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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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Using SYCLomatic to Migrate CUDA Code to oneAPI Adapting NVIDIA GPU

Using SYCLomatic to Migrate CUDA Code to oneAPI Adapting NVI...

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IEEE International Conference on Cluster Computing Workshops and Posters (CLUSTER WORKSHOPS)

作者： Wentao Liang Norihisa Fujita Ryohei Kobayashi Taisuke Boku Master's Program in Computer Science Degree Program in Systems and Information Engineering Graduate School of Science and Technology University of Tsukuba Center for Computational Sciences University of Tsukuba

ISBN: (数字)9798350383454

ISBN: (纸本)9798350383461

Nowadays, the use of accelerators in high performance computing has become more common than ever before. The most used accelerators must be the Graphics Processing Unit (GPU). It has emerged as an important component in most of the parallel computing scenarios, surpassing the capabilities of the traditional Central Processing Unit (CPU) in perspective of both performance and energy efficiency.

关键词： Codes Conferences High performance computing Graphics processing units Cluster computing Parallel processing Energy efficiency Central Processing Unit

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Machine-learning-based non-Newtonian fluid model with molecular fidelity

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Physical Review E 2020年第4期102卷 043309-043309页

作者： Huan Lei Lei Wu Weinan E Department of Computational Mathematics Science & Engineering and Department of Statistics & Probability Michigan State University East Lansing Michigan 48824 USA Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

We introduce a machine-learning-based framework for constructing continuum a non-Newtonian fluid dynamics model directly from a microscale description. Dumbbell polymer solutions are used as examples to demonstrate the essential ideas. To faithfully retain molecular fidelity, we establish a micro-macro correspondence via a set of encoders for the microscale polymer configurations and their macroscale counterparts, a set of nonlinear conformation tensors. The dynamics of these conformation tensors can be derived from the microscale model, and the relevant terms can be parametrized using machine learning. The final model, named the deep non-Newtonian model (DeePN2), takes the form of conventional non-Newtonian fluid dynamics models, with a generalized form of the objective tensor derivative that retains the microscale interpretations. Both the formulation of the dynamic equation and the neural network representation rigorously preserve the rotational invariance, which ensures the admissibility of the constructed model. Numerical results demonstrate the accuracy of DeePN2 where models based on empirical closures show limitations.

关键词： Learning Neuronal networks Complex fluids Non-Newtonian fluids Rheology Viscoelasticity Multiscale modeling

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Comparison of load path definitions in 2-D continuum structures

Comparison of load path definitions in 2-D continuum structu...

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作者： Marhadi, Kun S. Venkataraman., Satchi Computational Science Program San Diego State University San Diego CA 92182-1308 United States Department of Aerospace Engineering and Engineering Mechanics San Diego State University Mail Code 1308 5500 Campanile Drive San Diego CA 92182-1308 United States

ISBN: (纸本)9781563479731

The structural mechanics community has developed several methods to identify and visualize load paths in structures. There is no single accepted approach or method to characterize, quantify, visualize and tailor load paths. This paper compares various methods proposed to characterize and visualize load paths. The comparison is performed for a two-dimensional (2-D) rectangular plate under plane stress conditions arising from different loading and boundary conditions. The effectiveness and computational effort of each method are compared. The comparisons shows the methods provide different results and insights into the load transfer mechanisms. No single method appears to emerge as a clear choice for characterizing load paths. However, some methods provide more qualitative and quantitative information on the trajectory and efficiency of load transfer along load paths. Copyright © 2009 by the authors.

关键词： Rectangular plate

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Using DHP adaptive critic methods to tune a fuzzy automobile steering controller

Using DHP adaptive critic methods to tune a fuzzy automobile...

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Joint 9th IFSA World Congress and 20th NAFIPS International Conference

作者： Schultz, Larry J. Shannon, Thaddeus T. Lendaris, George G. Electrical Engineering Dept. Northwest Computational Intell. Portland State University P.O. Box 751 Portland OR 97207 United States Systems Science Ph.D Program Northwest Computational Intell. Portland State University P.O. Box 751 Portland OR 97207 United States

The approximate dynamic programming method known as Dual Heuristic programming (DHP) is applied to the design of a fuzzy controller for a 4-wheel, 2-axle vehicle. This controller is designed to guide an autonomous aut... 详细信息

关键词： Heuristic programming

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Deep potentials for materials science

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Materials Futures 2022年第2期1卷 89-115页

作者： Tongqi Wen Linfeng Zhang Han Wang Weinan E David J Srolovitz Department of Mechanical Engineering The University of Hong KongHong KongHong Kong Special Administrative Region of China DP Technology BeijingPeople’s Republic of China AI for Science Institute BeijingPeople’s Republic of China Laboratory of Computational Physics Institute of Applied Physics and Computational MathematicsBeijingPeople’s Republic of China HEDPS CAPTCollege of EngineeringPeking UniversityBeijingPeople’s Republic of China School of Mathematical Sciences Peking UniversityBeijingPeople’s Republic of China Department of Mathematics and Program in Applied and Computational Mathematics Princeton UniversityPrincetonNJUnited States of America International Digital Economy Academy(IDEA) ShenzhenPeople’s Republic of China

To fill the gap between accurate(and expensive)ab initio calculations and efficient atomistic simulations based on empirical interatomic potentials,a new class of descriptions of atomic interactions has emerged and been widely applied;*** learning potentials(MLPs).One recently developed type of MLP is the deep potential(DP)*** this review,we provide an introduction to DP methods in computational materials *** theory underlying the DP method is presented along with a step-by-step introduction to their development and *** also review materials applications of DPs in a wide range of materials *** DP Library provides a platform for the development of DPs and a database of extant *** discuss the accuracy and efficiency of DPs compared with ab initio methods and empirical potentials.

关键词： deep potential atomistic simulation machine learning potential neural network

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Numerical simulation on a reacting flow of a small gas turbine combustor with various spray conditions

Numerical simulation on a reacting flow of a small gas turbi...

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2010 Asia-Pacific International Symposium on Aerospace Technology, APISAT 2010

作者： Kim, Seihwan Jo, Sungjohyun Jeung, Inseuck Park, Heeho Na, Sangkwon Interdisciplinary Program in Computational Science and Technology Seoul National University Seoul Korea Republic of Department of Mechanical and Aerospace Engineering Seoul National University Seoul Korea Republic of Samsung Tech Win Co. Ltd. Gyeonggi Korea Republic of

ISBN: (纸本)9787561228999

According to the report, about 50% of helicopters in Korea are manufactured more than 30 years ago. For this reason, the large project on the development of the helicopter is proposed. In this research, relationship between the atomization properties and the characteristics of the reacting flow field in a small gas turbine engine are studied. In general, researches on the development of an injector need a lot of experiments. But those experiments always have the risks of explosion and an emission of toxic gases. Recently computational studies on a chemical reacting flow are widely used as the speed of CPU becomes faster. A spray structure can be expressed in terms of droplet size distribution, break-up length, spray angle, and penetration distance. Among those, the characteristics of the reacting flow field in the gas turbine engine according to various droplet sizes are investigated. Combustion chamber is modeled with 1. 3 million hybrid grid and n-pentane is used for the fuel. With those setting, spray droplet trajectory and temperature distribution are compared. For the cases with three different droplet's mean diameter, as the parcel size of the fuel decreases, reaction occurs faster in smaller area. But those small parcels cannot penetrate deeper, fuels is not equally distributed. Although heat transfer and diffusion occur, this inequality increases the pattern factor, important parameter on the combustor performance. Comparisons on the outlet temperature with two different sizes show that to get lower pattern factor, mean diameter of the spray parcels should be at least 80. This means that injection of smaller parcels than the specific value reduces overall performance of the engine. In this work, only the droplet size distribution and spray angle are considered. There are lots of variables to affect the injection properties, more researches are planed and we work on some of these.

关键词： CFD-ACE Gas turbine N-pentane Numerical simulation Reacting flow Subsonic

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Phage therapy

NATURE REVIEWS METHODS PRIMERS

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NATURE REVIEWS METHODS PRIMERS 2025年第1期5卷 1页

作者： [Anonymous] Human Microbiome Research Program Department of Bacteriology and Immunology Faculty of Medicine University of Helsinki Helsinki Finland European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Non-traditional Antibacterial Therapy (ESGNTA) Basel Switzerland Institute of Biomedical and Oral Research (IBOR) Faculty of Dental Medicine Hebrew University of Jerusaleum Jerusalem Israel The Israeli Phage Center (IPTC) of the Hebrew University and Hadassah Medical Center Jerusalem Israel Department of Clinical Microbiology and Infectious Diseases Hadassah–Hebrew University Medical Center Jerusalem Jerusalem Israel Laboratory of Gene Technology Department of Biosystems KU Leuven Leuven Belgium Leicester Centre for Phage Research Department of Genetics and Genome Biology University of Leicester Leicester UK Center for Evolutionary Hologenomics Globe Institute University of Copenhagen Copenhagen Denmark Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio) AIMST University Bedong Kedah Malaysia Laboratory of Phage Molecular Biology Institute of Immunology and Experimental Therapy Wrocław Poland Wrocław University of Science and Technology Faculty of Medicine Wrocław Poland Department of Biological Sciences University of Pittsburgh Pittsburgh PA USA Laboratory for Molecular and Cellular Technology Queen Astrid Military Hospital Brussels Belgium Department of Biological and Environmental Science Nanoscience Center University of Jyväskylä Jyväskylä Finland Chemical Engineering Department Loughborough University Loughborough UK

Bacteriophage (phages) are viruses that exclusively use bacterial cells for propagation, killing the bacterial host in the process. In phage therapy, phages are used to reduce bacterial numbers, thereby curing bacterial infections. Although this principle is conceptually straightforward, its practical application faces several hurdles. In this Primer, the practical aspects of phage therapy are outlined. We introduce the microbiological methods used to prepare and characterize phages and elucidate their interactions with bacteria. The discussion covers how the information in complete phage genome sequences is used, along with how RNA sequencing can enhance our understanding of phage biology. Selection parameters for therapeutic phages for clinical applications and key elements in industrial-scale phage production are provided. A summary of clinical trials both past and present, phage administration and dosing issues is analysed, as well as limitations associated with phage therapy and mitigation strategies. Finally, we speculate on the future of phage therapy.

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Diffusion suppression in gel dosimetry by addition of nanoclay

Diffusion suppression in gel dosimetry by addition of nanocl...

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World Congress on Medical Physics and Biomedical engineering

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

ISBN: (纸本)9783642293047

This paper reports diffusion suppression in gel dosimetery by using nanocomposite gel. A Fricke xylenol gel (FXG) and a dichromate gel (DCG) were selected for adding a small amount of nanoclay (Laponite XLG). The diffusion coefficient and T1 distribution were evaluated by irradiating the gel dosimeter with a heavy ion beam. As a result, these gels showed improvement in the diffusion coefficient. In particular, by addition of the clay, the DCG exhibited diffusion-free characteristics. Moreover, it exhibited high stability after irradiation. © 2013 Springer-Verlag.

关键词： Nanocomposites

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Influence of nonequilibrium lipid transport, membrane compartmentalization, and membrane proteins on the lateral organization of the plasma membrane

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Physical Review E 2010年第1期81卷 011908-011908页

作者： Jun Fan Maria Sammalkorpi Mikko Haataja Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) and Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544 USA

Compositional lipid domains (lipid rafts) in plasma membranes are believed to be important components of many cellular processes. The mechanisms by which cells regulate the sizes, lifetimes, and spatial localization of these domains are rather poorly understood at the moment. We propose a robust mechanism for the formation of finite-sized lipid raft domains in plasma membranes, the competition between phase separation in an immiscible lipid system and active cellular lipid transport processes naturally leads to the formation of such domains. Simulations of a continuum model reveal that the raft size distribution is broad and the average raft size is strongly dependent on the rates of cellular and interlayer lipid transport processes. We demonstrate that spatiotemporal variations in the recycling may enable the cell to localize larger raft aggregates at specific parts along the membrane. Moreover, we show that membrane compartmentalization may further facilitate spatial localization of the raft domains. Finally, we demonstrate that local interactions with immobile membrane proteins can spatially localize the rafts and lead to further clustering.

关键词： Cell membranes

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