A Thermodynamically Favoured Molecular Computer: Robust, Fast, Renewable, Scalable

Like life, computers are out-of-equilibrium.1,2 Thermodynamically favoured error states are thwarted by energetically-costly processes such as kinetic proofreading of biological polymers, error-correcting codes in computer data storage, and redundancy in molecular programming. Decades of theoretical work shows that unlike life thermodynamic computers can operate by drifting naturally to equilibrium.3,4 Similar ideas underlie machine learning models5 and search algorithms such as simulated annealing,6 although executed on non-equilibrium architectures at enormous energy cost.7 Physically implementing thermodynamically favoured computation is a decades-long challenge that could reduce dependence on fuel-consuming error-correction and precise kinetic control. Here, we demonstrate a thermodynamically favoured Scaffolded DNA Computer (SDC) on ten programs including MULTIPLICATION-by-3, DO_SCPLOWIVISIONC_SCPLOW-by-2, 8-bit PO_SCPLOWARITYC_SCPLOW-detection, and AO_SCPLOWDDITIONC_SCPLOW of up to 25-bit numbers. SDC algorithms have simple experimental protocols, can be reused dozens of times and small instances run in under a minute. The SDC is grounded in mathematical, physical and computer science principles that explain why the output is thermodynamically favoured, why no error-correction nor precise step-by-step kinetic control are required and how it is programmable and scalable. This work creates a new way to think about equilibrium computation in all manner of synthetic systems.