Modeling and Interacting with the Visible Molecular Cell

项目摘要/摘要 现在可以实现整个细胞的结构建模和可视化 原子水平上的细节。在这个项目中，我们将扩展以下功能 一种用于创建蜂窝环境的集成3D模型的方法， 从原子水平到细胞水平的桥梁。这些型号将提供 为了解细胞功能和疾病状态提供了前所未有的可能性， 为干预创造新的机会。他们还将挑战以下几个方面 生成、可视化和交互探索超大型3D所需的技术 和4D结构数据集。我们的目标是开发建模和可视化工具 使其他人能够开发、运行和分析这些复杂系统动态模拟 模特们。要使这一努力成为成功的工具，必须克服几个关键障碍 用于研究和科学教育，包括管理大量信息 数据库，用于自动建模的结构和相互作用的方法 拥挤细胞中的可溶性、纤维性和膜结合型分子组件 环境、可理解的可视化以及与这些大型和 异质模型。我们将以四个具体目标应对这些挑战： 1)用于复杂部件的中尺度建模的程序方法，例如 细菌类核糖体、肽多聚糖、脂多糖和多聚体； 2)用于管理复杂的多尺度数据的计算机辅助工具 指定细胞的3D中尺度模型； 3)开发快速有效的方法以允许显示和交互 这些复杂的中尺度模式； 4)将这些方法应用到细菌生物学研究中，并创建了一个Google 地球启发观众用于教育和外展。

Project Summary/Abstract It is now possible to approach the structural modeling and visualization of entire cells with detail at the atomic level. In this project, we will expand the capabilities of cellPACK, a method for creating integrative 3D models of cellular environments, bridging from the level of atoms to the level of cells. These models will provide unprecedented possibilities for the understanding of cellular function and disease states, enabling new opportunities for intervention. They will also challenge several aspects of the technologies needed to generate, visualize and interactively explore very large 3D and 4D structural datasets. Our goal is to develop the modeling and visualization tools that enable others to develop, run and analyze dynamic simulations of these complex models. Several critical barriers must be overcome to make this effort a successful tool for research and scientific education, including the management of large informational databases, methods for the automated modeling of the structure and interaction of soluble, fibrous, and membrane-bound molecular assemblies in crowded cellular environments, and comprehensible visualization of, and interaction with these large and heterogenous models. We will approach these challenges with four specific aims: 1) Procedural methods for mesoscale modeling of complex assemblies, such as the bacterial nucleoid, peptidoglycan, lipopolysaccharide, and polysomes; 2) Computer-assisted tools for the management of complex multiscale data for specifying 3D mesoscale models of cells; 3) Development of fast and effective methods to allow display of and interaction with these complex mesoscale models; 4) Application of these methods to research in bacterial biology and creation of a Google Earth inspired viewer for use in education and outreach.