Abstract
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. Assuming a fixed molecular population size and bimolecular reactions, CRNs are formally equivalent to population protocols, a model of distributed computing introduced by Angluin, Aspnes, Diamadi, Fischer, and Peralta (PODC 2004). The challenge of fast computation by CRNs (or population protocols) is to ensure that there is never a bottleneck “slow” reaction that requires two molecules (agent states) to react (communicate), both of which are present in low (O(1)) counts. It is known that CRNs can be fast in expectation by avoiding slow reactions with high probability. However, states may be reachable (with low probability) from which the correct answer may only be computed by executing a slow reaction. We deem such an event a speed fault. We show that the problems decidable by CRNs guaranteed to avoid speed faults are precisely the detection problems: Boolean combinations of questions of the form “is a certain species present or not?”. This implies, for instance, that no speed fault free CRN could decide whether there are at least two molecules of a certain species, although a CRN could decide this in “fast” expected time – i.e. speed fault free CRNs “can’t count.”
The third, and fourth authors were supported by the Molecular Programming Project under NSF grants 0832824 and 1317694, the first author was supposed by NSC grant number 101-2221-E-002-122-MY3, the second author was supported by NSF grants CCF-1049899 and CCF-1217770, the third author was supported by a Computing Innovation Fellowship under NSF grant 1019343, NSF grants CCF-1219274 and CCF-1162589, and the fourth author was supported by NIGMS Systems Biology Center grant P50 GM081879.
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References
Angluin, D., Aspnes, J., Diamadi, Z., Fischer, M., Peralta, R.: Computation in networks of passively mobile finite-state sensors. Distributed Computing 18, 235–253 (2006), Preliminary version appeared in PODC 2004
Angluin, D., Aspnes, J., Eisenstat, D.: Stably computable predicates are semilinear. In: PODC 2006: Proceedings of the Twenty-fifth Annual ACM Symposium on Principles of Distributed Computing, pp. 292–299. ACM Press, New York (2006)
Angluin, D., Aspnes, J., Eisenstat, D.: Fast computation by population protocols with a leader. Distributed Computing 21(3), 183–199 (2008); Preliminary version appeared in Dolev, S. (ed.) DISC 2006. LNCS, vol. 4167, pp. 61–75. Springer, Heidelberg (2006)
Cardelli, L.: Strand algebras for DNA computing. Natural Computing 10(1), 407–428 (2011)
Cardelli, L., Csikász-Nagy, A.: The cell cycle switch computes approximate majority. Scientific Reports 2 (2012)
Cardoza, E., Lipton, R.J., Meyer, A.R.: Exponential space complete problems for Petri nets and commutative semigroups (preliminary report). In: STOC 1976: Proceedings of the 8th Annual ACM Symposium on Theory of Computing, pp. 50–54. ACM (1976)
Chen, H.-L., Doty, D., Soloveichik, D.: Deterministic function computation with chemical reaction networks. Natural Computing (2013); Preliminary version appeared in DNA 2012. LNCS, vol. 7433, pp. 25–42. Springer, Heidelberg (2012)
Chen, Y.-J., Dalchau, N., Srinivas, N., Phillips, A., Cardelli, L., Soloveichik, D., Seelig, G.: Programmable chemical controllers made from DNA. Nature Nanotechnology 8(10), 755–762 (2013)
Condon, A., Hu, A., Maňuch, J., Thachuk, C.: Less haste, less waste: On recycling and its limits in strand displacement systems. Journal of the Royal Society Interface 2, 512–521 (2011); Preliminary version appeared in DNA 17 2011. LNCS, vol. 6937, pp. 84–99. Springer, Heidelberg (2011)
Dickson, L.E.: Finiteness of the odd perfect and primitive abundant numbers with n distinct prime factors. American Journal of Mathematics 35(4), 413–422 (1913)
Doty, D.: Timing in chemical reaction networks. In: SODA 2014: Proceedings of the 25th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 772–784 (January 2014)
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81(25), 2340–2361 (1977)
Karp, R.M., Miller, R.E.: Parallel program schemata. Journal of Computer and System Sciences 3(2), 147–195 (1969)
Petri, C.A.: Communication with automata. Technical report, DTIC Document (1966)
Soloveichik, D., Cook, M., Winfree, E., Bruck, J.: Computation with finite stochastic chemical reaction networks. Natural Computing 7(4), 615–633 (2008)
Soloveichik, D., Seelig, G., Winfree, E.: DNA as a universal substrate for chemical kinetics. Proceedings of the National Academy of Sciences 107(12), 5393 (2008); Preliminary version appeared in DNA Computing. LNCS, vol. 5347, pp. 57–69. Springer, Heidelberg (2009)
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Chen, HL., Cummings, R., Doty, D., Soloveichik, D. (2014). Speed Faults in Computation by Chemical Reaction Networks. In: Kuhn, F. (eds) Distributed Computing. DISC 2014. Lecture Notes in Computer Science, vol 8784. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-45174-8_2
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DOI: https://doi.org/10.1007/978-3-662-45174-8_2
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