Synthesizing minimal tile sets for patterned DNA self-assembly

Reference:

Mika Göös and Pekka Orponen. Synthesizing minimal tile sets for patterned DNA self-assembly. Technical Report cs.DS/0911.2924, arXiv.org, November 2009.

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.

Keywords:

DNA self-assembly, tilings, PATS problem, branch-and-bound algorithm

Suggested BibTeX entry:

@techreport{GoOr09,
    author = {Mika Göös and Pekka Orponen},
    institution = {arXiv.org},
    month = {November},
    number = {cs.DS/0911.2924},
    pages = {14},
    title = {Synthesizing minimal tile sets for patterned {DNA} self-assembly},
    type = {Technical Report},
    year = {2009},
}

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