XTile: An Error Correction Package for DNA Self-Assembly

Anshul Chaurasia, Sudhanshu Dwivedi, Prateek Jain and and Manish K. Gupta
Laboratory of Natural Information Processing
Dhirubhai Ambani Institute of Information and Communication Technology (DA-IICT),
Gandhinagar, India
Home Page: http://www.guptalab.org


Self-assembly is a process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. It has been predicted that in future self-assembly will become an important tool in the fields of bio-molecular computation, nano-technology and medicine. However robustness (i.e. error correction) is a key challenge in realizing the potential of self-assembly. In earlier works many authors have proposed several combinatorial error correction schemes to control errors having a close analogy with the coding theory such as Winfree's proofreading scheme and its generalizations by Chen and Goel and compact scheme of Reif, Sahu and Yin. In this work, we report an error correction package XTile that can be used to create input files to the Xgrow simulator of Erik Winfree by providing the design logic of the tiles and it also allows the user to apply proofreading, snake and compact error correction schemes. We also give a tile set for multiplying two binary numbers.

Keywords: DNA Self-Assembly, Error Correction, DNA Computer, Multiplier

XTile Home Page: http://www.guptalab.org/xtile