docs/REFERENCES.md

Primary-source bibliography and access notes

Literature search date: 19 September 2026. Bibliographic dates use publication records, not search-engine crawl dates. This is a targeted scientific prior-art search; no patent freedom-to-operate conclusion is offered. Citations identify enabling evidence, not endorsement of this proposal. No external figures or source PDFs are redistributed.

R1. Rothemund, P. W. K. (2006). Folding DNA to create nanoscale shapes and patterns. Nature. Publisher. DOI: 10.1038/nature04586. Scaffolded DNA origami; publisher abstract/bibliographic record accessed.

R2. Ke, Y., Ong, L. L., Shih, W. M., and Yin, P. (2012). Three-dimensional structures self-assembled from DNA bricks. Science 338, 1177-1183. Primary record. DOI: 10.1126/science.1227268. PubMed and publisher records accessed; PMC full-text access was blocked during one attempt.

R3. Tian, Y. et al. (2020). Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels. Nature Materials 19, 789-796. Publisher. DOI: 10.1038/s41563-019-0550-x. Direct precedent for material voxels; publisher abstract and originating laboratory summary accessed.

R4. Luu, M. T. et al. (2024). Reconfigurable nanomaterials folded from multicomponent chains of DNA origami voxels. Science Robotics 9, eadp2309. Publisher. DOI: 10.1126/scirobotics.adp2309. Indexed primary title/abstract found; direct publisher page failed during access. No precise method parameter is imported from this source.

R5. Ong, L. L. et al. (2017). Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components. Nature 552, 72-77. Primary record. DOI: 10.1038/nature24648. Bibliography verified in PubMed and author institution record.

R6. Wintersinger, C. M. et al. (2023; online 2022). Multi-micron crisscross structures grown from DNA-origami slats. Nature Nanotechnology 18, 281-289. Publisher. DOI: 10.1038/s41565-022-01283-1. Publisher abstract accessed; includes more than 1,000 addressable slats from a combinatorial strand library. Correction restores missing supplementary data; author code.

R7. Demaine, E. D. et al. (2008 preprint). Staged Self-Assembly: Nanomanufacture of Arbitrary Shapes with O(1) Glues. Author preprint. Formal staged tile model, not an experimental constant-glue fabricator.

R8. Demaine, E. D., Fekete, S. P., Scheffer, C., and Schmidt, A. (2015 preprint). New Geometric Algorithms for Fully Connected Staged Self-Assembly. Author preprint. Fully connected polyominoes and polylogarithmic stages under a formal model.

R9. Murugan, A., Zeravcic, Z., Brenner, M. P., and Leibler, S. (2015; preprint 2014). Multifarious assembly mixtures: Systems allowing retrieval of diverse stored structures. Author preprint. Shared-component competing-target model; abstract accessed.

R10. Benoist, F., and Sartori, P. (2026). Assembly Factors Resolve Speed and Encoding Bottlenecks in Multifarious Self-Assembly. PRX Life 4, 033021; published 27 August 2026. Publisher. DOI: 10.1103/5w6h-l93l. Primary abstract and publication record accessed. This recent prior art limits claims about inventing kinetic/encoding bottleneck relief.

R11. Chen, Z. et al. (2019; online 2018). Programmable design of orthogonal protein heterodimers. Nature 565, 106-111. Publisher. DOI: 10.1038/s41586-018-0802-y. Publisher abstract and extended-data descriptions accessed; selected robust designs are not evidence that arbitrary protein voxels share their stability.

R12. Michelson, A., Flanagan, T. J., Lee, S.-W., and Gang, O. (2023). High-strength, lightweight nano-architected silica. Cell Reports Physical Science 4, 101475. Publisher. DOI: 10.1016/j.xcrp.2023.101475. Primary indexed record and originating laboratory publication list accessed; not a source for a ready-made coating recipe in this release.

R13. Kulikowski, J. et al. (2024). DNA-silica nanolattices as mechanical metamaterials. Matter. Publisher. DOI: 10.1016/j.matt.2024.03.020. Author dataset accessed; indexed publisher abstract used. Direct full-text page was unavailable in one attempt.

R14. Gerling, T., Kube, M., Kick, B., and Dietz, H. (2018). Sequence-programmable covalent bonding of designed DNA assemblies. Science Advances 4, eaau1157. Primary record. DOI: 10.1126/sciadv.aau1157. Author full text. Designed ultraviolet-induced thymine crosslinks; this does not establish engineering-grade inorganic fusion.

R15. King, N. P. et al. (2012). Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 336, 1171-1174. Primary record. DOI: 10.1126/science.1219364. Primary abstract/bibliography accessed.

R16. Hopfield, J. J. (1974). Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. PNAS 71, 4135-4139. Primary record. DOI: 10.1073/pnas.71.10.4135. Driven discrimination precedent.

R17. Murugan, A., Huse, D. A., and Leibler, S. (2012). Speed, dissipation, and error in kinetic proofreading. PNAS. Publisher. DOI: 10.1073/pnas.1119911109. Primary record accessed; time/energy/error trade-offs.

R18. Winfree, E., and Bekbolatov, R. (2004 proceedings of DNA 2003). Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly. LNCS 2943, 126-144. Publisher. DOI: 10.1007/978-3-540-24628-2_13. Publisher abstract accessed.

R19. Soloveichik, D., and Winfree, E. (2008). Combining self-healing and proofreading in self-assembly. Author manuscript. Author PDF accessed through indexed text. Existing theoretical repair/self-assembly work.

R20. Wang, Y. et al. (2012). Colloids with valence and specific directional bonding. Nature 491, 51-55. Publisher. DOI: 10.1038/nature11564. Primary indexed record accessed.

R21. Park, S. Y. et al. (2008). DNA-programmable nanoparticle crystallization. Nature 451, 553-556. Publisher. DOI: 10.1038/nature06508. Primary publication record accessed.

R22. Cote, A. P. et al. (2005). Porous, crystalline, covalent organic frameworks. Science 310, 1166-1170. Primary record. DOI: 10.1126/science.1120411. Primary bibliography verified.

R23. Kurihara, K. et al. (2011). Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA. Nature Chemistry 3, 775-781. Publisher. DOI: 10.1038/nchem.1127. Primary abstract accessed; restricted synthetic-compartment result.

R24. Cheung, K. C., and Gershenfeld, N. (2013). Reversibly assembled cellular composite materials. Science 341, 1219-1221. Author manuscript. DOI: 10.1126/science.1240889. Primary bibliographic record and author PDF accessed.

R25. Kim, S. O. et al. (2003). Epitaxial self-assembly of block copolymers on lithographically defined nanopatterned substrates. Nature 424, 411-414. Primary record. DOI: 10.1038/nature01775. Hybrid directed-assembly precedent.

R26. Kuzyk, A. et al. (2012). DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483, 311-314. Publisher. DOI: 10.1038/nature10889. Author preprint abstract accessed. Evidence that nanoparticle organization can produce designed optical function; the proposed planar sensor is not copied experimental data.

R27. Serreli, V., Lee, C.-F., Kay, E. R., and Leigh, D. A. (2007). A molecular information ratchet. Nature 445, 523-527. Primary record. DOI: 10.1038/nature05452. Primary abstract accessed; energy-driven molecular motion, not a perpetual machine.

R28. Doty, D., Lutz, J. H., Patitz, M. J., Schweller, R. T., Summers, S. M., and Woods, D. (2012; preprint 2011). The tile assembly model is intrinsically universal. Author preprint. Abstract and author text accessed. Model-specific computational universality.

R29. Jacobs, W. M., Reinhardt, A., and Frenkel, D. (2015). Rational design of self-assembly pathways for complex multicomponent structures. PNAS 112, 6313-6318. Publisher. DOI: 10.1073/pnas.1502210112. Author preprint abstract accessed; nucleation and time-dependent protocols.

R30. Saha, R. et al. (2025). Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures. Nature Communications 16, 11392. Publisher. DOI: 10.1038/s41467-025-66195-9. Author preprint and PubMed accessed. Direct prior art for shared scaffold routing, reusable staples, and geometric/interaction programming.

R31. Zykov, V., Mytilinaios, E., Adams, B., and Lipson, H. (2005). Self-reproducing machines. Nature 435, 163-164. Author laboratory. DOI: 10.1038/435163a. Publisher access failed; originating laboratory material is the evidence route for restricted modular robotics.

R32. Li, H., Eddaoudi, M., O'Keeffe, M., and Yaghi, O. M. (1999). Design and synthesis of an exceptionally stable and highly porous metal-organic framework. Nature 402, 276-279. Publisher. DOI: 10.1038/46248. Primary abstract and bibliographic record accessed.