Supplementary Files for "Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly"

Publication: Nature 625: 500-507 (January 18, 2024)

• Paper (9.9 MB, 21 pages)
• for Figure Source Data Excel Files, see v3 below
• Supplementary Information including Data Appendix (85 MB, 189 pages)
• for oxDNA simulation files, see v2 below
• Code and data (1.2 GB)
• 01-merging: designing the tile set and layout
• 02-sequence-design: converting abstract tiles to SST sequencees for strands
• 03-nucleation-modesl-and-training: SGM and WNM and pixel-to-tile map
• 04-data-analysis: run code and make plots
• ECHO scripts
• MNIST training
• nucleation with depletion: mass-action model
• place cell comparison
• xgrow simulations
• design files
• model data
• experimental data

• Paper (7.6 MB, 24 pages)
• Figure Source Data Excel Files (60 KB to 3.2 MB)
  • for Figure 2: fig2.xlsx
  • for Figure 3: fig3.xlsx
  • for Figure 4: fig4.xlsx
  • for Figure 5: fig5.xlsx
  • for Figure 6: fig6.xlsx
• Supplementary Information and Data Appendix (86 MB, 188 pages)
• Section 1: Self-assembly and neural networks
• Section 2: Nucleation models and pattern recognition training
• Section 3: Fluorescence readout, shape layouts, and simulated structures
• Section 4: Sequences
• Section 5: Flag patterns
• Section 6: Pattern recognition
• For oxDNA simulation files, see v2 below
• Code and further data coming soon!

• Paper (26 MB, 22 pages)
• Supplementary Information and Data Appendix (84 MB, 174 pages)
• oxDNA simulations in a coarse-grained molecular dynamics model.
  • Movies showing the relaxation of full shapes (H A M) from an initially almost-flat (and thus strained) configuration. These are meant just to visuallize the structures, not to make any strong scientific claim. Note that simulation parameters were changed during some of the simulations, in order to prevent the highly-strained and thus unnatural initial configurations from pulling themselves apart. The SI discusses more about how the simulations were made and how to interpret them. The movies are in WebM format and should play in your browser. In our experience they may or may not play smoothly in Safari, but consistently work in Chrome.
• Data files for oxDNA simulations of structures
  H: topology file h.top (334 KB), mean structure file h-mean.dat (3.8 MB), deviation analysis file h-deviations.json (395 KB), movie trajectory file h-trajectory.dat (WARNING! 5.0 GB compressed)
  A: topology file a.top (346 KB), mean structure file a-mean.dat (3.9 MB), deviation analysis file a-deviations.json (410 KB), movie trajectory file a-trajectory.dat (WARNING! 2.4 GB compressed)
  M: topology file m.top (334 KB), mean structure file m-mean.dat (3.8 MB), deviation analysis file m-deviations.json (387 KB), movie trajectory file m-trajectory.dat (WARNING! 4.7 GB compressed)
• To view the simulation trajectories in your web browser with interactive zoom and rotation, you can use the Sulc group's oxView. For us, the easiest and most reliable method is to download corresponding .top and .dat files, make sure your browser didn't rename them, then simultaneously drag and drop them into the oxView window. (For mean structures, also include the .json file.) They should automatically load and index. Then you can play/pause/zoom/rotate to your heart's content.

• Paper (19 MB, 21 pages)
• Supplementary Information and Data Appendix (84 MB, 158 pages)