Single half-sarcomere wtih series compliance

Overview

This demo shows how to simulate a single half-sarcomere that is connected in series with a linear spring.

What this demo does

This demo:

  • Runs a single simulation in which a single half-sarcomere connected in series with a linear spring is activated and deactivated by step changes in the Ca2+ concentration
  • Plots a summary of the simulation

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/myofibrils/hs_with_sec/base/setup.json"
  • You should see text appearing in the terminal window, showing that the simulations are running. When it finishes (this may take a few minutes), you should see something similar to the image below.

Viewing the results

All of the results from the simulation are written to files in <FiberSim_repo>/demo_files/myofibrils/hs_with_sec/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. Note the complex time-course of relaxation.

How this worked

The myofibril was defined by adding a series elastic stiffness sc_k_stiff to the muscle section of <FiberSim_repo>/demo_files/myofibrils/hs_with_sec/base/model.json.

  "muscle": {
    "no_of_half_sarcomeres": 1,
    "no_of_myofibrils": 1,
    "sc_k_stiff": 3000,
    "initial_hs_length": 1100,
    "prop_fibrosis": 0.0,
    "prop_myofilaments": 0.5,
    "m_filament_density": 0.407e15
  }

If the sc_k_stiffness is not provided, FiberCpp assumes that it is infinite (that is, there is no series compliance).

The characterization defined in the setup.json is similar to those defined for the single trials except that pCa_step_up_s and pCa_step_down_s were added to set the time intervals for the change in Ca2+ concentration.

{
  "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": 9,
            "pCa_values": [4.5],
            "sim_duration_s": 1.0,
            "time_step_s": 0.001,
            "pCa_step_up_s": 0.1,
            "pCa_step_down_s": 0.7,
            "output_image_formats": [ "png" ],
            "figures_only": "False",
            "trace_figures_on": "False"
        }
    ]
  }
}