CAREER: Coding for Composite DNA Storage

DNA具有高密度、高稳定性等特点，是一种非常有吸引力的存储介质。 DNA存储系统包括将二进制信息编码为DNA链、合成（产生DNA分子）、存储、测序（阅读DNA链）和解码二进制信息。其中，合成是其高成本的主要瓶颈，每个核苷酸位置的成本约为0.10美元。传统上，信息由四种类型的DNA核苷酸表示，即腺嘌呤（A），胞嘧啶（C），鸟嘌呤（G）和胸腺嘧啶（T）;因此合成每比特信息至少需要0.05美元。另一方面，一种称为复合DNA存储的新兴技术通过所有四种类型的核苷酸的概率来表示信息，从而导致更高的信息密度和更低的每比特合成成本。该项目研究复合DNA存储的编码，寻求通过复合DNA字母表示二进制信息的有效方法，以实现成本效益，可靠，安全和大规模的信息存储。在复合DNA存储中，复合DNA字母由服从预定概率质量函数的多条链中相同位置的所有四种标准核苷酸（A、C、G、T）的混合物组成。在本项目中，将考虑复合DNA符号的选择和存储通道的各种因素，确定信息密度的基本限制和相应的可实现方案。此外，还将探索信息理论安全以对抗对抗性攻击。作为独特的特征，秘密信息可以通过仅阅读多个储存容器的混合DNA链而不是阅读所有容器的标准DNA来潜在地解码。此外，将检查从含有许多复合链的储存容器中鉴定给定的复合DNA链，以便于大规模储存。最后，理论方案将通过编写软件工具和进行实验来模拟和验证。因此，包括通道特性和复合DNA符号选择的理论模型将得到进一步改进。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。

DNA, with remarkable properties of high density and stability, is an appealing storage medium. The DNA storage system involves encoding the binary information to DNA strands, synthesis (producing DNA molecules), storage, sequencing (reading DNA strands), and decoding the binary information. Among them, synthesis is a major bottleneck for its high cost, which is approximately $0.10 per nucleotide position. Conventionally, information is represented by the four types of DNA nucleotides, namely, adenine (A), cytosine (C), guanine (G), and thymine (T); hence synthesis requires at least $0.05 per bit of information. An emerging technology called composite DNA storage, on the other hand, represents information by probabilities of all four types of nucleotides, leading to higher information density and lower synthesizing cost per bit by several orders of magnitude. This project investigates coding for composite DNA storage that seeks efficient methods to represent binary information by composite DNA letters so as to enable cost-effective, reliable, secure, and large-scale information storage. The activities in this project will be an important step towards the ubiquitous application of DNA storage in a broad range of applications.In composite DNA storage, a composite DNA letter constitutes a mixture of all four standard nucleotides (A, C, G, T) in the same position among multiple strands obeying a predetermined probability mass function. In this project, the fundamental limit on the information density and the corresponding achievable schemes will be established considering the choice of the composite DNA symbols and the various factors of the storage channel. Moreover, information-theoretic security will be explored to combat adversarial attacks. As a unique feature, secret information can be potentially decoded by reading only the mixed DNA strands of multiple storage vessels, instead of reading all vessels for standard DNA. In addition, the identification of a given composite DNA strand from a storage vessel containing many composite strands will be inspected in order to facilitate large-scale storage. Finally, the theoretical schemes will be simulated and verified by writing software tools and conducting experiments. Accordingly, theoretical models including channel characteristics and composite DNA symbol choices will be further improved.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.