Abstract
We introduce the problem of staged self-assembly of one-dimensional nanostructures, which becomes interesting when the elements are labeled (e.g., representing functional units that must be placed at specific locations). In a restricted model in which each operation has a single terminal assembly, we prove that assembling a given string of labels with the fewest steps is equivalent, up to constant factors, to compressing the string to be uniquely derived from the smallest possible context-free grammar (a well-studied O(log n)-approximable problem) and that the problem is NP-hard. Without this restriction, we show that the optimal assembly can be substantially smaller than the optimal context-free grammar, by a factor of \(\Omega(\sqrt{n/\log n})\) even for binary strings of length n. Fortunately, we can bound this separation in model power by a quadratic function in the number of distinct glues or tiles allowed in the assembly, which is typically small in practice.
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Notes
Personal communication with Hyunmin Yi, 2008–2010.
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Acknowledgments
We thank Martin Demaine, André Schulz, Diane Souvaine, and Hyunmin Yi for helpful discussions, and anonymous reviewers for helpful suggestions.
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Demaine, E.D., Eisenstat, S., Ishaque, M. et al. One-dimensional staged self-assembly. Nat Comput 12, 247–258 (2013). https://doi.org/10.1007/s11047-012-9359-0
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DOI: https://doi.org/10.1007/s11047-012-9359-0