A Simple Intracellular Calcium Diffusion Problem


  • These step-by-step instructions will guide you through setting up and running a simple biotransport problem from scratch.
  • This example models the diffusion of calcium in a cell in the presence of an immobilized buffer such as troponin C. Calcium flux across the cell membrane (the top and bottom edges of the mesh) is preset as a 20 ms inward-pulse followed by a time-varying outward flux that returns the system to initial conditions. The membrane currents approximate the activity of the L-type calcium channel and Na/Ca exchanger during an atrial myocyte action potential.
  • An automated script that runs this tutorial is included in the Continuity installation: examples\biotransport01\2D_ca_diffusion.py. To run it, click File→Read script→Python or session script

Start Continuity

Create Mesh

Formulate Biotransport Problem

  • If the Electrophysiology menu is not loaded, select File→Load Continuity Modules…

    • Select electrophysiology and click OK

    • The menu bar should now show the Electrophysiology command
  • Electrophysiology→Edit→Ionic Model…

    • In the Select Model tab, find EP_Ca_diffusion in the list of models, and select it.

    • Click on the Submit tab (the very last tab) and then click the Submit button

  • View→Change Renderer…

    • Click OpenMesh radio button

    • Click OK to change renderer

  • View→Set Divisions…

    • Enter 4 for Number of Divisions: and click OK

  • Mesh→Render→Elements…

    • Click surfaces radio button

    • Click Render to display mesh surface

    • The mesh should now look similar to the first screenshot on the top of this page. If the color seems washed out, try rotating the mesh a little bit (use the looped arrow button on the toolbar)

Compute and Render Solutions

Pre-built model

This cont6 file contains all data and parameters before the Electrophysiology solve: bt_model.cont6