CAREER: Coding for Composite DNA Storage

DNA具有密度高、稳定性好等特点，是一种极具吸引力的存储介质。DNA存储系统包括将二进制信息编码成DNA链、合成(生产DNA分子)、存储、测序(读取DNA链)和解码二进制信息。其中，合成是一大瓶颈，因为其成本较高，每个核苷酸位置约为0.10美元。传统上，信息是由四种类型的DNA核苷酸表示的，即腺嘌呤(A)、胞嘧啶(C)、鸟嘌呤(G)和胸腺嘧啶(T)；因此，合成每一位信息至少需要0.05美元。另一方面，一种名为复合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，导致更高的信息密度和更低的每比特合成成本几个数量级。本项目研究复合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，从而实现经济、可靠、安全和大规模的信息存储。该项目的活动将是朝着DNA存储在广泛应用中无处不在的应用迈出的重要一步。在复合DNA存储中，复合DNA字母由位于相同位置的所有四个标准核苷酸(A，C，G，T)在多条链中的混合物组成，并且服从预定的概率质量函数。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，建立信息密度的基本限制和相应的可实现方案。此外，还将探索信息论安全，以对抗对手攻击。作为一项独特的功能，秘密信息可以通过只读取多个存储容器的混合DNA链，而不是读取所有容器的标准DNA来潜在地解码。此外，将检查从包含许多复合DNA链的存储容器中识别给定的复合DNA链的情况，以促进大规模存储。最后，通过编写软件工具和进行实验，对理论方案进行了仿真验证。因此，包括渠道特征和复合DNA符号选择在内的理论模型将进一步完善。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。

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.