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Synthesis of Tile Sets for DNA Self-Assembly

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2 Author(s)
Xiaojun Ma ; Northeastern Univ., Boston ; Fabrizio Lombardi

This paper addresses the issues revolving around the synthesis of tile sets for DNA self-assembly as a promising approach for IC manufacturing in the nanoscale. As for a finite pattern, synthesis for minimizing tile or bond types is equivalent to a minimum graph coloring problem, two greedy algorithms that reduce the number of tiles (PATS_Tile) or bonds (PATS_Bond) in synthesized tile sets are proposed and evaluated. Both algorithms are O(l4) for a square pattern of dimension l. It is shown by simulation that PATS_Tile has a better average performance if both types of reduction must be accomplished.

Published in:

IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems  (Volume:27 ,  Issue: 5 )