ANNaMo_files

Code and examples for the ANNaMo model.

The simulation code

ANNaMo simulations are run with oxDNA. The repository contains a snapshot dated 05/02/2024, which can be compiled with the following commands:

cd oxDNA
mkdir build
cd build
cmake .. -DPython=On
make install -j6
make rovigatti tostiguerra -j6

At the end of the compilation stage, the oxDNA executable will be placed in the build/bin folder, and the oxpy Python bindings will be installed on the system. Check the oxDNA docs for additional information.

Note that ANNaMo is implemented as an oxDNA plugin, which means that input files should contain the correct plugin_search_path values.

File formats

The configuration file has the same format as oxDNA. By contrast, the topology file is unique to ANNaMo. The first line specifies the total number of beads and the total number of strands. The subsequent lines specify the id, type, and connectivity of each bead, two lines per bead. The syntax is the following:

ID type number_bonded_beads
ID_bonded_bead1 ID_bonded_bead2

The beads are listed on a per-strand basis: an empty line signals that all the beads of a strand have been specified. As an example, here is the topology of a 2-strand system made of 3 beads each:

6 2
0 1 1
1
1 2 2
0 2
2 3 1
1

3 5 1
4
4 6 2
3 5
5 7 1
4

The bead type is used in the dHdS_matrix.dat files to specify the $\Delta H$ and $\Delta S$​ associated to each bead pair. This is done using the following syntax:

dH[type_1][type_2] = delta_H
dS[type_1][type_2] = delta_S

By default, all unspecified interactions are set to 0.

As an example, this is the dHdS_matrix.dat file from the examples/DNA_duplexes/3beads/couple10 folder, whose topology file was shown earlier:

dH[1][2] = -1.5
dS[1][2] = -6.1
dH[1][5] = 4.766666666666667
dS[1][5] = 6.699999999999999
dH[1][6] = 0.36666666666666664
dS[1][6] = -2.2
dH[1][7] = -18.833333333333332
dS[1][7] = -53.8
dH[2][5] = -0.33333333333333337
dS[2][5] = -6.0
dH[2][6] = -28.233333333333334
dS[2][6] = -73.9
dH[2][7] = -1.3333333333333333
dS[2][7] = -5.9
dH[3][5] = -17.733333333333334
dS[3][5] = -48.6
dH[3][6] = -5.733333333333333
dS[3][6] = -18.2
dH[3][7] = -2.833333333333333
dS[3][7] = -13.0
dH[6][7] = -4.0
dS[6][7] = -13.2

where we omitted all the entries equal to zero.

Example simulations

The examples folder contains all the files required to run simulations of the systems showcased in the paper. Each leaf subfolder contains the following files:

• input is the oxDNA input file.
• topology.dat is the topology file.
• dHdS_matrix.dat specifies the interactions between beads in terms of $\Delta H$ and $\Delta S$​​.

Head over to examples/README.md and examples/FFS/README.md for more details.

Additional scripts

The scripts folder contains additional utility scripts.

Forward flux sampling (FFS)

The FFS simulations in the paper have been run with the ffs_flux.py and ffs_shoot.py scripts. Defining $A$ and $B$ as the two metastable states between which the rate should be computed and $\lambda_i$ as the $i$-th interface that separates them, ffs_flux.py is used to obtain an estimate of the flux exiting from $A$, while ffs_shoot.py evaluates the probability that $\lambda_i$ is crossed.

Both scripts take a file as input and require the oxpy and numpy Python packages to be installed. A runnable example containing one of the systems undergoing a toehold-mediated strand displacement process studied in the paper can be found in the examples/FFS folder.