Force velocity

Overview

This demo shows how to simulate force-velocity and force-power curves.

What this demo does

This demo:

  • Runs a simulation in which a half-sarcomere is activated in pCa 4.5 and held isometric.
    • This determines the isometric force.
  • The code then runs a set of simulations in which the half-sarcomere is activated in pCa 4.5 and, once force has reached steady-state, allowed to shorten against different fractions of the isometric force.
  • Force-velocity and force-power curves are fitted to the simulation data.

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/isotonic/force_velocity/base/setup.json"

Viewing the results

All of the results from the isotonic simulations are written to files in <FiberSim_repo>/demo_files/isotonic/force_velocity/sim_data/isotonic/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.

The file fv_traces_1.png shows the loaded shortening segment of the simulation in more details.

The file fv_and_power.png shows the force-velocity and force-power curves.

Finally, data derived from the simulations are tabulated in fv_analysis.xlsx.

How this worked

The setup file follows the normal template. The experimental protocols are defined by the characterization element. See the table below for more details.

{
  "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": "force_velocity",
        "pCa": 4.5,
        "hs_lengths": [1100],
        "m_n": 4,
        "randomized_repeats": 1,
        "length_fit_mode": "exponential",
        "time_step_s": 0.001,
        "sim_duration_s": 0.5,
        "sim_release_s": 0.4,
        "rel_isotonic_forces": [0.03, 0.04, 0.075, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.85, 0.875, 0.9, 0.925, 0.95],
        "fit_time_s": [ 0.41, 0.49 ],
        "relative_to": "this_file",
        "sim_folder": "../sim_data",
        "output_image_formats": [ "png" ],
        "figures_only": "False",
        "trace_figures_on": "False"
      }
    ]
  }
}
Parameter Value Comments
type force_velocity  
pCa float The pCa value for the tests (as in this example)
  “pCa_50” Alternative mode, which runs isotonic shortening at pCa50. If this mode is selected, an additional parameter pCa_values must also be provided. FiberPy will run isometric simulations with these values to determine the pCa50. Example, "pCa_values": [9, 6.5, 6.3, 6.1, 5.9, 5.7, 5.5, 5.3, 4.5]
hs_lengths (optional) array of floats array of hs_lengths to run the simulations at. FiberPy uses the hs_length in the model file if not provided
randomized_repeats (optional) integer number of repeats to run at each length with different seeds
length_fit_mode “linear” fits shortening velocity with a straight line
  “exponential” fits shortening velocity with an exponential and extrapolates to the onset of shortening to establish fastest shortening (useful for traces where shortening slows progressively during shortening)
time_step_s float time step in seconds for simulation
sim_duration_s float total duration in seconds of each simulation
sim_release_s float time in seconds at which muscle starts to shorten isotonically
rel_isotonic_forces array of floats the forces (relative to isometric) which the muscle shortens against
fit_time_s [2 element array of floats] time range (in seconds) over which to fit shortening velocity