Abstract
DNA tile self-assembly have been demonstrated to be used to solve graph theory or combinatorial optimization problem because of its high-density storage and huge-scale parallel computing ability. In this paper, tile self-assembly have been shown to be used for solving the maximum matching problem by mainly constructing four sub-systems which are seed configuration system, nondeterministic guess system, verification system and output system. These systems can be used to probabilistically get the feasible solution of the problem. The model can successfully perform the maximum matching problem in polynomial time with distinct tile types, parallel and at very low cost.
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References
Adleman, L.M.: Molecular computation of solutions to combinatorial problems. Science 266, 1021–1024 (1994)
Winfree, E., Liu, F.R., Wenzler, L.A., Seeman, N.C.: Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998)
Winfree, E., Eng, T., Rozenberg, G.: String tile models for DNA computing by self-assembly. In: Condon, A., Rozenberg, G. (eds.) DNA 2000. LNCS, vol. 2054, pp. 63–88. Springer, Heidelberg (2001)
Winfree, E.: Algorithmic self-assembly of DNA. Ph.D. Dissertation, California Institute of Technology (1998)
Winfree, E., Liu, F., Wenzler, L.A.: Design and self-assembly of 2D DNA crystals. Nature 394, 539–544 (1998)
Seeman, N.C.: DNA nanotechnology: novel DNA constructions. Annu. Rev. Biophys. Biomol. Struct. 27, 225–248 (1998)
Gehani, A., LaBean, T.H., Reif, J.H.: DNA-based cryptography. In: 5th DIMACS Workshop on DNA Based Computers. MIT (1999)
Mao, C., Sun, W., Seeman, N.C.: Designed two-dimensional DNA Holliday junction arrays visualized by atomic force microscopy. J. Am. Chem. Soc. 121, 5437–5443 (1999)
Mao, C., LaBean, T.H., Reif, J.H.: Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407, 493–496 (2000)
Carbone, A., Seeman, N.C.: Circuits and programmable self-assembling DNA structures. PNAS 99, 12577–12582 (2002)
Carbone, A., Seeman, N.C.: Molecular tiling and DNA self-assembly. In: Jonoska, N., Păun, G., Rozenberg, G. (eds.) Aspects of Molecular Computing. LNCS, vol. 2950, pp. 61–83. Springer, Heidelberg (2003)
Rothemund, P., Papadakis, N., Winfree, E.: Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol. 2(12), 2041–2053 (2004)
Brun, Y.: Arithmetic computation in the tile assembly model: addition and multiplication. Theor. Comput. Sci. 378(1), 17–31 (2007)
Zhang, X.C., Wang, Y.F., Chen, Z.H.: Arithmetic computation using self-assembly of DNA tiles: subtraction and division. Prog. Nat. Sci. 19(3), 377–388 (2009)
Lin, M.Q., Xu, J., Zhang, D.F.: 3D DNA self-assembly model for graph vertex coloring. J. Comput. Theor. Nanosci. 7(1), 246–253 (2010)
Pan, L.Q., Xu, J., Liu, Y.C.: A surface-based DNA algorithm for the minimal vertex problem. Prog. Nat. Sci. 13, 81–84 (2003)
Pan, L.Q., Liu, G.W., Xu, J.: Solid phase based DNA solution of the coloring problem. Prog. Nat. Sci. 14, 104–107 (2004)
Liu, W.B., Gao, L., Wang, S.D.: A surface-based DNA algorithm for maximal matching problem. Acta Electronica Sin. 31(10), 1496–1500 (2003)
Barish, R., Rothemund, P., Winfree, E.: Two computational primitives for algorithmic self-assembly: copying and counting. Nano Lett. 5(12), 2586–2592 (2005)
Wang, H.: Proving theorems by pattern recognition I. Bell Syst. Tech. J. 40, 1–42 (1961)
Song, T., Pan, L.: Spiking neural P systems with rules on synapses working in maximum spikes consumption strategy. IEEE Trans. Nanobiosci. 14(1), 38–44 (2015)
Song, T., Pan, L.: Spiking neural P systems with rules on synapses working in maximum spiking strategy. IEEE Trans. NanoBiosci. 14(4), 465–477 (2015)
Song, T., Pan, L., Jiang, K., et al.: Normal forms for some classes of sequential spiking neural P systems. IEEE Trans. NanoBiosci. 12(3), 255–264 (2013)
Song, T., Pan, L., Păun, G.: Asynchronous spiking neural P systems with local synchronization. Inf. Sci. 219, 197–207 (2013)
Song, T., Pan, L., Wang, J., et al.: Normal forms of spiking neural P systems with anti-spikes. IEEE Trans. NanoBiosci. 11(4), 352–359 (2012)
Zhang, X., Pan, L., Paun, A.: On the universality of axon P systems. IEEE Trans. Neural Netw. Learn. Syst. (2015). doi:10.1109/TNNLS.2015.2396940
Shi, X., Wang, Z., Deng, C., Song, T., Pan, L., Chen, Z.: A novel bio-sensor based on DNA strand displacement. PLoS One 9, e108856 (2014)
Acknowledgments
The authors thank the financial support for the work from Chinese National Natural Science Foundation (61379059, 61472293), the Fundamental Research Funds for the Central Universities (CZZ13003, CZQ12006).
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Zhang, H., Qiang, X., Zhang, K. (2015). Application of DNA Self-assembly for Maximum Matching Problem. In: Gong, M., Linqiang, P., Tao, S., Tang, K., Zhang, X. (eds) Bio-Inspired Computing -- Theories and Applications. BIC-TA 2015. Communications in Computer and Information Science, vol 562. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-49014-3_55
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DOI: https://doi.org/10.1007/978-3-662-49014-3_55
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