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High-order continuum kinetic method for modeling plasma dynamics in phase space

AIP Conference Proceedings 2014年第1期1639卷 146-149页

作者： G. V. Vogman P. Colella U. Shumlak Applied Science & Technology Program University of California Berkeley Berkeley CA 94720 USA Computational Research Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA and Department of Electrical Engineering & Computer Science University of California Berkeley CA 94720 USA Aerospace & Energetic Research Program University of Washington Seattle WA 98195 USA

Continuum methods offer a high-fidelity means of simulating plasma kinetics. While computationally intensive, these methods are advantageous because they can be cast in conservation-law form, are not susceptible to noise, and can be implemented using high-order numerical methods. Advances in continuum method capabilities for modeling kinetic phenomena in plasmas require the development of validation tools in higher dimensional phase space and an ability to handle non-cartesian geometries. To that end, a new benchmark for validating Vlasov-Poisson simulations in 3D (x,vx,vy) is presented [1]. The benchmark is based on the Dory-Guest-Harris instability and is successfully used to validate a continuum finite volume algorithm. To address challenges associated with non-cartesian geometries, unique features of cylindrical phase space coordinates are described. Preliminary results of continuum kinetic simulations in 4D (r,z,vr,vz) phase space are presented.

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A web-based, hospital-wide health care-associated bloodstream infection surveillance and classification system: Development and evaluation

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JMIR Medical Informatics 2015年第3期3卷 e31页

作者： Tseng, Yi-Ju Wu, Jung-Hsuan Lin, Hui-Chi Chen, Ming-Yuan Ping, Xiao-Ou Sun, Chun-Chuan Shang, Rung-Ji Sheng, Wang-Huei Chen, Yee-Chun Lai, Feipei Chang, Shan-Chwen Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan Computational Health Informatics Program Boston Children's Hospital Boston MA United States Department of Electrical Engineering National Taiwan University Taipei Taiwan Center for Infection Control National Taiwan University Hospital Taipei Taiwan National Taiwan University Hospital Information Systems Office Taipei Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei Taiwan Department of Internal Medicine National Taiwan University Hospital and College of Medicine Taipei Taiwan National Health Research Institutes National Institute of Infectious Diseases and Vaccinology Miaoli Taiwan

Background: Surveillance of health care-associated infections is an essential component of infection prevention programs, but conventional systems are labor intensive and performance dependent. Objective: To develop an automatic surveillance and classification system for health care-associated bloodstream infection (HABSI), and to evaluate its performance by comparing it with a conventional infection control personnel (ICP)-based surveillance system. Methods: We developed a Web-based system that was integrated into the medical information system of a 2200-bed teaching hospital in Taiwan. The system automatically detects and classifies HABSIs. Results: In this study, the number of computer-detected HABSIs correlated closely with the number of HABSIs detected by ICP by department (n=20;r=.999 P<.001) and by time (n=14;r=.941;P<.001). Compared with reference standards, this system performed excellently with regard to sensitivity (98.16%), specificity (99.96%), positive predictive value (95.81%), and negative predictive value (99.98%). The system enabled decreasing the delay in confirmation of HABSI cases, on average, by 29 days. Conclusions: This system provides reliable and objective HABSI data for quality indicators, improving the delay caused by a conventional surveillance system. © 2020 JMIR Publications Inc. All rights reserved.

关键词： Health care-associated infection Infection control Information systems Surveillance Web-based services

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Toward the Multi-scale Simulation for a Human Body Using the Next-generation Supercomputer

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Procedia IUTAM 2014年 10卷 193-200页

作者： Yoichiro Matsumoto Satoshi Ii Seiji Shiozaki Kazuyasu Sugiyama Shu Takagi School of Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan Department of Mechanical Science and Bioengineering Osaka University 1-1 Machikaneyama Toyonaka Osaka 560-0043 Japan Computational Science Research Program RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan

We have developed novel numerical methods for fluid-structure and fluid-membrane interaction problems. The basic equation set is formulated in a full Eulerian framework. The method is based on the finite difference volume-of-fluid scheme with fractional step algorithm. It is validated through a numerical solution to a deformable vesicle problem, and applied to blood flows including red blood cells (RBCs) and platelets. Further, to gain insight into the mechanism of thrombus formation, a stochastic Monte Carlo model to describe the platelet-vessel wall interaction is incorporated into the Eulerian method. The effect of the RBCs on the platelet motion is discussed.

关键词： Eulerian method fluid-structure interaction blood flow stochastic Monte Carlo method

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Discrete time optimal control applied to pest control problems

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Involve 2014年第4期7卷 479-489页

作者： Ding, Wandi Hendon, Raymond Cathey, Brandon Lancaster, Evan Germick, Robert Department of Mathematical Sciences Middle Tennessee State University Murfreesboro 37132 TN United States Computational Science Program Middle Tennessee State University Murfreesboro 37132 TN United States Department of Physics and Astronomy University of Tennessee Knoxville Knoxville 37996 TN United States Department of University Studies Middle Tennessee State University Murfreesboro 37132 TN United States Department of Electrical Engineering University of Tennessee Knoxville 37996 TN United States

We apply discrete time optimal control theory to the mathematical modeling of pest control. Two scenarios: biological control and the combination of pesticide and biological control are considered. The goal is maximizing the “valuable” population, minimizing the pest population and the cost to apply the control strategies. Using the extension of Pontryagin’s maximum principle to discrete system, the adjoint systems and the characterization of the optimal pest controls are derived. Numerical simulations of various cases are provided to show the effectiveness of our methods. © 2014 Mathematical sciences Publishers.

关键词： biological pest control discrete model optimal control pesticide

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Abstracts from the 8th International Conference on cGMP Generators, Effectors and Therapeutic Implications : Bamberg, Germany. 23-25 June, 2017

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BMC pharmacology & toxicology 2017年第SUPPL 1期18卷 64-64页

作者： Todd Milne, G. Sandner, Peter Lincoln, Kathleen A. Harrison, Paul C. Chen, Hongxing Wang, Hong Clifford, Holly Qian, Hu Sheng Wong, Diane Sarko, Chris Fryer, Ryan Richman, Jeremy Reinhart, Glenn A. Boustany, Carine M. Pullen, Steven S. Andresen, Henriette Moltzau, Lise Román Cataliotti, Alessandro Levy, Finn Olav Lukowski, Robert Frankenreiter, Sandra Friebe, Andreas Calamaras, Timothy Baumgartner, Robert McLaughlin, Angela Aronovitz, Mark Baur, Wendy Wang, Guang-Rong Kapur, Navin Karas, Richard Blanton, Robert Hell, Stefan Waldman, Scott A. Lin, Jieru E. Colon-Gonzalez, Francheska Kim, Gilbert W. Blomain, Erik S. Merlino, Dante Snook, Adam Erdmann, Jeanette Wobst, Jana Kessler, Thorsten Schunkert, Heribert Walter, Ulrich Pagel, Oliver Walter, Elena Gambaryan, Stepan Smolenski, Albert Jurk, Kerstin Zahedi, Rene Klinger, James R. Benza, Raymond L. Corris, Paul A. Langleben, David Naeije, Robert Simonneau, Gérald Meier, Christian Colorado, Pablo Chang, Mi Kyung Busse, Dennis Hoeper, Marius M. Masferrer, Jaime L. Jacobson, Sarah Liu, Guang Sarno, Renee Bernier, Sylvie Zhang, Ping Flores-Costa, Roger Currie, Mark Hall, Katherine Möhrle, Dorit Reimann, Katrin Wolter, Steffen Wolters, Markus Mergia, Evanthia Eichert, Nicole Geisler, Hyun-Soon Ruth, Peter Feil, Robert Zimmermann, Ulrike Koesling, Doris Knipper, Marlies Rüttiger, Lukas Tanaka, Yasutake Okamoto, Atsuko Nojiri, Takashi Kumazoe, Motofumi Tokudome, Takeshi Miura, Koichi Hino, Jun Hosoda, Hiroshi Miyazato, Mikiya Kangawa, Kenji Kapil, Vikas Ahluwalia, Amrita Paolocci, Nazareno Eaton, Philip Campbell, James C. Henning, Philipp Franz, Eugen Sankaran, Banumathi Herberg, Friedrich W. Kim, Choel Wittwer, M. Luo, Q. Kaila, V. Dames, S. A. Tobin, Andrew Alam, Mahmood Rudyk, Olena Krasemann, Susanne Hartmann, Kristin Prysyazhna, Oleksandra Zhang, Min Zhao, Lan Weiss, Astrid Schermuly, Ralph Moyes, Amie J. Chu, Sandy M. Baliga, Reshma S. Hobbs, Adrian J. Michalakis, Stylianos Mühlfriedel, Regine Schön, Christian Fischer, Dominik M. Wilhelm, Barbara Zobor, Ditta Kohl, Ironwood Pharmaceuticals Cambridge USA Bayer AG Drug Discovery - Cardiovascular Research Wuppertal Germany Department of Cardiometabolic Diseases Research Boehringer Ingelheim Pharmaceuticals Ridgefield USA Department of Small Molecule Drug Research Boehringer Ingelheim Pharmaceuticals Ridgefield USA Department of Pharmacology University of Oslo and Oslo University Hospital Oslo Norway Institute of Experimental Medical Research University of Oslo and Oslo University Hospital Oslo Norway Center for Heart Failure Research University of Oslo and Oslo University Hospital Oslo Norway Department of Pharmacology Toxicology and Clinical Pharmacy Institute of Pharmacy University of Tuebingen Tuebingen Germany Physiologisches Institut Universität Würzburg Würzburg Germany Molecular Cardiology Research Institute Tufts Medical Center Boston USA Present Affiliation: Division of Cardiology University of Pittsburgh Medical Center Pittsburgh USA Present Affiliation: Department of Medicine Brown University School of Medicine Providence USA Division of Cardiology Tufts Medical Center Boston USA Max Planck Institute for Biophysical Chemistry Göttingen and German Cancer Research Center (DKFZ) Heidelberg Germany Department of Pharmacology and Experimental Therapeutics Thomas Jefferson University Philadelphia USA Institut für Kardiogenetik and Universitäres Herzzentrum Lübeck Universität zu Lübeck Lübeck Germany & DZHK e.V. (German Center for Cardiovascular Research) Partner Site Hamburg/Kiel/Lübeck Lübeck Germany Deutsches Herzzentrum München Klinik für Herz- und Kreislauferkrankungen Technische Universität München Munich Germany Center for Thrombosis & Hemostasis Universitätsklinikum der Johannes Gutenberg-Universität Mainz Mainz Germany Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V Dortmund Germany Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences St. Petersburg Russia UCD Conway Institute UCD School of Medicine

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Calibrated Langevin-dynamics simulations of intrinsically disordered proteins

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Physical Review E 2014年第4期90卷 042709-042709页

作者： W. Wendell Smith Po-Yi Ho Corey S. O'Hern Department of Physics Yale University New Haven Connecticut 06520-8120 USA Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06520-8114 USA Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut 06520-8286 USA Department of Applied Physics Yale University New Haven Connecticut 06520-8267 USA Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA

We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules. Our CG model includes repulsive steric, attractive hydrophobic, and electrostatic interactions between residues and is calibrated to a large collection of single-molecule fluorescence resonance energy transfer data on the interresidue separations for 36 pairs of residues in five IDPs: α−, β−, and γ-synuclein, the microtubule-associated protein τ, and prothymosin α. We find that our CG model is able to recapitulate the average interresidue separations regardless of the choice of the hydrophobicity scale, which shows that our calibrated model can robustly capture the conformational dynamics of IDPs. We then employ our model to study the scaling of the radius of gyration with chemical distance in 11 known IDPs. We identify a strong correlation between the distance to the dividing line between folded proteins and IDPs in the mean charge and hydrophobicity space and the scaling exponent of the radius of gyration with chemical distance along the protein.

关键词： LANGEVIN equations SIMULATION methods & models CONFORMATIONAL analysis MICROTUBULE-associated proteins HYDROPHOBIC compounds

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Bound Analysis Through HDMR for Multivariate Data Modelling - CMMSE

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Journal of Mathematical Modelling and Algorithms 2013年第3期12卷 265-276页

作者： Tunga, M.Alper Demiralp, Metin Software Engineering Department Bahçeşehir University 34349 Istanbul Beşiktaş Turkey Informatics Institute Computational Science and Engineering Program Istanbul Technical University 34469 Istanbul Maslak Turkey

Multivariate data modelling problems consist of a number of nodes with associated function (class) values. The main purpose of these problems is to construct an analytical model to represent the characteristics of the problem under consideration. Because the devices, tools, and/or algorithms used to collect the data may have incapabilities or limited capabilities, the data set is likely to contain unavoidable errors. That is, each component of data is reliable only within an interval which contains the data value. To this end, when an analytical structure is needed for the given data, a band structure should be determined instead of a unique structure. As the multivariance of the given data set increases, divide-and-conquer methods become important in multivariate modelling problems. HDMR based methods allow us to partition the given multivariate data into less variate data sets to reduce the complexity of the given problem. This paper focuses on Interval Factorized HDMR method developed to determine an approximate band structure for a given multivariate data modelling problem having uncertainties on its nodes and function values. © 2012 Springer science+Business Media B.V.

关键词： Approximation Bound analysis High dimensional model representation Interpolation Multidimensional problems Multivariate functions

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Avian photoreceptor patterns represent a disordered hyperuniform solution to a multiscale packing problem

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Physical Review E 2014年第2期89卷 022721-022721页

作者： Yang Jiao Timothy Lau Haralampos Hatzikirou Michael Meyer-Hermann Joseph C. Corbo Salvatore Torquato Princeton Institute of the Science and Technology of Materials Princeton University Princeton New Jersey 08540 USA Materials Science and Engineering Arizona State University Tempe Arizona 85287 USA Department of Pathology and Immunology Washington University School of Medicine St. Louis Missouri 63110 USA Department of Systems Immunology Helmholtz Centre for Infection Research Braunschweig Germany Center for Advancing Electronics Dresden TU Dresden 01062 Dresden Germany Department of Chemistry Department of Physics Program in Computational and Applied Mathematics Princeton University Princeton New Jersey 08544 USA

Optimal spatial sampling of light rigorously requires that identical photoreceptors be arranged in perfectly regular arrays in two dimensions. Examples of such perfect arrays in nature include the compound eyes of insects and the nearly crystalline photoreceptor patterns of some fish and reptiles. Birds are highly visual animals with five different cone photoreceptor subtypes, yet their photoreceptor patterns are not perfectly regular. By analyzing the chicken cone photoreceptor system consisting of five different cell types using a variety of sensitive microstructural descriptors, we find that the disordered photoreceptor patterns are “hyperuniform” (exhibiting vanishing infinite-wavelength density fluctuations), a property that had heretofore been identified in a unique subset of physical systems, but had never been observed in any living organism. Remarkably, the patterns of both the total population and the individual cell types are simultaneously hyperuniform. We term such patterns “multihyperuniform” because multiple distinct subsets of the overall point pattern are themselves hyperuniform. We have devised a unique multiscale cell packing model in two dimensions that suggests that photoreceptor types interact with both short- and long-ranged repulsive forces and that the resultant competition between the types gives rise to the aforementioned singular spatial features characterizing the system, including multihyperuniformity. These findings suggest that a disordered hyperuniform pattern may represent the most uniform sampling arrangement attainable in the avian system, given intrinsic packing constraints within the photoreceptor epithelium. In addition, they show how fundamental physical constraints can change the course of a biological optimization process. Our results suggest that multihyperuniform disordered structures have implications for the design of materials with novel physical properties and therefore may represent a fruitful area for future research

关键词： PHOTORECEPTORS ARRAY processing BIRDS MULTISCALE modeling SAMPLING (Signal processing) EPITHELIUM

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Association between GWAS-identified lung adenocarcinoma susceptibility loci and EGFR mutations in never-smoking Asian women, and comparison with findings from Western populations

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Human molecular genetics 2017年第2期26卷 454-465页

作者： Wei Jie Seow Keitaro Matsuo Chao Agnes Hsiung Kouya Shiraishi Minsun Song Hee Nam Kim Maria Pik Wong Yun-Chul Hong H Dean Hosgood Zhaoming Wang I-Shou Chang Jiu-Cun Wang Nilanjan Chatterjee Margaret Tucker Hu Wei Tetsuya Mitsudomi Wei Zheng Jin Hee Kim Baosen Zhou Neil E Caporaso Demetrius Albanes Min-Ho Shin Lap Ping Chung She-Juan An Ping Wang Hong Zheng Yasushi Yatabe Xu-Chao Zhang Young Tae Kim Xiao-Ou Shu Young-Chul Kim Bryan A Bassig Jiang Chang James Chung Man Ho Bu-Tian Ji Michiaki Kubo Yataro Daigo Hidemi Ito Yukihide Momozawa Kyota Ashikawa Yoichiro Kamatani Takayuki Honda Hiromi Sakamoto Hideo Kunitoh Koji Tsuta Shun-Ichi Watanabe Hiroshi Nokihara Yohei Miyagi Haruhiko Nakayama Shingo Matsumoto Masahiro Tsuboi Koichi Goto Zhihua Yin Jianxin Shi Atsushi Takahashi Akiteru Goto Yoshihiro Minamiya Kimihiro Shimizu Kazumi Tanaka Tangchun Wu Fusheng Wei Jason Y Y Wong Fumihiko Matsuda Jian Su Yeul Hong Kim In-Jae Oh Fengju Song Victor Ho Fun Lee Wu-Chou Su Yuh-Min Chen Gee-Chen Chang Kuan-Yu Chen Ming-Shyan Huang Pan-Chyr Yang Hsien-Chih Lin Yong-Bing Xiang Adeline Seow Jae Yong Park Sun-Seog Kweon Chien-Jen Chen Haixin Li Yu-Tang Gao Chen Wu 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 Charles Lawrence Laurie Burdett Meredith Yeager Kevin B Jacobs Amy Hutchinson Sonja I Berndt Xingzhou He Wei Wu Junwen Wang Yuqing Li Jin Eun Choi Kyong Hwa Park Sook Whan Sung Li Liu Chang Hyun Kang Lingmin Hu Chung-Hsing Chen Tsung-Ying Yang Jun Xu Peng Guan Wen Tan Chih-Liang Wang Alan Dart Loon Sihoe Ying Chen Yi Young Choi Jen-Yu Hung Jun Suk Kim Ho-Il Yoon Qiuyin Cai Chien-Chung Lin In Kyu Park Ping Xu Jing Dong Christopher Kim Qincheng He Reury-Perng Perng Chih-Yi Chen Roel Vermeulen Junjie Wu Wei-Yen Lim Kun-Chieh Chen John K C Chan Minjie Chu Yao-Jen Li Jihua Li Hongyan Chen Chong-Jen Yu Li Jin Yen-Li Lo Ying-Hsiang Chen Joseph F Fraumeni Jie Liu Taiki Yamaji Yang Yang Belynda Hicks Kathleen Wyatt Shengchao A Li Division of Cancer Epidemiology and Genetics National Cancer Institute Bethesda MD USA. Saw Swee Hock School of Public Health National University of Singapore and National University Health System Singapore. Division of Molecular Medicine Aichi Cancer Center Research Institute Nagoya Japan. Institute of Population Health Sciences National Health Research Institutes Zhunan Taiwan. Division of Genome Biology National Cancer Center Research Institute Tokyo Japan. Department of Statistics Sookmyung Women's University Seoul Republic of Korea. Department of Preventive Medicine Chonnam National University Medical School Gwangju Republic of Korea. Department of Pathology The University of Hong Kong Queen Mary Hospital Hong Kong. Department of Preventive Medicine Seoul National University College of Medicine Seoul Republic of Korea. Department of Epidemiology and Population Health Albert Einstein College of Medicine Bronx NY USA. Department of Computational Biology St. Jude Children's Research Hospital Memphis TN 38105 USA. National Institute of Cancer Research National Health Research Institutes Zhunan Taiwan. Ministry of Education Key Laboratory of Contemporary Anthropology School of Life Sciences Fudan University Shanghai People's Republic of China. State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai People's Republic of China. Division of Thoracic Surgery Kinki University School of Medicine Sayama Japan. Division of Epidemiology Department of Medicine Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center Nashville TN USA. Department of Integrative Bioscience & Biotechnology Sejong University Seoul Republic of Korea. Department of Epidemiology School of Public Health China Medical University Shenyang People's Republic of China. Guangdong Lung Cancer Institute Medical Research Center and Cancer Center of Guangdong General Hospital Guangdong Academy of Medical Sciences Guangzhou People's Republic

To evaluate associations by EGFR mutation status for lung adenocarcinoma risk among never-smoking Asian women, we conducted a meta-analysis of 11 loci previously identified in genome-wide association studies (GWAS). Genotyping in an additional 10,780 never-smoking cases and 10,938 never-smoking controls from Asia confirmed associations with eight known single nucleotide polymorphisms (SNPs). Two new signals were observed at genome-wide significance (P < 5 × 10-8), namely, rs7216064 (17q24.3, BPTF), for overall lung adenocarcinoma risk, and rs3817963 (6p21.3, BTNL2) which is specific to cases with EGFR mutations. In further sub-analyses by EGFR status, rs9387478 (ROS1/DCBLD1) and rs2179920 (HLA-DPB1) showed stronger estimated associations in EGFR-positive compared to EGFR-negative cases. Comparison of the overall associations with published results in Western populations revealed that the majority of these findings were distinct, underscoring the importance of distinct contributing factors for smoking and non-smoking lung cancer. Our results extend the catalogue of regions associated with lung adenocarcinoma in non-smoking Asian women and highlight the importance of how the germline could inform risk for specific tumour mutation patterns, which could have important translational implications.

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Implementation of OpenMP and MPI hybrid parallelization to Monte Carlo dose simulation for particle therapy

Implementation of OpenMP and MPI hybrid parallelization to M...

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World Congress on Medical Physics and Biomedical engineering

作者： Furuta, T. Ishikawa, K.L. Fukunishi, N. Noda, S. Takagi, S. Maeyama, T. Fukasaku, K. Himeno, R. RIKEN Computational Science Research Program Wako Japan University of Tokyo Department of Nuclear Engineering and Management Graduate School of Engineering Tokyo Japan RIKEN Nishina Center for Accelerator-Based Science Wako Japan RIKEN Advanced Center for Computing and Communication Wako Japan University of Tokyo Department of Mechanical Engineering Tokyo Japan Himon'ya Hospital Department of Neurosurgery Tokyo Japan

ISBN: (纸本)9783642293047

We report a successful implementation of the sharedmemory parallelization using OpenMP to the dose calculation by the Monte Carlo particle and heavy-ion transport code PHITS. The OpenMP shared-memory parallelization is better suited than the MPI distributed-memory parallelization which is originally implemented in the PHITS code in the case of human voxel data which requires a large memory space. We have confirmed that the same results can be obtained with and without the shared-memory parallelization by the modified PHITS code. Sufficiently high OpenMP parallelization efficiency (92.4% with 8 parallelized cores within a single node) is achieved even when the special treatment for accessing memory to avoid memory contentions is taken into account. We implement the OpenMP parallelization on top of the MPI parallelization originally included in PHITS so that the modified code works in a hybrid way such that the distributed-memory parallelization for different nodes by MPI and the shared-memory parallelization among the cores in a single node by OpenMP. The performance has been checked on supercomputers: RICC and K computer. © 2013 Springer-Verlag.

关键词： Supercomputers

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