dnafold: codes for simulating DNA origami folding

access our user guide at https://daniel-duke.github.io/dnafold-docs/

Quick start (bash instructions in parentheses, replace <PATH_TO_DNAFOLD> with wherever you put the files):

1. Make sure you have git and gnu make installed, and a c++ compiler.
2. Clone this repository ("git clone https://github.com/marcello-deluca/dnafold")
3. in either WSL, a Linux OS (we have tested on Ubuntu and CentOS), or Mac OS, enter the "src" directory ("cd <PATH_TO_DNAFOLD>/src")
4. build the software by running make ("make")
5. There is now an executable in <PATH_TO_DNAFOLD> assuming compilation did not fail.
6. You can now run examples in the "examples" folder:
7. Navigate to the "examples" folder ("cd <PATH_TO_DNAFOLD>/examples/")
8. Navigate to one of the examples, e.g. 3D_4HB ("cd 3D_4HB")
9. Run the included input file: ("../../dnafold input.txt")
10. The program will automatically parse the design file and run a simulation of its self assembly, in either a forced or unforced manner depending upon the user setting.

Descriptions of each example:

• 3D_4HB: small 4HB structure, unguided. Assembles in under 5 minutes on most computers.
• laughing_face: a large structure (1456 beads / 11,648 nucleotides). Takes around 20 minutes. More diffusion will improve the final quality, but forced assembly can also make the structure topologically trapped.
• 2D_donut: a moderate structure which self-assembles into a rectangle with a hole in the middle by force. Assembles in a few minutes.
• 32HB: the 32HB structure that we folded in our manuscript, except assembled by force so that you can watch it fold quickly. Folds in 20-30 minutes.

Note that in all cases the total simulation time is much longer than the approximate folding time, so you can just quit the simulation using ctrl-c when you are satisfied with the folding progress having visualized the structure (see below); quoted times are based on how long it took for these devices to fold satisfactorily, not for the simulation to complete all timesteps.

To visualize simulation results using OVITO visualization software (https://ovito.org): You have two options.

The most rudimentary just shows particle locations:

• Just open the .dat file (e.g., in the 32HB folder, "32HB.dat")

The nicer version also shows the backbone of the ssDNA scaffold and staples:

• Open the topology file (e.g., in the 32HB folder, once the simulation is run: "32HB.dat_TOPOLOGY.dat") and select "bond" or "molecular" style
• On the right side of the page, under the "Visual elements" pane, select "Bonds". Increase the bond width to 2.8. If flat shading is enabled, turn it off. Select "Particles" and change the standard radius to 1.4 and radius scaling to 100%.
• under the "add modification" selection pane on the top right, select "load trajectory"
• navigate down to the panel titled "external file" and click the folder icon, then select the .dat file containing the trajectory (e.g. "32HB.dat").
• OVITO should automatically detect that this file is formatted as a LAMMPS dump file; under the box "Trajectory Source: LAMMPS dump", select the additional option "file contains multiple timesteps" or "file contains time series" if it is not checked automatically.
• You should now get a nice trajectory with all of the particle motion and with all of the backbone bonds filled in.