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MATMyoSim

Protocol

In MATMyoSim, protocols are text files that contain 4 columns of data. Each row in the file defines the properties for the corresponding time-step in the simulation.

The fields are as follows

  • dt
    • the duration of the time-step in s
      • Note that this should be less than 1/(fastest rate) in your simulation
  • dhsl
    • the length-change in nm per half-sarcomere imposed during each time-step
  • pCa
    • the activating Ca2+ concentration for the time-step where pCa = -log10[Ca2+]
  • Mode
    • one of:
      • -2 which means length control, that is the length of the muscle system is controlled
      • -1 which means potentially slack, that is the system is under length control, but it could have fallen slack if the muscle is being shortened quickly.
        • If the muscle falls slack, the half-sarcomeres shorten at their Vmax and the total length of the half-sarcomeres will be longer than the length of the muscle system.
        • This is useful for simulations of k_tr maneuvers and muscles that are being shortened at or faster than Vmax.
      • x >= 0.0 which means tension control, that is the muscle system will change length so that the force per unit area is equal to the value of x

Example

Here is an artificially simple example

dt     dhsl  Mode  pCa
0.001  0     -2    9
0.001  0     -2    9
0.001  0     -2    4.5
0.001  0     -2    4.5
0.001  0     -2    4.5
0.001  0.5   -2    4.5
0.001  0.5   -2    4.5
0.001  -10   -1    4.5
0.001  0     100    4.5
0.001  0     100    4.5

This protocol defines a simulation that lasts 10 ms (10 time-steps of 0.001 s)

  • The first 2 time-steps are at pCa 9.0 and isometric.
  • The next 3 time-steps are at pCa 4.5 and isometric.
  • The next 2 time-steps at at pCa 4.5 but the system is stretched by 0.5 nm per half-sarcomere in each one.
  • The next time step shortens the muscle by 10 nm per half-sarcomere and the software checks to see if the system has fallen slack.
  • The last 2 time-steps are under tension control so that the muscle adopts the length at which force per unit area is equal to 100 N m-2

More examples

To see more examples, look at the demos