SI2-SSE: Collaborative Research: Integrated Tools for DNA Nanostructure Design and Simulation

SI2-SSE：合作研究：DNA 纳米结构设计和模拟的集成工具

• 批准号: 1740282
• 负责人: Shawn Douglas
• 金额: $ 25万
• 依托单位: University of California-San Francisco
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2020-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1740282&HistoricalAwards=false
• 关键词: SI2; SSE; Collaborative; Research; Integrated

Nanotechnology could one day revolutionize several activities of great importance to our national interest, including how we manufacture consumer products, how we diagnose and treat disease, and how we detect and neutralize threats to our defense. One promising approach to atomically precise construction is adapting molecular building blocks from living organisms such as DNA, RNA, and proteins, and repurposing them to self-assemble into prescribed shapes, devices, and materials. A key bottleneck to progress is the complexity of designing, building, and testing nanostructures comprised of thousands or millions of atoms. The goal of this project is to accelerate development of bio-inspired nanostructures by integrating two widely adopted software tools used in bio-nanostructure design and physics-based molecular simulation. The products of this effort will enhance our fundamental capability to understand and precisely engineer self-assembled biomolecular nanostructures, which, when coupled with experimental validation in the laboratory, will enable future demand-meeting applications of bionanotechnology.Toward realizing the goal of programming matter with nanoscale precision, this project will develop software interfaces between two classes of molecular design programs that, until now, have been evolving independently from one another. A widely adopted DNA structure design program, Cadnano, will be extended to utilize the results of physics-based microscopic simulations, enabling an iterative structure design process. A leading molecular graphics program, VMD (Visual Molecular Dynamics), will be developed to seamlessly visualize Cadnano designs, provide their structural interpretation, and enable further modification of the structures using an arsenal of computational structural biology and nanotechnology tools. Both developments will utilize recent advances in cloud computing technologies, making the DNA structure design software available anywhere and to anyone in a platform-independent manner.This project is supported by the Office of Advanced Cyberinfrastructure in the Directorate for Computer & Information Science & Engineering and the Division of Civil, Mechanical and Manufacturing Innovation in the Directorate of Engineering.

纳米技术有朝一日可能会给几项对我们的国家利益具有重大意义的活动带来革命性的变化，包括我们如何制造消费品，我们如何诊断和治疗疾病，以及我们如何检测和消除对我们国防的威胁。一种有希望的原子精确构建方法是修改来自DNA、RNA和蛋白质等活有机体的分子构建块，并重新调整它们的用途，使其自组装成指定的形状、设备和材料。进展的一个关键瓶颈是设计、建造和测试由数千或数百万个原子组成的纳米结构的复杂性。该项目的目标是通过集成生物纳米结构设计和基于物理的分子模拟中广泛使用的两个软件工具来加速生物启发纳米结构的开发。这项工作的成果将增强我们理解和精确设计自组装生物分子纳米结构的基本能力，再加上实验室中的实验验证，将使未来的生物纳米技术应用能够满足需求。为了实现以纳米级精度对物质进行编程的目标，该项目将开发两类分子设计程序之间的软件接口，到目前为止，这两类程序一直是独立进化的。被广泛采用的DNA结构设计程序CadNano将被扩展，以利用基于物理的微观模拟的结果，使迭代结构设计过程成为可能。将开发一种领先的分子图形程序VMD(可视化分子动力学)，以无缝地可视化CadNano设计，提供结构解释，并使用大量计算结构生物学和纳米技术工具对结构进行进一步修改。这两项发展都将利用云计算技术的最新进展，使DNA结构设计软件以独立于平台的方式随时随地供任何人使用。该项目得到了计算机与信息科学与工程局的高级网络基础设施办公室和工程局的土木、机械和制造创新司的支持。