Define your own scheme

If you need to define your own kinetic scheme, you’ll need to write some MATLAB code.

Here are the steps to add a new scheme called my_scheme

• Define your kinetic scheme and write down equations for the fluxes between each transition. These will become a set of ordinary differential equations that define the rate of change of each population.

• Then write a new function update_my_scheme.m that solves the rate equations. Save this in repo\code\@half_sarcomere
  • use update_3state_with_SRX.m as an example.
• Then add a new case in repo\code\@half_sarcomere\evolve_kinetics.m so that it reads

  switch (obj.kinetic_scheme)
  case 'my_scheme'
    update_my_scheme(obj, time_step)
  end
  

• Then add a new case in to the constructor in repo\code\@half_sarcomere\half_sarcomere.m
  • This code should initialise the y_vector holding the cross-bridge populations and the thin filament state variables.

• Then add the method update_my_scheme(obj, time_step) to the “other methods in half-sarcomere.m

• Then add a new case in to repo\code\@half_sarcomere\implement_time_step.m
  • This code should unpack the y_vector holding the cross-bridge populations
• Then add a new case in repo\code\@half_sarcomere\update_forces.m
  • This code should be update obj.cb_force with the force generated by the cross-bridges in each attached state in your scheme
• Then add a new case in repo\code\@half_sarcomere\check_new_forces.m
  • This code should calculate delta_cb_force which is the change in the cross-bridge force if the half-sarcomere is stretched by delta_hs_length
• Then add a new case in to the constructor in repo\code\@simulation\simulation.m
  • This code should initialise the cross-bridge populations.
• Then add a new case in to implement_protocol in repo\code\@simulation\simulation.m
  • This code should store the cross-bridge populations in the output structure.
• Then add a new case in repo\code\@simulation\draw_rates.m
  • This code should create a figure showing the rate functions for your scheme. The plots can be as simple or as sophisticated as you like.
• Then add a new case in repo\code\@simulation\show_output.m
  • This code should show the cross-bridge distributions for your chosen scheme.

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