Saving your model and running a Force Velocity simulation

Saving your model

After defining everything of your model, you will save the model. Click Save in the menu bar.

Enter a model name and note (optional), and click on the Save button.

Running a Force Velocity simulation

Go back to your Dashboard page, and then click on the Run Simulation button on the row corresponding to the model that you have saved.

Then click on the Force Velocity radio button from the Observations in the Simulation Setup dialog. See Force Velocity Relationship if you want to know what is the Force Velocity Relationship test.

Click on the Submit button.

When the simulation job is successfully submitted by XB Modeler, the notification dialog appears on your screen. Then click on the Close button.

Getting simulation results

When the simulation is finished, you receive an email notification as follows.

Dear your_username,

Your force velocity simulation has been completed.
You can download the result from Simulation Results page in your dashboard.

model name : tutorial MH-3-state model
model note : with constant transition rates
state names: [P_XB, XB_PreR, XB_PostR]

Click on the Simulation Results button in your dashboard page.

Click on the Plot button in the top row that corresponds to the latest simulation result.

Then plots of the results appear. You will see the relations between several variables (1: Force(kPa), 2:Shortening velocity(μm), 3:Efficiency, 4: Work rate (J/m³), ATP consumption rate(J/m³)). Here the shortening velocity is for a half sarcomere. The ATP consumption rate is converted by the hydrolysis energy (E_ATP) given in the Common parameters form of the Edit Parameters menu. In the current model, all the transition rates are constant, thus the ATP consumption rates does not depends on the shortening velocity. The weak non-linearity of the force velocity relationship is due to the non-linear nature of the myosin arm spring as introduced in Property of myosin arm spring.

What is missing?

What is missing in the current model is relationship of the ATP energy and the myosin arm spring energy given by a head rotation. For example, if you define a larger stroke distance (X_STROKE) enough to produce the strain energy much larger than the ATP energy, you will get efficiency larger than 100%. This means that you have to control a transition accompanied by a head rotation as it does not contradict the law of statistical physics. One possibility is to define the transition rate based on the Boltzmann factor as introduced in Toward energy-aware model.