Programming and Simulating Chemical Reaction Networks on a Surface Royalsocietypublishing.Org/Journal/Rsif Samuel Clamons1, Lulu Qian1,2 and Erik Winfree1,2,3
Programming and simulating chemical reaction networks on a surface royalsocietypublishing.org/journal/rsif Samuel Clamons1, Lulu Qian1,2 and Erik Winfree1,2,3 1Bioengineering, 2Computer Science, and 3Computation and Neural Systems, California Institute of Technology, Research Pasadena, CA 91125, USA SC, 0000-0002-7993-2278; LQ, 0000-0003-4115-2409; EW, 0000-0002-5899-7523 Cite this article: Clamons S, Qian L, Winfree Models of well-mixed chemical reaction networks (CRNs) have provided a solid foundation for the study of programmable molecular systems, but the E. 2020 Programming and simulating chemical importance of spatial organization in such systems has increasingly been reaction networks on a surface. J. R. Soc. recognized. In this paper, we explore an alternative chemical computing Interface 17: 20190790. model introduced by Qian & Winfree in 2014, the surface CRN, which uses http://dx.doi.org/10.1098/rsif.2019.0790 molecules attached to a surface such that each molecule only interacts with its immediate neighbours. Expanding on the constructions in that work, we first demonstrate that surface CRNs can emulate asynchronous and synchro- nous deterministic cellular automata and implement continuously active Received: 23 November 2019 Boolean logic circuits. We introduce three new techniques for enforcing syn- Accepted: 30 April 2020 chronization within local regions, each with a different trade-off in spatial and chemical complexity. We also demonstrate that surface CRNs can manu- facture complex spatial patterns from simple initial conditions and implement interesting swarm robotic behaviours using simple local rules. Throughout all example constructions of surface CRNs, we highlight the trade-off between Subject Category: the ability to precisely place molecules and the ability to precisely control mol- Life Sciences–Engineering interface ecular interactions.
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