Abstract
This paper proposes a biological cell-based communication protocol to enable communication between biological nanodevices. Inspired by existing communication network protocols, our solution combines two molecular computing techniques (DNA and enzyme computing), to design a protocol stack for molecular communication networks. Based on computational requirements of each layer of the stack, our solution specifies biomolecule address encoding/decoding, error correction and link switching mechanisms for molecular communication networks.
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References
Hiyama, S., Moritani, Y., Suda, T., Egashera, R., Enomoto, A., Moore, M., Nakano, T.: Mole-cular Communication. In: Proc. NSTI Nanotech Conference and Trade Show, Anaheim, vol. 3, pp. 391–394 (May 2005)
Alfano, G., Morandi, D.: On Information Transmission Among Nanomachines. In: 1st International Conference on Nano-Networks (Nano-Net), Lousanne, Switzerland (2006)
Benenson, Y., Shapiro, E.: Molecular Computing Machines. In: Dekker Encyclopaedia of Nanoscience and Nanotechnology, pp. 2043–2055. Marcel Dekker, New York (2004)
Markevich, N., Hoek, J., Kholodenko, B.: Signalling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J. Cell Biology 164(3), 353 (2004), http://www.jcb.org/cgi/reprint/164/3/353
Stetter, M., Schurmann, B., Hofstetter, M.: Logical Nano-Computation in Enzyme Reaction Networks. In: Proceedings of BIONETICS 2006, Cavalese, Italy (2006)
Sauro, H., Kholodenko, B.: Quantitative analysis of signalling networks. Prog, in Biophysics & Mol. Biology 86, 5–43 (2004)
Cooper, G.: The cell, a molecular approach, pp. 545–549, ISBN 0-87893-119-8
Komarova, N., Zou, X., Nie, Q., Bardwell, L.: A theoretical framework for specificity in cell signalling. Mol. Syst. Biol. (October 2005)
Moritani, Y., Hyama, S., Suda, T.: A Communication Interface Using Vesicles Embedded with Channel Forming Proteins in Molecular Communication. In: Proceedings of BIONETICS 2007, Budapest, Hungary (2007)
Nakano, T., Suda, T., Koujin, T., Haraguchi, T., Hiraoka, Y.: Molecular Communication through Gap Junction Channels: System Design, Experiments and Modeling. In: Proceedings of 2nd International Conference on Bio-inspired models of Network, Information, and Computing Systems, Budapest, Hungary (2007)
Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., Shapiro, E.: An Autonomous Molecular Computer for Logical Control of Gene Expression. Nature 429, 423–429 (2004)
De Silva, A.P., Uchiyama, S.: Molecular Logic and Computing. Nature Nanotechnology 2 (July 2007)
Niazof, T., Baron, R., Katz, E., Ioubashevski, O., Willner, I.: Concatenated logic gates using four coupled biocatalysts operating in series. In: PNAS, Niazov, November 14 (2006)
Cavalcanti, R., Freitas Jr., A.: Nanorobotics Control Design: A Collective behaviour ap-proach for medicine. IEEE Transaction on NanoBioscience 4(2) (June 2005)
Abelson, H., Allen, D., Coore, D., Hanson, C., Homsy, G., Knight, T.F., Nagpal, R., Rauch, E., Sussman, G., Weiss, R.: Amorphous Computing. Communications of the ACM 43(5) (May 2001)
Fedichkin, L., Katz, E., Privman, V.: Error Correction and Digitalization Concepts in Bio-chemical Computing. J. Comput. Theor. Nanosci. 5, 36–43 (2008)
Liu, S., Gaudiot, J.: DNA-based Killer Automaton: the Innovative Nanomedicine. In: Proc. NSTI Nanotech Conference and Trade Show, Boston, Massachusetts (May 2006)
Valiunas, V., Polosina, Y.Y., Miller, H., Potapova, I.A., Valiuniene, L., Doronin, S., Mathias, R.T., Robinson, R.B., Rosen, M.R., Cohen, I.S., Brink, P.R.: Connexin-specific cell-to-cell transfer of short interfering RNA by gap junctions. J. Physiol. 568(2), 459–468 (2005)
Önfelt, B., Nedvetzki, S., Benninger, R.K.P., Purbhoo, M.A., Sowinski, S., Hume, A.N., Seabra, M.C., Neil, M.A.A., French, P.M.W., Davis, D.M.: Structurally Distinct Membrane Nanotubes between Human Macrophages Support Long-Distance Vesicular Traffic or Surfing of Bacteria. FEBS Lett. 581(11), 2194–2201 (2007)
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© 2009 ICST Institute for Computer Science, Social Informatics and Telecommunications Engineering
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Walsh, F. et al. (2009). Hybrid DNA and Enzyme Based Computing for Address Encoding, Link Switching and Error Correction in Molecular Communication. In: Cheng, M. (eds) Nano-Net. NanoNet 2008. Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, vol 3. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02427-6_7
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DOI: https://doi.org/10.1007/978-3-642-02427-6_7
Publisher Name: Springer, Berlin, Heidelberg
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