CNS Core: Medium: Thermodynamically-driven design of high capacity, practical DNA-based data storage systems

CNS 核心：中：高容量、实用的基于 DNA 的数据存储系统的热力学驱动设计

• 批准号: 1901324
• 负责人: James Tuck
• 金额: $ 121.6万
• 依托单位: North Carolina State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-10-01 至 2024-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1901324&HistoricalAwards=false
• 关键词: CNS; Core; Medium; Thermodynamically; driven

The idea of storing information in deoxyribonucleic acid (DNA) first arose a few decades ago. DNA is intriguing as a storage medium due to its high density, long half-life of over 100 years, and low maintenance costs. There is renewed interest in DNA as a storage medium due to society's growing demand for large volumes of permanent data storage. However, it also poses many new challenges. Unlike electronic media that physically orders its data, DNA strands are stored in a very small space without any order. This project seeks to understand how DNA strands can be designed using a thermodynamically-driven approach.The project will develop a set of computational and physical tools that enable truly extreme-scale DNA storage systems. A key goal is a set of generalizable design principles for DNA-based storage systems garnered through a deep fundamental understanding of how DNA sequences translate into physical interactions derived from a statistical thermodynamic framework. From this thermodynamic framework, the project will engineer specific data manipulations to make random access and searching for data more efficient and create overall effective architectures for DNA storage systems. The tasks of the project involve exploring, developing models, and testing key thermodynamic knobs for tuning strand interactions.If the project is successful, it may help lay the foundation to make DNA-based storage practical and affordable. With that, long-term, reliable storage of information may become more abundant. The project will also train multiple Ph.D. students and undergraduate students in related areas of synthetic biology and computer systems engineering. Their training will include interacting with the project leaders, taking coursework relevant to the project, carrying out research tasks, writing and critiquing articles for publication, and presenting their work. The project will also broaden participation in computing through outreach to underserved communities in the areas around North Carolina State University.The results of this project will be made available through a public website at http://go.ncsu.edu/dna-storage. The website and data collected in the project will be available for at least five years after the end of the project and will remain available until such provision is no longer practical.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

在脱氧核糖核酸（DNA）中存储信息的想法最初出现在几十年前。DNA作为存储介质非常有趣，因为它的密度高、半衰期长（超过100年）和维护成本低。由于社会对大量永久数据存储的需求不断增长，人们对DNA作为存储介质重新产生了兴趣。然而，它也提出了许多新的挑战。不像电子媒介，它的数据是按物理顺序排列的，DNA链存储在一个非常小的空间里，没有任何顺序。该项目旨在了解如何使用计算机驱动的方法设计DNA链。该项目将开发一套计算和物理工具，使真正的极端规模的DNA存储系统成为可能。一个关键的目标是一套基于DNA的存储系统的可推广的设计原则，通过对DNA序列如何转化为来自统计热力学框架的物理相互作用的深刻基本理解而获得。从这个热力学框架中，该项目将设计特定的数据操作，使随机访问和搜索数据更有效，并为DNA存储系统创建整体有效的架构。该项目的任务包括探索，开发模型，并测试关键的热力学旋钮调谐链相互作用。如果该项目是成功的，它可能有助于奠定基础，使基于DNA的存储实用和负担得起的。这样，长期、可靠的信息存储可能会变得更加丰富。该项目还将培养多名博士。学生和本科生在合成生物学和计算机系统工程的相关领域。 他们的培训将包括与项目负责人互动，参加与项目相关的课程，执行研究任务，撰写和评论文章以供出版，并展示他们的工作。该项目还将通过向北卡罗来纳州州立大学周围地区服务不足的社区进行推广，扩大对计算的参与，该项目的结果将通过一个公共网站http://go.ncsu.edu/dna-storage公布。该网站和项目中收集的数据将在项目结束后至少五年内可用，并将一直可用，直到这种提供不再实用。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Dynamic and scalable DNA-based information storage

• DOI: 10.1038/s41467-020-16797-2
• 发表时间: 2020-06-12
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Lin, Kevin N.;Volkel, Kevin;Keung, Albert J.
• 通讯作者: Keung, Albert J.

DINOS: Data INspired Oligo Synthesis for DNA Data Storage

• DOI: 10.1145/3510853
• 发表时间: 2022-03
• 期刊: ACM Journal on Emerging Technologies in Computing Systems (JETC)
• 作者: Kevin Volkel;Kyle J Tomek;Albert J. Keung;James M. Tuck