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.

纳米技术可能有一天可以彻底改变一些对我们国家利益的重要活动，包括我们如何生产消费产品，如何诊断和治疗疾病以及我们如何发现和中和对防御的威胁。一种有希望的原子上精确结构的方法是从生物，RNA和蛋白质等生物体中调整分子构建块，并将其重新用于自我组装成处方的形状，设备和材料。进步的关键瓶颈是设计，建造和测试纳米结构的复杂性，该纳米结构由数千或数百万个原子组成。该项目的目的是通过集成在生物纳米结构设计和基于物理学的分子模拟中使用的两种广泛采用的软件工具来加速生物启发的纳米结构的开发。 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彼此独立发展。广泛采用的DNA结构设计程序Cadnano将扩展以利用基于物理学的显微镜模拟的结果，从而实现迭代结构设计过程。将开发领先的分子图形程序VMD（视觉分子动力学），以无缝可视化Cadnano设计，提供结构解释，并使用计算结构生物学和纳米技术工具的库来进一步修改结构。这两种开发都将利用云计算技术的最新进展，使DNA结构设计软件在任何地方都能提供，并以平台独立的方式提供给任何人。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以及工程工程局的民用，机械和制造创新部的支持。