Modeling and Interacting with the Visible Molecular Cell

项目概要/摘要 现在可以接近整个细胞的结构建模和可视化 原子级的细节。在这个项目中，我们将扩展 cellPACK是一种创建细胞环境的综合3D模型的方法， 从原子水平到细胞水平的桥梁。这些模型将提供 为理解细胞功能和疾病状态提供了前所未有的可能性， 创造新的干预机会。他们还将挑战的几个方面， 生成、可视化和交互式探索超大型3D所需的技术 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的动态模拟 模型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，包括大型信息管理 数据库，用于结构和相互作用的自动建模的方法， 在拥挤的细胞中，可溶性、纤维状和膜结合的分子组装体 环境，以及可理解的可视化，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)复杂组件的中尺度建模的过程方法，例如 细菌类核、肽聚糖、脂多糖和多核糖体; 2)用于管理复杂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，以便展示和互动 这些复杂的中尺度模型 4)将这些方法应用于细菌生物学研究并创建Google 地球启发查看器用于教育和推广。

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.