Counting, Computing, and Pattern Recognition with Self-Assembling Non-Reciprocal DNA Tiles

Tim E. Veenstra; René van Roij; Marjolein Dijkstra

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arXiv · 2510.19503

Counting, Computing, and Pattern Recognition with Self-Assembling Non-Reciprocal DNA Tiles

Tim E. Veenstra·René van Roij·Marjolein Dijkstra

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Abstract

Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into multiple target structures can perform basic computational tasks analogous to those of finite-state automata when equipped with programmable non-reciprocal interactions that drive controlled dynamical transitions between these structures. By establishing design rules for multifarious self-assembly while budgeting the energy input required to drive these non-equilibrium transitions, we demonstrate that these systems can execute a wide variety of tasks including counting, computing modulo functions, and recognizing specific input patterns. This framework integrates memory, sensing, and actuation within a single physical platform, paving the way toward energy-efficient physical computation embedded in materials ranging from DNA and enzymes to proteins and colloids.

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Tim E. Veenstra, René van Roij, Marjolein Dijkstra. 2025-10-22. Counting, Computing, and Pattern Recognition with Self-Assembling Non-Reciprocal DNA Tiles. https://arxiv.org/abs/2510.19503

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