IEEE Trans Vis Comput Graph. 2018 Jan;24(1):862-872. doi: 10.1109/TVCG.2017.2744258. Epub 2017 Aug 29.
We present the first approach to integrative structural modeling of the biological mesoscale within an interactive visual environment. These complex models can comprise up to millions of molecules with defined atomic structures, locations, and interactions. Their construction has previously been attempted only within a non-visual and non-interactive environment. Our solution unites the modeling and visualization aspect, enabling interactive construction of atomic resolution mesoscale models of large portions of a cell. We present a novel set of GPU algorithms that build the basis for the rapid construction of complex biological structures. These structures consist of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures. The compartments are defined using volume voxelization of triangulated meshes. For membranes, we present an extension of the Wang Tile concept that populates the bilayer with individual lipids. Soluble molecules are populated within compartments distributed according to a Halton sequence. Fibrous structures, such as RNA or actin filaments, are created by self-avoiding random walks. Resulting overlaps of molecules are resolved by a forced-based system. Our approach opens new possibilities to the world of interactive construction of cellular compartments. We demonstrate its effectiveness by showcasing scenes of different scale and complexity that comprise blood plasma, mycoplasma, and HIV.
我们提出了在交互式可视环境中对生物介观进行综合结构建模的第一种方法。这些复杂的模型可以包含多达数百万个具有定义原子结构、位置和相互作用的分子。以前，只能在非视觉和非交互式环境中尝试构建这些模型。我们的解决方案将建模和可视化方面结合在一起，使构建大比例细胞的原子分辨率介观模型能够实现交互式构建。我们提出了一组新的 GPU 算法，为快速构建复杂的生物结构奠定了基础。这些结构由多个膜封闭的隔室组成，包括可溶性分子和纤维结构。隔室使用三角网格的体素化进行定义。对于膜，我们提出了 Wang 平铺概念的扩展，该扩展使用单个脂质填充双层。可溶性分子根据 Halton 序列分布在隔室中。纤维结构，如 RNA 或肌动蛋白丝，通过自回避随机游走创建。通过基于力的系统解决分子的重叠问题。我们的方法为交互式构建细胞隔室的世界开辟了新的可能性。我们通过展示不同规模和复杂性的场景来展示其有效性，这些场景包括血浆、支原体和 HIV。
