Bridging DNA Storage and Computation: An Integrated Framework for Efficient Biomolecular Data Management

In the era of rapid technological advancements, Cyber-Physical Systems (CPS) play a pivotal role in sectors like healthcare and industrial automation. However, with the escalating demand for data storage in CPS, traditional storage media may be inadequate in the future. DNA (deoxyribonucleic acid) storage is emerging as a promising alternative, given its high density, long-term durability, and stability. However, several challenges persist in DNA storage, notably the high costs and large time consumption associated with accessing DNA data. Fortunately, DNA computing technology presents a possible solution to these challenges. This direct computation method offers time and cost savings and enhanced computational efficiency. In this work, we present DCDS (DNA Computer with DNA Storage) to ensure efficient data access, and propose the DCA (dual-phase clustering approach) to mitigate contamination and errors during data transportation. DCDS holds the potential to enhance the efficiency with high accuracy of DNA computing systems significantly. DCA leads to a time savings of 87--91% on the DNA Computer unit, mainly by reducing unnecessary cleaning steps in DMF (Digital Microfluidics).