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2015 | OriginalPaper | Chapter

Scalable Design of Logic Circuits Using an Active Molecular Spider System

Authors : Dandan Mo, Matthew R. Lakin, Darko Stefanovic

Published in: Information Processing in Cells and Tissues

Publisher: Springer International Publishing

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Abstract

As spatial locality leads to advantages of computation speed-up and sequence reuse in molecular computing, molecular walkers that exhibit localized reactions are of interest for implementing logic computations. We use molecular spiders, which are a type of molecular walkers, to implement logic circuits. We develop an extended multi-spider model with a dynamic environment where signal transmission is triggered locally, and use this model to implement three basic gates (AND, OR, NOT) and a mechanism to cascade the gates. We use a kinetic Monte Carlo algorithm to simulate gate computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity.

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Literature
1.
go back to reference Antal, T., Krapivsky, P.L.: Molecular spiders with memory. Phys. Rev. E 76(2), 021121 (2007)CrossRef Antal, T., Krapivsky, P.L.: Molecular spiders with memory. Phys. Rev. E 76(2), 021121 (2007)CrossRef
2.
go back to reference Chandran, H., Gopalkrishnan, N., Phillips, A., Reif, J.: Localized hybridization circuits. In: Cardelli, L., Shih, W. (eds.) DNA 17 2011. LNCS, vol. 6937, pp. 64–83. Springer, Heidelberg (2011) CrossRef Chandran, H., Gopalkrishnan, N., Phillips, A., Reif, J.: Localized hybridization circuits. In: Cardelli, L., Shih, W. (eds.) DNA 17 2011. LNCS, vol. 6937, pp. 64–83. Springer, Heidelberg (2011) CrossRef
3.
go back to reference Dannenberg, F., Kwiatkowska, M., Thachuk, C., Turberfield, A.J.: DNA Walker circuits: computational potential, design, and verification. In: Soloveichik, D., Yurke, B. (eds.) DNA 2013. LNCS, vol. 8141, pp. 31–45. Springer, Heidelberg (2013) CrossRef Dannenberg, F., Kwiatkowska, M., Thachuk, C., Turberfield, A.J.: DNA Walker circuits: computational potential, design, and verification. In: Soloveichik, D., Yurke, B. (eds.) DNA 2013. LNCS, vol. 8141, pp. 31–45. Springer, Heidelberg (2013) CrossRef
4.
go back to reference Lund, K., Manzo, A.J., Dabby, N., Michelotti, N., Johnson-Buck, A., Nangreave, J., Taylor, S., Pei, R., Stojanovic, M.N., Walter, N.G., et al.: Molecular robots guided by prescriptive landscapes. Nature 465(7295), 206–210 (2010)CrossRef Lund, K., Manzo, A.J., Dabby, N., Michelotti, N., Johnson-Buck, A., Nangreave, J., Taylor, S., Pei, R., Stojanovic, M.N., Walter, N.G., et al.: Molecular robots guided by prescriptive landscapes. Nature 465(7295), 206–210 (2010)CrossRef
5.
go back to reference Muscat, R.A., Strauss, K., Ceze, L., Seelig, G.: DNA-based molecular architecture with spatially localized components. ACM SIGARCH Comput. Architect. News 41, 177–188 (2013). ACMCrossRef Muscat, R.A., Strauss, K., Ceze, L., Seelig, G.: DNA-based molecular architecture with spatially localized components. ACM SIGARCH Comput. Architect. News 41, 177–188 (2013). ACMCrossRef
6.
go back to reference Padilla, J.E., Liu, W., Seeman, N.C.: Hierarchical self assembly of patterns from the Robinson tilings: DNA tile design in an enhanced tile assembly model. Nat. Comput. 11(2), 323–338 (2012)MathSciNetCrossRef Padilla, J.E., Liu, W., Seeman, N.C.: Hierarchical self assembly of patterns from the Robinson tilings: DNA tile design in an enhanced tile assembly model. Nat. Comput. 11(2), 323–338 (2012)MathSciNetCrossRef
7.
go back to reference Pei, R., Taylor, S.K., Stefanovic, D., Rudchenko, S., Mitchell, T.E., Stojanovic, M.N.: Behavior of polycatalytic assemblies in a substrate-displaying matrix. J. Am. Chem. Soc. 128(39), 12693–12699 (2006)CrossRef Pei, R., Taylor, S.K., Stefanovic, D., Rudchenko, S., Mitchell, T.E., Stojanovic, M.N.: Behavior of polycatalytic assemblies in a substrate-displaying matrix. J. Am. Chem. Soc. 128(39), 12693–12699 (2006)CrossRef
8.
go back to reference Qian, L., Winfree, E.: Scaling up digital circuit computation with DNA strand displacement cascades. Science 332(6034), 1196–1201 (2011)CrossRef Qian, L., Winfree, E.: Scaling up digital circuit computation with DNA strand displacement cascades. Science 332(6034), 1196–1201 (2011)CrossRef
9.
go back to reference Samii, L., Blab, G.A., Bromley, E.H.C., Linke, H., Curmi, P.M.G., Zuckermann, M.J., Forde, N.R.: Time-dependent motor properties of multipedal molecular spiders. Phys. Rev. E 84, 031111 (2011)CrossRef Samii, L., Blab, G.A., Bromley, E.H.C., Linke, H., Curmi, P.M.G., Zuckermann, M.J., Forde, N.R.: Time-dependent motor properties of multipedal molecular spiders. Phys. Rev. E 84, 031111 (2011)CrossRef
10.
go back to reference Semenov, O., Mohr, D., Stefanovic, D.: First-passage properties of molecular spiders. Phys. Rev. E 88(1), 012724 (2013)CrossRef Semenov, O., Mohr, D., Stefanovic, D.: First-passage properties of molecular spiders. Phys. Rev. E 88(1), 012724 (2013)CrossRef
11.
go back to reference Semenov, O., Olah, M.J., Stefanovic, D.: Mechanism of diffusive transport in molecular spider models. Phys. Rev. E 83(2), 021117 (2011)CrossRef Semenov, O., Olah, M.J., Stefanovic, D.: Mechanism of diffusive transport in molecular spider models. Phys. Rev. E 83(2), 021117 (2011)CrossRef
12.
go back to reference Semenov, O., Olah, M.J., Stefanovic, D.: Multiple molecular spiders with a single localized source—the one-dimensional case. In: Cardelli, L., Shih, W. (eds.) DNA 17 2011. LNCS, vol. 6937, pp. 204–216. Springer, Heidelberg (2011) CrossRef Semenov, O., Olah, M.J., Stefanovic, D.: Multiple molecular spiders with a single localized source—the one-dimensional case. In: Cardelli, L., Shih, W. (eds.) DNA 17 2011. LNCS, vol. 6937, pp. 204–216. Springer, Heidelberg (2011) CrossRef
13.
go back to reference Wickham, S.F., Bath, J., Katsuda, Y., Endo, M., Hidaka, K., Sugiyama, H., Turberfield, A.J.: A DNA-based molecular motor that can navigate a network of tracks. Nat. Nanotechnol. 7(3), 169–173 (2012)CrossRef Wickham, S.F., Bath, J., Katsuda, Y., Endo, M., Hidaka, K., Sugiyama, H., Turberfield, A.J.: A DNA-based molecular motor that can navigate a network of tracks. Nat. Nanotechnol. 7(3), 169–173 (2012)CrossRef
Metadata
Title
Scalable Design of Logic Circuits Using an Active Molecular Spider System
Authors
Dandan Mo
Matthew R. Lakin
Darko Stefanovic
Copyright Year
2015
DOI
https://doi.org/10.1007/978-3-319-23108-2_2

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