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

有一天，纳米技术可能会彻底改变对我们国家利益非常重要的几项活动，包括我们如何制造消费品，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。一种很有前途的原子精确构建方法是适应来自生物体的分子构建块，如DNA、RNA和蛋白质，并重新利用它们自组装成规定的形状、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整合两种广泛应用于生物纳米结构设计和基于物理的分子模拟的软件工具来加速生物启发纳米结构的发展。这一努力的成果将提高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，当与实验室的实验验证相结合时，将使生物纳米技术的未来需求满足应用。为了实现以纳米级精度编程物质的目标，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，这两类分子设计程序一直是彼此独立发展的。广泛采用的DNA结构设计程序Cadnano将扩展到利用基于物理的微观模拟结果，从而实现迭代结构设计过程。一个领先的分子图形程序，VMD（视觉分子动力学），将开发无缝可视化Cadnano设计，提供它们的结构解释，并允许使用计算结构生物学和纳米技术工具库进一步修改结构。这两项开发都将利用云计算技术的最新进展，使DNA结构设计软件以一种与平台无关的方式在任何地方提供给任何人。该项目由计算机与信息科学与工程理事会的先进网络基础设施办公室和工程理事会的土木、机械和制造创新司提供支持。

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.