Srilakshmi Pattabiraman, University of Illinois Urbana-Champaign: “Coding for Polymer and DNA Based Storage”

Position: PhD Candidate

Current Institution:University of Illinois Urbana-Champaign

Abstract: Coding for Polymer and DNA Based Storage

Coding for Polymer and DNA Based Storage To address the emerging needs for large data volume archiving it is of great importance to identify new nanoscale recording media. Our work focuses on two such molecular storage platforms. 1) In Polymer-based storage platforms two molecules that significantly differ in their masses represent the bits 0 and 1 and are used as building blocks in the process of synthesizing user-defined information content. The synthetic polymers are read by mass spectrometers that break multiple copies of the polymer uniformly at random thereby fragmenting the string into substrings. The masses of these substrings are reported as the output of the system. We propose a new family of codes that allows for both unique string reconstruction and correction of multiple mass errors. Noting that these polymers are stored and read together we design codebooks such that multiple strings can be reconstructed based on their joint mass spectrometry readouts. 2) In one DNA-based data storage system nanoscopic holes are punched into the sugar-phosphate backbone of one strand of a double-stranded DNA molecule. A “hole” indicates the value 1 while the absence of a hole indicates the value 0. Multiple copies of the same DNA strands are punched to bear different patterns and are mixed and stored in a single microwell. The mixture with various punch patterns is then sequenced and the strings are read together. However multiple holes punched in proximity results in poorer quality outputs leading to a constraint on the runlength of 0s between pairs of 1s. Our goal is to construct a binary code such that multiple strings can be sequenced and read simultaneously with precision. We address this problem by introducing a new runlength limited group testing paradigm.


I am a 4th year graduate student at the University of Illinois Urbana-Champaign in the Department of Electrical and Computer Engineering. I am advised by Prof. Olgica Milenkovic. I am drawn towards mathematical challenges in Combinatorics Coding Theory Detection and Estimation and Statistical Learning Theory. Presently my research focuses on alternatives to the current digital archival storage platforms. I have allied research interests in phylogeny and sequence alignment. I earned my masterÂ’s in Electrical and Computer Engineering from The University of Texas at Austin in December 2017. Previously I obtained my B. Tech. degree in Instrumentation and Control Engineering from National Institute of Technology Trichy India in 2015.