AF Medium: DNA-based Data Storage and Computing Materials

全球数据的指数增长与摩尔定律最近的终结不谋而合，因此需要替代的、新的大规模数据存储和计算形式，超越传统的基于硅的设备。虽然DNA通常被认为是地球上所有生命的蓝图材料，但作为一种合成材料，它也提供了非常密集的信息存储介质和高度并行的计算能力。在目前的奖项中，研究人员研究了将DNA用于超高密度数据存储和计算。DNA数据文件被封装在纳米级的数据包中，以研究如何在同一分子文件系统中实现随机访问存储器和高度并行计算。DNA还将被构建成2D超分子组件，以探索用于超高密度数据存储和检索的空间模式。这些数据存储和计算架构将被用来模仿传统的基于硅的计算中常见的神经网络。该项目的结果将导致基本的理解，这将指导下一代信息存储和检索系统，远远超过当前固态设备的能力。研究生正在接受融合了计算机科学、化学和DNA纳米技术的跨学科培训。这位研究人员正在接待来自当地和全国大学的代表不足的少数族裔和女性，以帮助培养多样化的下一代计算机科学家和工程师。这项工作的成果正在通过已建立的协议和在线传播的开源软件工具进行分发。在本奖项中，DNA纳米技术和DNA折纸被用于数据存储和计算。DNA文件被封装在二氧化硅纳米颗粒中，用于信息编码和条形码，在解决方案中提供随机访问存储器和高度并行计算。同时，2D DNA折纸超结构被用作自组装块来组织和寻址存储在空间上的信息，DNA折纸被用作使用染料、纳米颗粒和量子点实现的标记有“二维码”的存储块。在二氧化硅纳米颗粒和DNA折纸中，单链DNA条形码和标签之间的广泛杂交被用于探索用于联想记忆和数据分类的分子计算算法。关联交互映射是在与关联信息相关的杂交空间中探索的。总而言之，这些基于解决方案的结构化2D DNA存储系统为开发新的基于DNA的信息存储体系结构提供了独特的机会，这种体系结构使用关联分子计算来模拟神经网络。这一奖项的结果将导致基于DNA的分层存储系统的基本原则，用于下一代信息存储和检索。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

The exponential growth of worldwide data coincides with the recent end of Moore’s Law and therefore calls for alternative, new forms of large-scale data storage and computation that go beyond conventional silicon-based devices. While DNA is commonly known as the material that is the blueprint for all life on earth, as a synthetic material it also offers an extraordinarily dense information-storage medium and highly parallel computing capabilities. In the current award, the investigator studies the use of DNA for ultra-high-density data storage and computing. DNA data files are encapsulated within nanometer-scale packets to investigate how to enable random-access memory and highly parallel computation within the same molecular file system. DNA will also be structured into 2D supra-molecular assemblies to explore spatial patterning for ultra-dense data storage and retrieval. These data-storage and computing architectures will be used to mimic neural networks commonly found in conventional silicon-based computing. Results of this project will lead to fundamental understanding that will guide next-generation information-storage and -retrieval systems that far exceed current capabilities of solid-state devices. Graduate students are being trained in an interdisciplinary manner integrating computer science, chemistry, and DNA nanotechnology. The investigator is hosting host under-represented minorities and women from local and national colleges to help nurture a diverse set of next-generation computer scientists and engineers. Results of this work are being distributed through established protocols and open source software tools disseminated online.In the present award, DNA nanotechnology and DNA origami are used for data storage and computing. DNA files are encapsulated within silica nanoparticles for information encoding and barcoding, offering both random-access memory and highly parallel computation in solution. In parallel, 2D DNA origami superstructures are used as self-assembly blocks to organize and address information stored spatially, with DNA origami serving as memory blocks labeled with “QR codes” implemented using dyes, nanoparticles, and quantum dots. Extensive hybridization between single-stranded DNA barcodes and labels are used in both silica nanoparticles and DNA origami to explore molecular computing algorithms for associative memory and data sorting. Associative interaction maps are explored in hybridization space correlated with associative information. Together, these solution-based and structured 2D DNA memory systems offer unique opportunities for developing new DNA-based information storage architectures that mimic neural networks using associative molecular computation. Results of this award will lead to fundamental principles of hierarchical DNA-based memory systems for next-generation information storage and retrieval.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.