SI2006 track 4 Continuity Exercises

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Contents

Tuesday

Getting Started

1D,2D,3D / Linear vs Cubic / Local vs arclength derivatives

Coordinate Systems

Fibers and Fields

Biotransport

Fitting

Wednesday

Introduction to Continuity Electrophysiology Module

Suggested experimentation

Now that you are familiar with the electrophysiology module in Continuity, you can try and make changes to the pickle files. You are welcome to try out your own ideas, but we have provided some suggestions below.

  • Change the electrode position from [0.6 0.2 0.0] to [ -0.1 0.2 0.0]. How does it differ? How does it differ at [0.25 0.5 0.0]?
  • Open the node form in Excel and change the diffusion coefficients. What happens when you increase the diffusion? What happens when you decrease it?
  • Try running with Puglisi-Bers instead of Beeler-Reuter. How much longer does it take to solve to 300 ms? Compare the action potentials and ECGs obtained with PB with those from BR.
  • Refine the mesh 2*2 so that you end up with 128 elements. How much longer does it take to solve?
  • Try selecting the "Explicit" time-stepping method. Note that you will probably have to run with a time step of 0.01 (instead of 0.1). If you do not change the time step, chances are, the program will almost certainly crash. Compare the time it takes to solve explicitly compared with implicitly - you will see why we almost always choose implicit!

Ionic Current Models and the Continuity Equation Editor

Thursday

  1. Passive Cube
  2. Passive Prolate
  3. Active Prolate
  4. Tricubic Cartesian Canine Model coupled to circulatory model

Friday

files for today

  1. Passive Cube
  2. Passive Prolate
  3. Active Prolate
  4. Tricubic Cartesian Canine Model coupled to circulatory model

More Examples

  • pcty/examples/biomechanics01/ (simple prolate passive)
  • pcty/examples/biomechanics02/ (simple cube passive)
  • pcty/examples/biomechanics03/ (passive pig model)
  • pcty/examples/biomechanics04/ (simple cube active)
  • pcty/examples/biomechanics05/ (passive rabbit)
  • pcty/examples/biomechanics06/ (2 ventricle dog passive)
  • pcty/examples/biomechanics07/ (1 ventricle dog passive)
  • pcty/examples/biomechanics08/ (refined cube active)
  • pcty/examples/biomechanics09/ (refined dog circulatory)
  • pcty/examples/biomechanics10/ (active prolate)
  • pcty/examples/biomechanics11/ (refined dog ischemic)
  • pcty/examples/biomechanics12/ (cylinder passive)


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