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Title: Programming and simulating chemical reaction networks on a surface
Models of well-mixed chemical reaction networks (CRNs) have provided a solid foundation for the study of programmable molecular systems, but the importance of spatial organization in such systems has increasingly been recognized. In this paper, we explore an alternative chemical computing model introduced by Qian & Winfree in 2014, the surface CRN, which uses 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 synchronous deterministic cellular automata and implement continuously active Boolean logic circuits. We introduce three new techniques for enforcing synchronization within local regions, each with a different trade-off in spatial and chemical complexity. We also demonstrate that surface CRNs can manufacture 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 the ability to precisely place molecules and the ability to precisely control molecular interactions. Finally, we provide a Python simulator for surface CRNs with an easy-to-use web interface, so that readers may follow along with our examples or create their own surface CRN designs.  more » « less
Award ID(s):
1813550
PAR ID:
10198326
Author(s) / Creator(s):
; ;
Date Published:
Journal Name:
Journal of The Royal Society Interface
Volume:
17
Issue:
166
ISSN:
1742-5689
Page Range / eLocation ID:
20190790
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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