Steps

Overview

This demo shows how to simulate the force responses to steps of different sizes.

What this demo does

This demo:

• Runs a set of simulations with step stretches of different sizes imposed at different activation levels

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/length_changes/steps/base/setup.json"
  

Viewing the results

All of the results from the simulations are written to files in <FiberSim_repo>/demo_files/length_changes/steps/sim_output

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

The file rates.png summarizes the kinetic scheme.

How this worked

The setup file follows the normal template. The experimental protocols are defined by the characterization element.

The new feature in this demo are the specifications for length steps.

    "length_step_nm" : [0, 3, 6, -3, -6],
    "length_step_s": 2,
    "length_step_ramp_s": 0.001

This means, for each pCa value, run 5 trials where a step is imposed at 2 s that is complete within 0.001 s and is one of the following values 0, 3, 6, -3, -6 nm.

{
  "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": "pCa_length_control",
            "relative_to": "this_file",
            "sim_folder": "../sim_data",
            "m_n": 16,
            "pCa_values": [9.0, 6.3, 6.1, 6.0, 4.5],
            "sim_duration_s": 3.5,
            "time_step_s": 0.001,
            "pCa_step_up_s": 0.05,
            "k_tr_start_s": 3.0,
            "k_tr_duration_s": 0.02,
            "k_tr_ramp_s": 0.001,
            "k_tr_magnitude_nm": 0,
            "k_tr_fit_time_s": [3.025, 3.95],
            "length_step_nm" : [0, 3, 6, -3, -6],
            "length_step_s": 2,
            "length_step_ramp_s": 0.001,
            "output_image_formats": [ "png" ],
            "figures_only": "False",
            "trace_figures_on": "False"
        }
    ]
  }
}