Arbitrary loads

Overview

This demo shows how to simulate a muscle that is subjected to a time-varying load while activated by a single stimulus.

What this demo does

This demo:

• Runs a single simulation which switches from isometric to force control with an arbitrary signal with a single electrical stimulus activating the muscle

Instructions

If you need help with these step, check the installation instructions.

• Open an Anaconda prompt
• Activate the FiberSim environment
• Change directory to <FiberSim_repo>/code/FiberPy/FiberPy
• Run the command

   python FiberPy.py characterize "../../../demo_files/electrical_stimulation/arbirary_load/base/setup.json"
  

Viewing the results

All of the results from the simulation are written to files in <FiberSim_repo>/demo_files/electrical_stimulation/arbirary_load/sim_data/sim_output

The file superposed_traces.png shows pCa, length, force per cross-sectional area (stress), and thick and thin filament properties plotted against time.

The file rates.png summarizes the kinetic scheme.

How this worked

The setup file is very similar to that used in the prior examples except that a load_file element has been added to the data structure.

{
  "FiberSim_setup":
  {
    "FiberCpp_exe": {
      "relative_to": "this_file",
      "exe_file": "../../../../bin/FiberCpp.exe"
    },
    "model": {
      "relative_to": "this_file",
      "options_file": "sim_options.json",
      "model_files": ["model.json"]
    },
    "characterization": [
        {
            "type": "twitch",
            "relative_to": "this_file",
            "sim_folder": "../sim_data",
            "m_n": 4,
            "protocol":
            {
                "protocol_folder": "../protocols",
                "data": [
                    {
                        "time_step_s": 0.001,
                        "n_points": 400,
                        "stimulus_times_s": [0.1],
                        "Ca_content": 1e-3,
                        "stimulus_duration_s": 0.01,
                        "k_leak": 6e-4,
                        "k_act": 8.2e-2,
                        "k_serca": 20,
                        "load_file": "../test_load/test_load.txt"
                    }
                ]
            },
            "output_image_formats": [ "png" ],
            "figures_only": "False",
            "trace_figures_on": "False"
        }
    ]
  }
}

Here load_file points to a text file with 400 values, arranged one per line.

Values are as follows:

• -2 means hold muscle at fixed length
• any float >= 0 means adjust muscle length to keep force at that float

The demo file is shown below:

-2
-2
-2
<SNIP>
-2
-2
-2
200
399.97
599.91
799.79
999.58
1199.3
1398.9
1598.3
1797.6
1996.7
2195.6
<SNIP>
7075.3
6887.9
6699.8