Synthesizing Minimal Tile Sets for Patterned DNA Self-assembly

  • Mika Göös
  • Pekka Orponen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6518)

Abstract

The Pattern self-Assembly Tile set Synthesis (PATS) problem is to determine a set of coloured tiles that self-assemble to implement a given rectangular colour pattern. We give an exhaustive branch-and-bound algorithm to find tile sets of minimum cardinality for the PATS problem. Our algorithm makes use of a search tree in the lattice of partitions of the ambient rectangular grid, and an efficient bounding function to prune this search tree. Empirical data on the performance of the algorithm shows that it compares favourably to previously presented heuristic solutions to the problem.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Mika Göös
    • 1
  • Pekka Orponen
    • 1
  1. 1.Department of Information and Computer ScienceAalto University School of Science and Technology (TKK)AaltoFinland

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