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从电子尺度到细胞尺度的光合作用能量转换过程的多尺度建模与动态可视化。

Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales.

作者信息

Sener Melih, Levy Stuart, Stone John E, Christensen A J, Isralewitz Barry, Patterson Robert, Borkiewicz Kalina, Carpenter Jeffrey, Hunter C Neil, Luthey-Schulten Zaida, Cox Donna

机构信息

Beckman Institute, University of Illinois at Urbana-Champaign.

Advanced Visualization Laboratory, NCSA, University of Illinois at Urbana-Champaign.

出版信息

Parallel Comput. 2020 May;102. doi: 10.1016/j.parco.2020.102698. Epub 2020 Dec 15.

Abstract

Conversion of sunlight into chemical energy, namely photosynthesis, is the primary energy source of life on Earth. A visualization depicting this process, based on multiscale computational models from electronic to cell scales, is presented in the form of an excerpt from the fulldome show . This accessible visual narrative shows a lay audience, including children, how the energy of sunlight is captured, converted, and stored through a chain of proteins to power living cells. The visualization is the result of a multi-year collaboration among biophysicists, visualization scientists, and artists, which, in turn, is based on a decade-long experimental-computational collaboration on structural and functional modeling that produced an atomic detail description of a bacterial bioenergetic organelle, the chromatophore. Software advancements necessitated by this project have led to significant performance and feature advances, including hardware-accelerated cinematic ray tracing and instanced visualizations for efficient cell-scale modeling. The energy conversion steps depicted feature an integration of function from electronic to cell levels, spanning nearly 12 orders of magnitude in time scales. This atomic detail description uniquely enables a modern retelling of one of humanity's earliest stories-the interplay between light and life.

摘要

将阳光转化为化学能,即光合作用,是地球上生命的主要能量来源。基于从电子尺度到细胞尺度的多尺度计算模型,以穹顶影院完整节目片段的形式呈现了这一过程的可视化展示。这个通俗易懂的视觉叙事向包括儿童在内的普通观众展示了阳光的能量是如何通过一系列蛋白质被捕获、转化和储存,从而为活细胞提供动力的。该可视化展示是生物物理学家、可视化科学家和艺术家多年合作的成果,而这一合作又基于长达十年的关于结构和功能建模的实验与计算合作,该合作产生了对一种细菌生物能量细胞器——载色体的原子细节描述。该项目所需的软件进步带来了显著的性能和功能提升,包括硬件加速的电影光线追踪和用于高效细胞尺度建模的实例化可视化。所描绘的能量转换步骤展示了从电子水平到细胞水平功能的整合,时间尺度跨越近12个数量级。这种原子细节描述独特地使得能够对人类最古老的故事之一——光与生命之间的相互作用进行现代重述。

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