GPU-Accelerated Atom and Dynamic Bond Visualization Using Hyperballs: A Unified Algorithm for Balls, Sticks, and Hyperboloids
GPU-Accelerated Atom and Dynamic Bond Visualization Using Hyperballs: A Unified Algorithm for Balls, Sticks, and Hyperboloids
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DOI：
10.1002/jcc.21861
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发表时间：
2011-10-01
影响因子：
3
通讯作者：
Baaden, Marc
中科院分区：
文献类型：
--
作者：
Chavent, Matthieu;Vanel, Antoine;Baaden, Marc
图形处理单元(GPU)上的光线投射为分子可视化打开了新的可能性。我们描述了各种分子表示的实现和计算，例如甘草、球棒、空间填充的范德华球和使用GPU近似的溶剂可访问的表面。我们引入了HyperBalls，一种改进的球杆表示法，取代了管，通过双曲面将原子球连接起来，从而可以平滑地连接它们。这种类型的描述对于表示动态现象特别有用，例如非共价键的演化。此外，它还非常适合表示粗粒度模型和弹簧网络。所有这些表示都可以由一个通用的代数方程定义，该方程适用于光线投射技术，并且非常适合在GPU上执行。使用GPU功能，该实现可以常规、准确和交互地呈现从几个原子到包含超过500,000个粒子的巨大大分子组件的分子。在简单的情况下，仅基于球体，我们已经能够顺利地显示多达200万个原子。(C)2011年威利期刊公司J Comput Chem 32：2924-2934,2011
Ray casting on graphics processing units (GPUs) opens new possibilities for molecular visualization. We describe the implementation and calculation of diverse molecular representations such as licorice, ball-and-stick, space-filling van der Waals spheres, and approximated solvent-accessible surfaces using GPUs. We introduce HyperBalls, an improved ball-and-stick representation replacing tubes, linking the atom spheres by hyperboloids that can smoothly connect them. This type of depiction is particularly useful to represent dynamic phenomena, such as the evolution of noncovalent bonds. It is furthermore well suited to represent coarse-grained models and spring networks. All these representations can be defined by a single general algebraic equation that is adapted for the ray-casting technique and is well suited for execution on the GPU. Using GPU capabilities, this implementation can routinely, accurately, and interactively render molecules ranging from a few atoms up to huge macromolecular assemblies with more than 500,000 particles. In simple cases, based only on spheres, we have been able to display up to two million atoms smoothly. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2924-2934, 2011