Abstract
In this paper, we introduce the following problem in the theory of algorithmic self-assembly: given an input shape as the seed of a tile-based self-assembly system, design a finite tile set that can, in some sense, uniquely identify whether or not the given input shape–drawn from a very general class of shapes–matches a particular target shape. We first study the complexity of correctly identifying squares. Then we investigate the complexity associated with the identification of a considerably more general class of non-square, hole-free shapes.
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References
Abel, Z., Benbernou, N., Damian, M., Demaine, E., Demaine, M., Flatland, R., Kominers, S., Schweller, R.: Shape replication through self-assembly and RNAse enzymes. In: SODA 2010: Proceedings of the Twentyfirst Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 1045–1064 (2010)
Adleman, L.: Toward a mathematical theory of self-assembly (extended abstract), Tech. Report 00-722, University of Southern California (2000)
Adleman, L., Cheng, Q., Goel, A., Huang, M.-D., Wasserman, H.: Linear self-assemblies: Equilibria, entropy and convergence rates. In: Sixth International Conference on Difference Equations and Applications. Taylor and Francis, Abington (2001)
Andersen, E.S., Dong, M., Nielsen, M.M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M.M., Sander, B., Stark, H., Oliveira, C.L.P., Pedersen, J.S., Birkedal, V., Besenbacher, F., Gothelf, K.V., Kjems, J.: Self-assembly of a nanoscale dna box with a controllable lid. Nature 459(7243), 73–76 (2009)
Barish, R.D., Schulman, R., Rothemund, P.W., Winfree, E.: An information-bearing seed for nucleating algorithmic self-assembly. Proceedings of the National Academy of Sciences 106(15), 6054–6059 (2009)
Cheng, Q., Aggarwal, G., Goldwasser, M.H., Kao, M.-Y., Schweller, R.T., de Espanés, P.M.: Complexities for generalized models of self-assembly. SIAM Journal on Computing 34, 1493–1515 (2005)
Demaine, E.D., Demaine, M.L., Fekete, S.P., Ishaque, M., Rafalin, E., Schweller, R.T., Souvaine, D.L.: Staged self-assembly: nanomanufacture of arbitrary shapes with O(1) glues. Natural Computing 7(3), 347–370 (2008)
Fu, Y., Schweller, R.: Temperature 1 self-assembly: Deterministic assembly in 3d and probabilistic assembly in 2d. In: Proceedings of the ACM-SIAM Symposium on Discrete Algorithms (SODA 2011) (to appear, 2011)
Gu, H., Chao, J., Xiao, S.-J., Seeman, N.C.: A proximity-based programmable dna nanoscale assembly line. Nature 465(7295), 202–205 (2010)
Hartgerink, J.D., Beniash, E., Stupp, S.I.: Self-Assembly and Mineralization of Peptide-Amphiphile Nanofibers. Science 294(5547), 1684–1688 (2001)
Kalsin, A.M., Fialkowski, M., Paszewski, M., Smoukov, S.K., Bishop, K.J.M., Grzybowski, B.A.: Electrostatic Self-Assembly of Binary Nanoparticle Crystals with a Diamond-Like Lattice. Science 312(5772), 420–424 (2006)
Luhrs, C.: Polyomino-safe DNA self-assembly via block replacement. In: Goel, A., Simmel, F.C., Sosík, P. (eds.) DNA14. LNCS, vol. 5347, pp. 112–126. Springer, Heidelberg (2008)
Lund, K., Manzo, A.J., Dabby, N., Michelotti, N., Johnson-Buck, A., Nangreave, J., Taylor, S., Pei, R., Stojanovic, M.N., Walter, N.G., Winfree, E., Yan, H.: Molecular robots guided by prescriptive landscapes. Nature 465(7295), 206–210 (2010)
Majumder, U., LaBean, T.H., Reif, J.H.: Activatable tiles for compact error-resilient directional assembly. In: 13th International Meeting on DNA Computing (DNA 13), Memphis, Tennessee, June 4-8 (2007)
Rothemund, P.W.K.: Folding DNA to create nanoscale shapes and patterns. Nature 440(7082), 297–302 (2006)
Rothemund, P.W.K., Winfree, E.: The program-size complexity of self-assembled squares (extended abstract). In: STOC 2000: Proceedings of the Thirty-second Annual ACM Symposium on Theory of Computing, pp. 459–468. ACM, New York (2000)
Rothemund, P.W.K., Papadakis, N., Winfree, E.: Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biology 2(12), 2041–2053 (2004)
Soloveichik, D., Winfree, E.: Complexity of self-assembled shapes. SIAM Journal on Computing 36(6), 1544–1569 (2007)
Tang, Z., Zhang, Z., Wang, Y., Glotzer, S.C., Kotov, N.A.: Self-Assembly of CdTe Nanocrystals into Free-Floating Sheets. Science 314(5797), 274–278 (2006)
Vitányi, P., Li, M.: An introduction to kolmogorov complexity and its applications. Springer, Heidelberg (1997)
Winfree, E.: Algorithmic self-assembly of DNA, Ph.D. thesis, California Institute of Technology (June 1998)
Winfree, E.: Simulations of computing by self-assembly, Tech. Report CaltechCSTR:1998.22, California Institute of Technology (1998)
Winfree, E.: Self-healing tile sets. In: Chen, J., Jonoska, N., Rozenberg, G. (eds.) Nanotechnology: Science and Computation. Natural Computing Series, pp. 55–78. Springer, Heidelberg (2006)
Winfree, E., Yang, X., Seeman, N.C.: Universal computation via self-assembly of dna: Some theory and experiments. In: DNA Based Computers II. DIMACS, vol. 44, pp. 191–213. American Mathematical Society, Providence (1996)
Yan, H., Park, S.H., Finkelstein, G., Reif, J.H., LaBean, T.H.: DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires. Science 301(5641), 1882–1884 (2003)
Zeng, H., Li, J., Liu, J.P., Wang, Z.L., Sun, S.: Exchange-coupled nanocomposite magnets by nanoparticle self-assembly. Nature 420(6914), 395–398 (2002)
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Patitz, M.J., Summers, S.M. (2010). Identifying Shapes Using Self-assembly. In: Cheong, O., Chwa, KY., Park, K. (eds) Algorithms and Computation. ISAAC 2010. Lecture Notes in Computer Science, vol 6507. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-17514-5_39
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DOI: https://doi.org/10.1007/978-3-642-17514-5_39
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