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Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing

机译:利用GPU加速的光线跟踪对光合膜进行原子细节可视化

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摘要

The cellular process responsible for providing energy for most life on Earth, namely, photosynthetic light-harvesting, requires the cooperation of hundreds of proteins across an organelle, involving length and time scales spanning several orders of magnitude over quantum and classical regimes. Simulation and visualization of this fundamental energy conversion process pose many unique methodological and computational challenges. We present, in two accompanying movies, light-harvesting in the photosynthetic apparatus found in purple bacteria, the so-called chromatophore. The movies are the culmination of three decades of modeling efforts, featuring the collaboration of theoretical, experimental, and computational scientists. We describe the techniques that were used to build, simulate, analyze, and visualize the structures shown in the movies, and we highlight cases where scientific needs spurred the development of new parallel algorithms that efficiently harness GPU accelerators and petascale computers. (C) 2015 Elsevier B.V. All rights reserved.
机译:负责为地球上大多数生命提供能量的细胞过程,即光合作用的光捕获,需要细胞器中数百种蛋白质的合作,涉及长度和时间尺度,跨越量子和经典机制,跨越了几个数量级。此基本能量转换过程的仿真和可视化带来了许多独特的方法和计算挑战。在两部附带的电影中,我们介绍了紫色细菌(所谓的染色体)中发现的光合作用装置中的光波收集。这些电影是三十年建模工作的结晶,具有理论,实验和计算科学家的协作。我们描述了用于构建,模拟,分析和可视化电影中显示的结构的技术,并重点介绍了由于科学需求而促使人们开发可有效利用GPU加速器和petascale计算机的新型并行算法的情况。 (C)2015 Elsevier B.V.保留所有权利。

著录项

  • 来源
    《Parallel Computing》 |2016年第7期|17-27|共11页
  • 作者单位

    Univ Illinois, Beckman Inst, 405 N Mathews Ave, Urbana, IL 61801 USA;

    Univ Illinois, Beckman Inst, 405 N Mathews Ave, Urbana, IL 61801 USA;

    Univ Illinois, Beckman Inst, 405 N Mathews Ave, Urbana, IL 61801 USA;

    Univ Illinois, Beckman Inst, 405 N Mathews Ave, Urbana, IL 61801 USA;

    Univ Illinois, Beckman Inst, 405 N Mathews Ave, Urbana, IL 61801 USA;

    Univ Illinois, Dept Phys, 1110 W Green St, Urbana, IL 61801 USA;

    Univ Illinois, Beckman Inst, 405 N Mathews Ave, Urbana, IL 61801 USA;

    Univ Illinois, Beckman Inst, 405 N Mathews Ave, Urbana, IL 61801 USA;

    Univ Illinois, Beckman Inst, 405 N Mathews Ave, Urbana, IL 61801 USA;

    Univ Illinois, Beckman Inst, 405 N Mathews Ave, Urbana, IL 61801 USA|Univ Illinois, Dept Phys, 1110 W Green St, Urbana, IL 61801 USA;

    Univ Illinois, Beckman Inst, 405 N Mathews Ave, Urbana, IL 61801 USA;

    Univ Sheffield, Dept Mol Biol & Biotechnol, Western Bank, Sheffield S10 2TN, S Yorkshire, England;

    Univ Sheffield, Dept Mol Biol & Biotechnol, Western Bank, Sheffield S10 2TN, S Yorkshire, England;

    Cornell Univ, Sch Appl & Engn Phys, 271 Clark Hall, Ithaca, NY 14853 USA|Kavli Inst Cornell Nanoscale Sci, 420 Phys Sci Bldg, Ithaca, NY 14853 USA;

    Univ Sheffield, Dept Mol Biol & Biotechnol, Western Bank, Sheffield S10 2TN, S Yorkshire, England;

    Univ Illinois, Beckman Inst, 405 N Mathews Ave, Urbana, IL 61801 USA|Univ Illinois, Dept Phys, 1110 W Green St, Urbana, IL 61801 USA;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    Photosynthesis; Parallel molecular dynamics; Parallel ray tracing; GPU computing;

    机译:光合作用平行分子动力学平行光线追踪GPU计算;

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