• Simmel, F. C. in Visions of DNA Nanotechnology at 40 for the Next 40: A Tribute to Nadrian C. Seeman (eds Jonoska, N. & Winfree, E.) 17–29 (Springer, 2023).

  • Wolpert, D. H. The stochastic thermodynamics of computation. J. Phys. A Math. Theor. 52, 193001 (2019).

    Article 
    ADS 
    MathSciNet 

    Google Scholar 

  • Doty, D., Rogers, T. A., Soloveichik, D., Thachuk, C. & Woods, D. Thermodynamic binding networks. In Proc. DNA23: The 23rd International Conference on DNA Computing and Molecular Programming Vol. 10467, 249–266 (Springer, 2017).

  • Bennett, C. H. The thermodynamics of computation—a review. Int. J. Theor. Phys. 21, 905–940 (1982).

    Article 
    CAS 

    Google Scholar 

  • Du, Y. & Mordatch, I. Implicit generation and modeling with energy based models. In Proc. Advances in Neural Information Processing Systems Vol. 32 (eds Wallach, H. et al.) (Curran Associates, 2019).

  • Kirkpatrick, S., Gelatt, C. D. Jr & Vecchi, M. P. Optimization by simulated annealing. Science 220, 671–680 (1983).

    Article 
    ADS 
    MathSciNet 
    CAS 
    PubMed 

    Google Scholar 

  • Frank, M. P. & Conte, T. M. Reversible computing technology is essential for sustainable growth of the digital economy. Preprint at www.sandia.gov/app/uploads/sites/210/2022/06/FrankConte-HotCarbon22-v4SAND.pdf (2022).

  • Demaine, E. D., Lynch, J. F., Mirano, S. & Tyagi, A. Energy-efficient algorithms. In Proc. ACM Conference on Innovations in Theoretical Computer Science 321–332 (ACM, 2016).

  • Landauer, R. Irreversibility and heat generation in the computing process. IBM J. Res. Dev. 5, 183–191 (1961).

    Article 
    MathSciNet 

    Google Scholar 

  • Ouldridge, T. E. The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics. Nat. Comput. 17, 3–29 (2018).

    Article 
    MathSciNet 
    CAS 
    PubMed 

    Google Scholar 

  • King, A. D. et al. Quantum critical dynamics in a 5,000-qubit programmable spin glass. Nature 617, 61–66 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Adleman, L. M. Molecular computation of solutions to combinatorial problems. Science 266, 1021–1024 (1994).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Woods, D. et al. Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. Nature 567, 366–372 (2019).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Evans, C. G., O’Brien, J., Winfree, E. & Murugan, A. Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly. Nature 625, 500–507 (2024).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Schulman, R., Yurke, B. & Winfree, E. Robust self-replication of combinatorial information via crystal growth and scission. Proc. Natl Acad. Sci. USA 109, 6405–6410 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fern, J. & Schulman, R. Design and characterization of DNA strand-displacement circuits in serum-supplemented cell medium. ACS Synth. Biol. 6, 1774–1783 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Srinivas, N., Parkin, J., Seelig, G., Winfree, E. & Soloveichik, D. Enzyme-free nucleic acid dynamical systems. Science 358, eaal2052 (2017).

    Article 
    PubMed 

    Google Scholar 

  • Bui, H. et al. Localized DNA hybridization chain reactions on DNA origami. ACS Nano 12, 1146–1155 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Chatterjee, G., Dalchau, N., Muscat, R. A., Phillips, A. & Seelig, G. A spatially localized architecture for fast and modular DNA computing. Nat. Nanotechnol. 12, 920–927 (2017).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Wang, B., Wang, S. S., Chalk, C., Ellington, A. D. & Soloveichik, D. Parallel molecular computation on digital data stored in DNA. Proc. Natl Acad. Sci. USA 120, e2217330120 (2023).

    Article 
    MathSciNet 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Song, T. & Qian, L. Heat-rechargeable computation in DNA logic circuits and neural networks. Nature 646, 315–322 (2025).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Qian, L. & Winfree, E. Scaling up digital circuit computation with DNA strand displacement cascades. Science 332, 1196–1201 (2011).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Wickham, S. F. J. et al. A DNA-based molecular motor that can navigate a network of tracks. Nat. Nanotechnol. 7, 169–173 (2012).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Thubagere, A. J. et al. A cargo-sorting DNA robot. Science 357, eaan6558 (2017).

    Article 
    PubMed 

    Google Scholar 

  • Wang, B., Chalk, C., Doty, D. & Soloveichik, D. Molecular computation at equilibrium via programmable entropy. Sci. Adv. 12, eadx3969 (2026).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nikitin, M. P. Non-complementary strand commutation as a fundamental alternative for information processing by DNA and gene regulation. Nat. Chem. 15, 70–82 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Castro, C. E. et al. A primer to scaffolded DNA origami. Nat. Methods 8, 221–229 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Shalaby, A., Thachuk, C. & Woods, D. Minimum free energy, partition function and kinetics simulation algorithms for a multistranded Scaffolded DNA Computer. In Proc. 29th International Conference on DNA Computing and Molecular Programming (DNA 29) Vol. 276, 1:1–1:22 (Schloss Dagstuhl, 2023).

  • Petrack, J., Evans, C. G., Cervera Roldan, A., Enayati, M. & Woods, D. Scaling up thermodynamically favoured scaffolded DNA computing by sculpting the energy landscape. In Proc. 32nd International Conference on DNA Computing and Molecular Programming (DNA32) Vol. 387, 7:1–7:22 (Schloss Dagstuhl, 2026).

  • Thachuk, C., Winfree, E. & Soloveichik, D. Leakless DNA strand displacement systems. In Proc. 21st International Conference on DNA Computing and Molecular Programming (eds Phillips, A. & Yin, P.) Vol. 9211, 133–153 (Springer, 2015).

  • Winfree, E. & Bekbolatov, R. Proofreading tile sets: error correction for algorithmic self-assembly. In Proc. 9th International Workshop on DNA Based Computers (eds Chen, J. & Reif, J.) Vol. 2943, 126–144 (Springer, 2004).

  • Evans, C. G. Crystals that count! Physical principles and experimental investigations of DNA tile self-assembly. PhD thesis, Caltech (2014).

  • Schulman, R., Wright, C. & Winfree, E. Increasing redundancy exponentially reduces error rates during algorithmic self-assembly. ACS Nano 9, 5760–5771 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Wang, B., Thachuk, C., Ellington, A. D., Winfree, E. & Soloveichik, D. Effective design principles for leakless strand displacement systems. Proc. Natl Acad. Sci. USA 115, E12182–E12191 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wang, B., Thachuk, C. & Soloveichik, D. Speed and correctness guarantees for programmable enthalpy-neutral DNA reactions. ACS Synth. Biol. 12, 993–1006 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lee Tin Wah, J., David, C., Rudiuk, S., Baigl, D. & Estevez-Torres, A. Observing and controlling the folding pathway of DNA origami at the nanoscale. ACS Nano 10, 1978–1987 (2016).

    Article 
    CAS 

    Google Scholar 

  • Dunn, K. E. et al. Guiding the folding pathway of DNA origami. Nature 525, 82–86 (2015).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Rossi-Gendron, C. et al. Isothermal self-assembly of multicomponent and evolutive DNA nanostructures. Nat. Nanotechnol. 18, 1311–1318 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhu, Y. et al. Accelerating DNA computing via freeze-thaw cycling. Sci. Adv. 9, eaax7983 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kennedy, T., Pearce, C. & Thachuk, C. Fast and robust strand displacement cascades via systematic design strategies. In Proc. 28th International Conference on DNA Computing and Molecular Programming (DNA 28) Vol. 238, 1:1–1:17 (Schloss Dagstuhl, 2022).

  • Song, T. et al. Fast and compact DNA logic circuits based on single-stranded gates using strand-displacing polymerase. Nat. Nanotechnol. 14, 1075–1081 (2019).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Yurke, B., Turberfield, A. J., Mills, A. P. Jr, Simmel, F. C. & Neumann, J. L. A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Liu, L. et al. Multifunctional clip strand for the regulation of DNA strand displacement and construction of complex DNA nanodevices. ACS Nano 15, 11573–11584 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Eshra, A., Shah, S., Song, T. & Reif, J. Renewable DNA hairpin-based logic circuits. IEEE Trans. Nanotechnol. 18, 252–259 (2019).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Garg, S. et al. Renewable time-responsive DNA circuits. Small 14, 1801470 (2018).

    Article 

    Google Scholar 

  • Genot, A. J., Bath, J. & Turberfield, A. J. Reversible logic circuits made of DNA. J. Am. Chem. Soc. 133, 20080–20083 (2011).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Song, X., Eshra, A., Dwyer, C. & Reif, J. Renewable DNA seesaw logic circuits enabled by photoregulation of toehold-mediated strand displacement. RSC Adv. 7, 28130–28144 (2017).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Hahn, J. & Shih, W. M. Thermal cycling of DNA devices via associative strand displacement. Nucleic Acids Res. 47, 10968–10975 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, X. et al. Enzyme-assisted waste-to-reactant transformation to engineer renewable DNA circuits. Chem. Commun. 55, 11615–11618 (2019).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Fornace, M. E., Porubsky, N. J. & Pierce, N. A. A unified dynamic programming framework for the analysis of interacting nucleic acid strands: enhanced models, scalability, and speed. ACS Synth. Biol. 9, 2665–2678 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Padirac, A., Fujii, T. & Rondelez, Y. Quencher-free multiplexed monitoring of DNA reaction circuits. Nucleic Acids Res. 40, e118 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • You, Y., Tataurov, A. V. & Owczarzy, R. Measuring thermodynamic details of DNA hybridization using fluorescence. Biopolymers 95, 472–486 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Doty, D. & Lee, B. UC-Davis-molecular-computing/nuad. GitHub (2022).

  • Stérin, T. tcosmo/cosmix. GitHub (2022).

  • Evans, C. G. Riverine. Zenodo (2022).

  • Evans, C. G. cgevans/qslib: v0.11.0 (v.0.11.0). Zenodo (2023).

  • Machinek, R. R. F., Ouldridge, T. E., Haley, N. E. C., Bath, J. & Turberfield, A. J. Programmable energy landscapes for kinetic control of DNA strand displacement. Nat. Commun. 5, 5324 (2014).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Olson, X. et al. Availability: a metric for nucleic acid strand displacement systems. ACS Synth. Biol. 6, 84–93 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Stérin, T., Eshra, A., Evans, C. G., Adio, J. & Woods, D. Data and code for “A Thermodynamically Favoured Molecular Computer: Robust, Fast, Renewable, Scalable”. Zenodo (2026).