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Published in: Natural Computing 1/2019

30-08-2018

Self-assembly of shapes at constant scale using repulsive forces

Authors: Austin Luchsinger, Robert Schweller, Tim Wylie

Published in: Natural Computing | Issue 1/2019

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Abstract

The algorithmic self-assembly of shapes has been considered in several models of self-assembly. For the problem of shape construction, we consider an extended version of the two-handed tile assembly model, which contains positive (attractive) and negative (repulsive) interactions. As a result, portions of an assembly can become unstable and detach. In this model, we utilize fuel-efficient computation to perform Turing machine simulations for the construction of the shape. In this paper, we show how an arbitrary shape can be constructed using an asymptotically optimal number of distinct tile types (based on the shape’s Kolmogorov complexity). We achieve this at O(1) scale factor in this straightforward model, whereas all previous results with sublinear scale factors utilize powerful self-assembly models containing features such as staging, tile deletion, chemical reaction networks, and tile activation/deactivation. Furthermore, the computation and construction in our result only creates constant-size garbage assemblies as a byproduct of assembling the shape.

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Footnotes
1
Note that only matching glues of the same type contribute a non-zero weight, whereas non-equal glues always contribute zero weight to the bond graph. Relaxing this restriction has been considered as well Cheng et al. (2005).
 
2
The strongest detaching force used in our construction is a \(\tau\) strength detachment, and since the internal bonds of our gadgets are meant to withstand even the strongest repulsive force, it follows that those bonds must be of strength at least \(2\tau\).
 
3
The formal theorem statement of Schweller and Sherman (2013) cites the product of the states and symbols of the Turing machine as the tile type cost. However, the actual cost is the number of transition rules, which is upper bounded by this product.
 
Literature
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go back to reference Cheng Q, Aggarwal G, Goldwasser MH, Kao MY, Schweller RT, de Espanés PM (2005) Complexities for generalized models of self-assembly. SIAM J Comput 34:1493–1515MathSciNetCrossRefMATH Cheng Q, Aggarwal G, Goldwasser MH, Kao MY, Schweller RT, de Espanés PM (2005) Complexities for generalized models of self-assembly. SIAM J Comput 34:1493–1515MathSciNetCrossRefMATH
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go back to reference Demaine ED, Patitz MJ, Schweller RT, Summers SM (2011) Self-assembly of arbitrary shapes using RNAse enzymes: meeting the Kolmogorov bound with small scale factor (extended abstract). In: Proceedings of the 28th international symposium on theoretical aspects of computer science (STACS’11) Demaine ED, Patitz MJ, Schweller RT, Summers SM (2011) Self-assembly of arbitrary shapes using RNAse enzymes: meeting the Kolmogorov bound with small scale factor (extended abstract). In: Proceedings of the 28th international symposium on theoretical aspects of computer science (STACS’11)
go back to reference Patitz MJ, Rogers TA, Schweller R, Summers SM, Winslow A (2016) Resiliency to multiple nucleation in temperature-1 self-assembly. In: Rondelez Y, Woods D (eds) DNA computing and molecular programming. Springer, Berlin Patitz MJ, Rogers TA, Schweller R, Summers SM, Winslow A (2016) Resiliency to multiple nucleation in temperature-1 self-assembly. In: Rondelez Y, Woods D (eds) DNA computing and molecular programming. Springer, Berlin
go back to reference Rothemund PWK, Winfree E (2000) The program-size complexity of self-assembled squares (extended abstract). In: Proceedings of the 32nd ACM symposium on theory of computing, STOC’00, pp 459–468 Rothemund PWK, Winfree E (2000) The program-size complexity of self-assembled squares (extended abstract). In: Proceedings of the 32nd ACM symposium on theory of computing, STOC’00, pp 459–468
go back to reference Schweller R, Sherman M (2013) Fuel efficient computation in passive self-assembly. In: SODA 2013: proceedings of the 24th annual ACM-SIAM symposium on discrete algorithms. SIAM, pp 1513–1525 Schweller R, Sherman M (2013) Fuel efficient computation in passive self-assembly. In: SODA 2013: proceedings of the 24th annual ACM-SIAM symposium on discrete algorithms. SIAM, pp 1513–1525
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Metadata
Title
Self-assembly of shapes at constant scale using repulsive forces
Authors
Austin Luchsinger
Robert Schweller
Tim Wylie
Publication date
30-08-2018
Publisher
Springer Netherlands
Published in
Natural Computing / Issue 1/2019
Print ISSN: 1567-7818
Electronic ISSN: 1572-9796
DOI
https://doi.org/10.1007/s11047-018-9707-9

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