Abstract
As the first step in studying cell-based computing, a new method of biomolecular computing by cells is proposed based on signaling pathways of kinases and phosphatases for phosphorylation-dephosphorylation (we call this method ”kinase computing” for short in the latter parts of this paper). As opposed to the Adleman-Lipton paradigm of DNA computing and other types of cell-based computing, the core mechanism of kinase computing that carries out recursive computation at the biological level is based on (1) encoding the information by phosphorylation and dephosphorylation, (2) running the selection operators by coupled pathways of kinases and phosphatases under certain conditions, and (3) readout by immunofluorescence analysis. The control schemes for the related synchronization processes in 3-SAT computation is studied to clarify the biological feasibility of kinase computing, in which the control-space complexity and time complexity are linear.
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References
Landweber, L.F., Kari, L.: The evolution of cellular computing: nature’s solution to a computational problem. BioSystem 52, 3–13 (1999)
Ehrenfeucht, A., Harju, T., Petre, I., Rozenberg, G.: Patterns of micronuclear genes in ciliates. In: Jonoska, N., Seeman, N.C. (eds.) DNA 2001. LNCS, vol. 2340, pp. 279–289. Springer, Heidelberg (2002)
Weiss, R., Knight Jr., T.F.: Engineered communications for microbial robotics. In: Condon, A., Rozenberg, G. (eds.) DNA 2000. LNCS, vol. 2054, pp. 1–16. Springer, Heidelberg (2001)
Păun, G.: From cells to computers: computing with membranes (P systems). BioSystem 59, 139–158 (2001)
Regev, A., Shapiro, E.: Cellular abstractions: computation. Nature 419, 343 (2001)
Liu, J.-Q., Shimohara, K.: Kinase Computing in GTPases: analysis and simulation. IPSJ 2001, 29–32 (2001) (in Japanese)
Kaibuchi, K., Kuroda, S., Amano, M.: Regulation of the cytoskeleton and cell adhesion by the Rho family GTPases in mammalian cells. Annu. Rev. Biochem. 68, 459–485 (1999)
Helmriech, E.J.M.: The Biochemistry of Cell Signaling. Oxford University Press, Oxford (2001)
Freeman, M.: Feedback control of intercellular signaling in development. Nature 408, 313–319 (2000)
Reif, J.H.: Successes and Challenges. Science 296, 478–479 (2002)
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Liu, JQ., Shimohara, K. (2004). Biomolecular Computing by Encoding of Regulated Phosphorylation-Dephosphorylation and Logic of Kinase-Phosphatase in Cells. In: Chen, J., Reif, J. (eds) DNA Computing. DNA 2003. Lecture Notes in Computer Science, vol 2943. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24628-2_21
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DOI: https://doi.org/10.1007/978-3-540-24628-2_21
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