Activation with a k_tr maneuver

Overview

This demo shows how to simulate a single k_tr experiment.

What this demo does

This demo:

  • Runs a single simulation in which a half-sarcomere is activated in pCa 4.5 and then subjected to a k_tr maneuver
  • 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/single_trials/k_tr/base/setup.json"

Viewing the results

All of the results from the simulation are written to files in <FiberSim_repo>/demo_files/single_trials/k_tr/sim_data/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.

Since the code simulated a ktr maneuver, FiberPy also created a figure showing the analyis of the tension recovery.

Data quantifying the ktr are written to <FiberSim_repo>/demo_files/single_trials/k_tr/sim_data/sim_output/k_tr_analysis.xlsx

How this worked

The only difference between this simulation and the isometric activation example are a few extra lines in the characteriztion structure of the setup file.

"characterization": [
        {
            "type": "pCa_length_control",
            "relative_to": "this_file",
            "sim_folder": "../sim_data",
            "m_n": 9,
            "pCa_values": [4.5],
            "sim_duration_s": 1.2,
            "time_step_s": 0.001,
            "pCa_step_up_s": 0.1,
            "k_tr_start_s": 0.6,
            "k_tr_duration_s": 0.02,
            "k_tr_ramp_s": 0.001,
            "k_tr_magnitude_nm": 100,
            "k_tr_fit_time_s": [0.625, 1.0],
            "output_image_formats": [ "png" ],
            "figures_only": "False",
            "trace_figures_on": "False"
        }

Note the parameters starting with k_tr. These describe:

Parameter Sets
k_tr_start_s The start time for the k_tr maneuver
k_tr_duration_s How long the k_tr lasts
k_tr_ramp_s The duration of the length changes
k_tr_magnitude_nm The magnitude of the length change (per half-sarcomere)
k_tr_fit_time_s The portion of the record that the code will fit a single exponential to