Abstract
The fields of DNA computing, molecular programming and DNA nanotechnology offer exciting new possibilities for organizing and manipulating matter at the nanoscale, and prompt us to think about computation in creative new ways. Molecules reacting in a test tube change state, and counts of molecules can in principle be used to simulate counter machines, all in a highly distributed, asynchronous and stochastic manner. In this talk I’ll give some background on models of molecular programming, focusing on Stochastic Chemical Reaction Networks, and describe some beautiful results and open problems pertaining to this model of computing.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340–2361 (1977)
Cook, M., Soloveichik, D., Winfree, E., Bruck, J.: Programmability of chemical reaction networks. In: Condon, A., Harel, D., Kok, J., Salomaa, A., Winfree, E. (eds.) Algorithmic Bioprocesses, pp. 543–584. Springer, Heidelberg (2009). https://doi.org/10.1007/978-3-540-88869-7_27
Soloveichik, D., Cook, M., Winfree, E., Bruck, J.: Computation with finite stochastic chemical reaction networks. Nat. Comput. 7(4), 615–633 (2008)
Angluin, D., Aspnes, J., Diamadi, Z., Fischer, M.J., Peralta, R.: Computation in networks of passively mobile finite-state sensors. Distrib. Comput. 18(4), 235–253 (2006)
Bower, J.M., Bolouri, H.: Computational Modeling of Genetic and Biochemical Networks. MIT Press, Cambridge (2004)
Cruise, J., Ganesh, A.: Probabilistic consensus via polling and majority rules. Queueing Syst. 78(2), 99–120 (2014)
Perron, E., Vasudevan, D., Vojnovic, M.: Using three states for binary consensus on complete graphs. In Proceedings of the 28th IEEE Conference on Computer Communications (INFOCOM), pp. 2527–2535. (2009)
Moussaïd, M., Kämmer, J.E., Analytis, P.P., Neth, H.: Social influence and the collective dynamics of opinion formation. PLoS ONE 8(11), e78433 (2013)
Angluin, D., Aspnes, J., Diamadi, Z., Fischer, M., Peralta, R.: Computation in networks of passively mobile finite-state sensors. Distrib. Comput. 18(4), 235–253 (2006)
Angluin, D., Aspnes, J., Eisentat, D.: Stably computable predicates are semi-linear. In: Proceedings of the Twenty-Fifth Annual ACM Symposium on Principles of Distributed Computing, pp. 292–299. ACM (2006)
Chen, H., Doty, D., Soloveichik, D.: Deterministic function computation with chemical reaction networks. Nat. Comput. 13(4), 517–534 (2014)
Angluin, D., Aspnes, J., Eisenstat, D.: A simple population protocol for fast robust approximate majority. Distrib. Comput. 21(2), 87–102 (2008)
Condon, A., Hajiaghayi, M., Kirkpatrick, D., Maňuch, J.: Simplifying analyses of chemical reaction networks for approximate majority. In: Brijder, R., Qian, L. (eds.) DNA 2017. LNCS, vol. 10467, pp. 188–209. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-66799-7_13
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG, part of Springer Nature
About this paper
Cite this paper
Condon, A. (2018). On Design and Analysis of Chemical Reaction Network Algorithms. In: Câmpeanu, C. (eds) Implementation and Application of Automata. CIAA 2018. Lecture Notes in Computer Science(), vol 10977. Springer, Cham. https://doi.org/10.1007/978-3-319-94812-6_1
Download citation
DOI: https://doi.org/10.1007/978-3-319-94812-6_1
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-94811-9
Online ISBN: 978-3-319-94812-6
eBook Packages: Computer ScienceComputer Science (R0)