SI2011 Mesoscale Modeling of Cardiac Myocytes

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General Information

The track is geared towards researchers in the computational biology field, who are interested in mesoscale modeling of cardiac myocytes and applications to other systems in translational research.

This track provides presentations and hands on tutorials on emerging software tools, and algorithms in mesocale modeling of cardiac myocytes. The topics include use of the FEniCS toolkit and adaptive finite element modeling in calcium signaling; use of GAMER in the generation of high quality mesh representation of subcellular structures; modeling of the T-tubular network in the simulation of CICR in cardiac myocytes.

Each session includes lectures and demonstrations or hands-on exercises.

Projected Outcome By the end of the sessions, the participants will be able to utilize the new tools from NBCR on mesoscale modeling and apply to their own research problems. Participants are encouraged to provide feedback and interact with the developers at all stages of the tools development.

Instructors: Johan Hake, Ph.D., Pete Kekenes-Huskey, Ph.D., Anushka Michailova, Ph.D., Zeyun Yu, Ph.D.

Time M-Th, 2:00 pm to 5:30 pm, Aug 1-5, 2011

Location Atkinson Hall (Calit2) Room 2004

Prerequisite Familiarity with Unix is recommended but NOT required.


  • Monday, Use of CSMOL in Mesoscale Simulation of Cardiac Myocyte Calcium Dynamics
    Instructor: Pete Kekenes-Huskey, Ph.D., Johan Hake, Ph.D., Anushka Michailova, Ph.D.
  • Tuesday Segmentation, Mesh Generation and Refinement using GAMer/Blender Interface
    Instructors: Johan Hake, Ph.D., 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 using IMOD. 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. Talk Tutorial
  • Wednesday, The use of the general reaction-diffusion solver: SubCell
    Instructor: Johan Hake, Ph.D., 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.
    Talk Tutorial
  • Thursday, 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.

Related Tracks from Previous SI

SI2010 Special Topics on Emerging Technologies

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