Abstract
We explore the computational power of biochemistry with respect to basic chemistry, identifying complexation as the basic mechanism that distinguishes the former from the latter. We use two process algebras, the Chemical Ground Form (CGF) which is equivalent to basic chemistry, and the Biochemical Ground Form (BGF) which is a minimalistic extension of CGF with primitives for complexation. We characterize an expressiveness gap: CGF is not Turing complete while BGF supports a finite precise encoding of Random Access Machines, a well-known Turing powerful formalism.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Busi, N., Gorrieri, R.: On the Computational Power of Brane Calculi. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 16–43. Springer, Heidelberg (2006)
Cardelli, L.: Artificial Biochemistry. In: Proc. of Algorithmic Bioprocesses. LNCS (to appear, 2008), http://lucacardelli.name
Cardelli, L.: On Process Rate Semantics. Theoretical Computer Science (in press, 2008), http://dx.doi.org/10.1016/j.tcs.2007.11.012
Cardelli, L., Pradalier, S.: Where Membranes Meet Complexes. In: Proc. of Concurrent Models in Molecular Biology (BioConcur. 2005) (2005)
Credi, A., Garavelli, M., Laneve, C., Pradalier, S., Silvi, S., Zavattaro, G.: Modelization and Simulation of Nano Devices in nano-kappa Calculus. In: Calder, M., Gilmore, S. (eds.) CMSB 2007. LNCS (LNBI), vol. 4695, pp. 168–183. Springer, Heidelberg (2007)
Danos, V., Feret, J., Fontana, W., Krivine, J.: Kappa Factory (2007), http://www.lix.polytechnique.fr/~krivine/kappaFactory.html
Danos, V., Laneve, C.: Formal molecular biology. Theoretical Computer Science 325(1), 69–110 (2004)
Kitano, H., Funahashi, A., Matsuoka, Y., Oda, K.: Using process diagrams for the graphical representation of biological networks. Nature Biotechnolgy 23, 961–966 (2005)
Kohn, K.W., Aladjem, M.I., Weinstein, J.N., Pommier, Y.: Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Molecular biology of the cell 17(1), 1–13 (2006)
Liekens, A.M.L., Fernando, C.T.: Turing complete catalytic particle computers. In: Almeida e Costa, F., Rocha, L.M., Costa, E., Harvey, I., Coutinho, A. (eds.) ECAL 2007. LNCS (LNAI), vol. 4648, pp. 1202–1211. Springer, Heidelberg (2007)
Magnasco, M.O.: Chemical Kinetics is Turing Universal. Physical Review Letters 78, 1190–1193 (1997)
McQuarrie, D.A.: Stochastic approach to chemical kinetics. Journal of Applied Probability 4, 413–478 (1967)
Milner, R.: Communication and Concurrency. Prentice-Hall, Englewood Cliffs (1989)
Minsky, M.L.: Computation: finite and infinite machines. Prentice-Hall, Englewood Cliffs (1967)
Priami, C., Quaglia, P.: Beta Binders for Biological Interactions. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 20–33. Springer, Heidelberg (2005)
Priami, C., Regev, A., Shapiro, E., Silverman, W.: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80, 25–31 (2001)
Soloveichik, D., Cook, M., Winfree, E., Bruck, J.: Computation with Finite Stochastic Chemical Reaction Networks. Natural Computing (in press, 2008), http://dx.doi.org/10.1007/s11047-008-9067-y
Zavattaro, G., Cardelli, L.: Termination Problems in Chemical Kinetics (2008), http://lucacardelli.name
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Cardelli, L., Zavattaro, G. (2008). On the Computational Power of Biochemistry. In: Horimoto, K., Regensburger, G., Rosenkranz, M., Yoshida, H. (eds) Algebraic Biology. AB 2008. Lecture Notes in Computer Science, vol 5147. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85101-1_6
Download citation
DOI: https://doi.org/10.1007/978-3-540-85101-1_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-85100-4
Online ISBN: 978-3-540-85101-1
eBook Packages: Computer ScienceComputer Science (R0)