Alistarh, Dan-AdrianIST Austria; Dudek, Bartłomiej; Kosowski, Adrian; Soloveichik, David; Uznański, Przemysław
In contrast to electronic computation, chemical computation is noisy and susceptible to a variety of sources of error, which has prevented the construction of robust complex systems. To be effective, chemical algorithms must be designed with an appropriate error model in mind. Here we consider the model of chemical reaction networks that preserve molecular count (population protocols), and ask whether computation can be made robust to a natural model of unintended “leak” reactions. Our definition of leak is motivated by both the particular spurious behavior seen when implementing chemical reaction networks with DNA strand displacement cascades, as well as the unavoidable side reactions in any implementation due to the basic laws of chemistry. We develop a new “Robust Detection” algorithm for the problem of fast (logarithmic time) single molecule detection, and prove that it is robust to this general model of leaks. Besides potential applications in single molecule detection, the error-correction ideas developed here might enable a new class of robust-by-design chemical algorithms. Our analysis is based on a non-standard hybrid argument, combining ideas from discrete analysis of population protocols with classic Markov chain techniques.
D. Alistarh - Supported by an SNF Ambizione Fellowship. A. Kosowski — Supported by Inria project GANG, ANR project DESCARTES, and NCN grant 2015/17/B/ST6/01897. D. Soloveichik — Supported by NSF grants CCF-1618895 and CCF-1652824.
155 - 171
DNA Computing and Molecular Programming
Alistarh D-A, Dudek B, Kosowski A, Soloveichik D, Uznański P. Robust detection in leak-prone population protocols. In: Vol 10467 LNCS. Springer; 2017:155-171. doi:10.1007/978-3-319-66799-7_11
Alistarh, D.-A., Dudek, B., Kosowski, A., Soloveichik, D., & Uznański, P. (2017). Robust detection in leak-prone population protocols (Vol. 10467 LNCS, pp. 155–171). Presented at the DNA Computing and Molecular Programming, Springer. https://doi.org/10.1007/978-3-319-66799-7_11
Alistarh, Dan-Adrian, Bartłomiej Dudek, Adrian Kosowski, David Soloveichik, and Przemysław Uznański. “Robust Detection in Leak-Prone Population Protocols,” 10467 LNCS:155–71. Springer, 2017. https://doi.org/10.1007/978-3-319-66799-7_11.
D.-A. Alistarh, B. Dudek, A. Kosowski, D. Soloveichik, and P. Uznański, “Robust detection in leak-prone population protocols,” presented at the DNA Computing and Molecular Programming, 2017, vol. 10467 LNCS, pp. 155–171.
Alistarh D-A, Dudek B, Kosowski A, Soloveichik D, Uznański P. 2017. Robust detection in leak-prone population protocols. DNA Computing and Molecular Programming, LNCS, vol. 10467 LNCS, 155–171.
Alistarh, Dan-Adrian, et al. Robust Detection in Leak-Prone Population Protocols. Vol. 10467 LNCS, Springer, 2017, pp. 155–71, doi:10.1007/978-3-319-66799-7_11.