Abstract:

Deoxyribonucleic Acid (DNA), with its ultra-high storage density and long durability, is a promising long-term archival storage medium and is attracting much attention today. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. Several studies have verified the feasibility of using DNA for archival storage with limited amounts of data. Since then, many encoding schemes have been proposed to enlarge DNA storage capacity by increasing DNA encoding density under certain bio-constraints. However, only increasing encoding density is insufficient because enhancing DNA storage capacity is a multifaceted problem. In this talk, we assume that random accesses are necessary for practical DNA archival storage. We first identify major factors affecting DNA tube storage capacity under current technologies. We then systematically investigate the practical DNA tube capacity with several popular encoding schemes. We found that the collisions between primers and DNA payload sequences severely limit the DNA tube capacity. Based on this discovery, we designed a new encoding scheme called Collision Aware Code (CAC) to trade some encoding density for the reduction of primer-payload collisions. Compared with the best result among the five existing encoding schemes, CAC can extricate 120% more primers from collisions and increase the DNA tube capacity from 211.96 GB to 295.11 GB. Besides, we also evaluate CAC’s recoverability from DNA storage errors. The result shows CAC is comparable to those of existing encoding schemes. We will also briefly discuss several other studies on DNA storage done by our group.

Bio:

David H.C. Du (杜宏章) – received his B.S. in mathematics from National Tsing-Hua University in 1974 and the M.S. and Ph.D. degrees in computer science from the University of Washington, Seattle, in 1980 and 1981, respectively. He is currently the Qwest Chair Professor at the Computer Science and Engineering Department, University of Minnesota, Minneapolis and was the Director of US National Science Foundation Industry/University Collaboration Research Center with Center Research in Intelligent Storage from 2009 to 2021. He is an IEEE Fellow and a Fellow of Minnesota Supercomputing Institute. He has done research in cyber security, sensor networks, multimedia computing, storage systems, high-speed networking, high-performance computing, and database design and CAD for VLSI circuits. His current research focuses on storage technologies/systems and vehicular networks. He has authored and co-authored more than 340 technical papers published in top conferences and referred journals. He has also graduated 68 Ph.D. and 100+ M.S. students in the past.