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Unique Assembly Verification in Two-Handed Self-Assembly

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Abstract

One of the most fundamental and well-studied problems in Tile Self-Assembly is the Unique Assembly Verification (UAV) problem. This algorithmic problem asks whether a given tile system uniquely assembles a specific assembly. The complexity of this problem in the 2-Handed Assembly Model (2HAM) at a constant temperature is a long-standing open problem since the model was introduced. Previously, only membership in the class coNP was known and that the problem is in P if the temperature is one (\(\tau =1\)). The problem is known to be hard for many generalizations of the model, such as allowing one step into the third dimension or allowing the temperature of the system to be a variable, but the most fundamental version has remained open. In this paper, we prove the UAV problem in the 2HAM is hard even with a small constant temperature (\(\tau = 2\)), and finally answer the complexity of this problem (open since 2013). Further, this result proves that UAV in the staged self-assembly model is coNP-complete with a single bin and stage (open since 2007), and that UAV in the q-tile model is also coNP-complete (open since 2004). We reduce from Monotone Planar 3-SAT with Neighboring Variable Pairs, a special case of 3SAT recently proven to be NP-hard. We accompany this reduction with a positive result showing that UAV is solvable in polynomial time with the promise that the given target assembly will have a tree-shaped bond graph, i.e., contains no cycles. We provide a \(\mathcal {O}(n^5)\) algorithm for UAV on tree-bonded assemblies when the temperature is fixed to 2, and a \(\mathcal {O}(n^5\log \tau )\) time algorithm when the temperature is part of the input.

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Notes

  1. While a formula may have multiple clauses without a parent, the authors of [26] show that by adding additional variables, an instance may be constructed with only a single root clause. For MP-3SAT-NVP, we need at least two clauses (one for the positive and negative sides).

  2. Without these base dominoes, variable gadgets could build without the full Bump due to backfilling or backwards growth. The dominoes ensure this can not happen.

  3. Having complimentary bump positions is equivalent to both representing the same assignment.

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Acknowledgements

This research was supported in part by National Science Foundation Grant CCF-1817602.

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Authors and Affiliations

  1. Department of Computer Science, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX, 78539-2999, USA

    David Caballero, Timothy Gomez, Robert Schweller & Tim Wylie

  2. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA

    Timothy Gomez

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  1. David Caballero
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Correspondence to Tim Wylie.

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To the best of our knowledge, we have no conflicts of interest related to the research. For publishing, Robert Schweller currently serves as an editor for the Algorithmica journal. For funding, Robert Schweller and Tim Wylie are PIs and received funding from the National Science Foundation (Grant CCF-1817602).

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Caballero, D., Gomez, T., Schweller, R. et al. Unique Assembly Verification in Two-Handed Self-Assembly. Algorithmica 85, 2427–2453 (2023). https://doi.org/10.1007/s00453-023-01103-5

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