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SDC: Scaffolded DNA Computers

SDC models simulate the systems in Stérin, T., Eshra, A., Adio, J., Evans, C. G. & Woods, D. A Thermodynamically Favoured Molecular Computer: Robust, Fast, Renewable, Scalable https://doi.org/10.1101/2025.07.16.664196 (2025).

There are currently two models in rgrow:

  • SDC: a 'standard' TAM-like kinetic model with strand/tile attachment and detachment based on stochastic chemical kinetics.
  • SDC1DBindReplace: the abstract, bind-replace model in S3.3 of the paper SI.

SDC

  • SDC models strand interactions at an attachment/detachment level, like the kTAM. On attaching, a strand is assumed to make all possible bonds with its neighbors and the scaffold, and detaches by simultaneously breaking all these bonds.
  • SDC implements optional event-level strand concentration depletion via event-skipping: rates for non-depleted attachments are used for choosing events, but events are skipped based on depletion. This works efficiently when compute strands are in reasonable excess: for example, if compute strand concentrations are 10 times the scaffold concentration, then at most, 10% of events would be skipped.

SDC1DBindReplace