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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.
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Computing Threshold Circuits with Bimolecular Void Reactions in Step Chemical Reaction Networks
Step Chemical Reaction Networks (step CRNs) are an augmentation of the Chemical Reaction Network (CRN) model where additional species may be introduced to the system in a sequence of “steps.” We study step CRN systems using a weak subset of reaction rules, void rules, in which molecular species can only be deleted. We demonstrate that step CRNs with only void rules of size (2,0) can simulate threshold formulas (TFs) under linear resources. These limited systems can also simulate threshold circuits (TCs) by modifying the volume of the system to be exponential. We then prove a matching exponential lower bound on the required volume for simulating threshold circuits in a step CRN with (2,0)-size rules under a restricted gate-wise simulation, thus showing our construction is optimal for simulating circuits in this way.
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- Award ID(s):
- 2329918
- PAR ID:
- 10562738
- Publisher / Repository:
- Springer Nature
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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