k_tr

This page shows how to reproduce a slack/re-stretch simulation for two conditions:

• Myosin heads are able to bind to the nearest actin binding site only (1 potential binding site)

• Myosin heads are able to bind to one of the three nearest acting binding sites (3 potential binding sites)

Getting ready

• Open an Anaconda Prompt

• Activate the FiberSim Anaconda Environment by executing:

  conda activate fibersim
  

• Change directory to <FiberSim_dir>/code/FiberPy/FiberPy, where <FiberSim_dir> is the directory where you installed FiberSim.

Run the simulations

• Type:

  python FiberPy.py run_batch "../../../manuscripts/2021b/k_tr/batch_k_tr.json"
  

• You should see text appearing in the terminal window, showing that the simulations are running. When it finishes (this may take ~20 min), you should see something similar to the image below.

Viewing the results

The figure showing results for both simulations is stored in <FiberSim_dir>/manuscripts/2021b/k_tr/sim_output/superposed_summary.png

Summary figures and results files for the individual simulations are also stored in <FiberSim_dir>/manuscripts/2021b/k_tr/sim_output.