Supplementary Files for "Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly"
Version 2: arXiv 2207.06399v2 (September 3, 2022)
- 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
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
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.
Version 1: arXiv 2207.06399v1 (July 13, 2022)
Watch this space for related code and things, once we get it cleaned up.