SI2012 Mesoscale Modeling of Cardiac Myocytes

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Use of Subcell in Mesoscale Simulation of Cardiac Myocyte Calcium Dynamics Instructor: Pete Kekenes-Huskey, Ph.D., Anushka Michailova, Ph.D.


Segmentation, Mesh Generation and Refinement using GAMer/Blender Interface Instructors: Pete Kekenes-Huskey, Ph.D.

This session starts with a brief introduction of segmentation of reconstructed EM images of mouse to obtain a realistic sub-cellular geometry. The rest of the session will be used to show how the mesh can be improved using GAMer within the GUI of Blender. Volumetric meshes which can be used in finite element simulations will finally be generated. Simple Blamer Tutorial Talk Tutorial


The use of the general reaction-diffusion solver: SubCell Instructor: Pete Kekenes-Huskey, Ph.D., Anushka Michailova, Ph.D.

SubCell provides a high level interface to declare and solve general reaction-diffusion equation on unstructured meshes. SubCell is based on the finite element library of FEniCS.

Opal Tutorial

Talk Tutorial


From Meshing to Model Building to Simulation of CICR using realistic models of cardiac myocytes Instructors: Zeyun Yu, Ph.D., Anushka Michailova, Ph.D.

This session introduces computational approaches to image pre-processing and boundary segmentation, and new developments of surface/volumetric mesh generation and quality improvement. We will also discuss finite element simulation of cardiac myocytes using realistic models extracted from imaging data.

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