Jeongnim Baczewski, Andrew Beaudet, Todd D. Benali, Anouar Bennett, M. Chandler Berrill, Mark A. Blunt, Nick S. Borda, Edgar Casula, Michele Ceperley, David M. Chiesa, Simone Clark, Bryan K. Clay, Raymond C. Delaney, Kris T. Dewing, Mark Esler, Kenneth P. Hao, Hongxia Heinonen, Olle Kent, Paul R.C. Krogel, Jaron T. Kylänpää, Ilkka Li, Ying Wai Lopez, M. Graham Luo, Ye Malone, Fionn D. Martin, Richard M. Mathuriya, Amrita McMinis, Jeremy Melton, Cody A. Mitas, Lubos Morales, Miguel A. Neuscamman, Eric Parker, William D. Flores, D. Pineda Romero, Nichols A. Rubenstein, Brenda M. Shea, Jacqueline A.R. Shin, Hyeondeok Shulenburger, Luke Tillack, Andreas Townsend, Joshua P. Tubman, Norm M. Goetz, Brett Vincent, Jordan E. Yang, D. ChangMo Yang, Yubo Zhang, Shuai Zhao, Luning Intel Corporation HillsboroOR987124 United States HEDP Theory Department Sandia National Laboratories AlbuquerqueNM87185 United States Department of Mechanical and Aerospace Engineering University of Virginia CharlottesvilleVA22904 United States Argonne Leadership Computing Facility Argonne National Laboratory ArgonneIL60439 United States Computational Science Division Argonne National Laboratory ArgonneIL60439 United States Department of Physics North Carolina State University RaleighNC27695 United States Computer Science and Mathematics Division Oak Ridge National Laboratory Oak RidgeTN37831 United States University Chemical Laboratory Lensfield Road CambridgeCB2 1EW United Kingdom Lawrence Livermore National Laboratory LivermoreCA94550 United States Sorbonne Université CNRS UMR 7590 IRD UMR 206 MNHN 4 Place Jussieu Paris75252 France Department of Physics University of Illinois UrbanaIL61801 United States Materials Research Laboratory University of California Santa BarbaraCA93106 United States Stone Ridge Technology Bel AirMD21015 United States Department of Chemistry Brown University ProvidenceRI02912 United States Material Science Division Argonne National Laboratory ArgonneIL60439 United States Northwestern-Argonne Institute for Science and Engineering Northwestern University EvanstonIL60208 United States Center for Nanophase Materials Sciences Oak Ridge National Laboratory Oak RidgeTN37831 United States Computational Sciences and Engineering Division Oak Ridge National Laboratory Oak RidgeTN37831 United States Materials Science and Technology Division Oak Ridge National Laboratory Oak Ridge TN37831 United States National Center for Computational Sciences Oak Ridge National Laboratory Oak RidgeTN37831 United States Department of Chemistry University of California BerkeleyCA94720 United States Chemical Sciences Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Department of M

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://***. Copyright © 2018, The Authors. All rights reserved.

关键词： Electronic structure

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