Please contact Dr. Patrick M. Boyle (pmjboyle@uw.edu) with any questions, concerns, complaints, or difficulties.

This dataset contains data required to reproduce computational simulations presented in the 2025 paper by Zenger et al.

Description of the data and file structure

The repository contains all finite element model files needed to rerun simulations in openCARP. These files have the basename ring_hemi_26mm. or ring_hemi_28mm.*, depending on model dimensions.

Specific finite element mesh file types:

.pts: description of points in Cartesian coordinates (spacial unit: microns)
.elem: description of how nodes (zero indexed) are interconnected by elements
.lon: fiber orientations for each element
.surf: description of mesh surface (zero indexed) triangulation
.xfrm / .mshz: saved transform / state files for model visualization

The .sv files contain initial conditions for all cell-scale ionic models used in simulation studies.

The file ring_hemi_TT2_final.par provides the baseline parameters used to run all simulations in this study.

The file ReproduceResults.sh is a driver script that can be run from the command line to produce the six exact simulations presented in Fig. 8A of the paper. Modifications to this script may be necessary to account for local machine settings. See documentation in script for more detail.

Key for interpreting filenames: 

• Finite element mesh filenames:
  • ring_hemi prefix: This refers to a model of a tissue ring subdivided into upper and lower hemispheres.
  • 26mm / 28mm suffix: This refers to the outer diameter of the ring model.
  • Specific file extensions:
    • .pts: Finite element nodes in Cartesian coordinates (x, y, z); units of microns
    • .elem: Finite element tetrahedral connectedness specifications, four nodes per element
    • .lon: Finite element fiber orientation vectors, assigned on an element-wise basis
    • .surf: Surface file containing node information for surfaces to be visualized
    • .xfrm: Geometric transform file for visualizing data in meshalyzer
    • _RenderVm.mshz: Saved state file for visualizing membrane voltage (Vm) in meshalyzer
• .sv extension: Save state data for OpenCARP ionic models
  • GTT2_fast prefix for .sv files: refers to the TT2 ionic model
  • [factor]xIKrIKs token: refers to the scaling factor applied to rapid and slow delayed rectifier potassium currents (IKr and IKs, respectively) in the TT2 ionic model
  • Normal / GrayZone token: Refers to model settings associated with normal human ventricular myocardium vs. tissue  in the vicinity of infarcted regions, which is affected by ionic remodeling (i.e., Gray Zone, Peri-Infarct Zone, Border Zone, etc.)
  • 10x1Hz_Prepace token: Describes the prepacing stimulation protocol, which involves delivery of 10 electrical stimuli at 1 Hz frequency; after the response from the final stimulus has resolved, the state of the ionic model is written into the .sv file
• ring_hemi_TT2_final.par: OpenCARP parameter file for running simulations in the ring model with the ten Tusscher 2006 (TT2) human ventricular ionic model (DOI: 10.1152/ajpheart.00109.2006)
• ReproduceResults.sh: Bash script to invoke commands for reproducing results

Example usage -- tested using openCARP v8.2 on Ubuntu 22.04.5

The command below (text following $) can be executed on a properly configured system. Example output of the script is also included.

$ bash -u ReproduceResults.sh;
Fig8A 2.6 cm Control -- last act. = 1499 ms; reentry: period = 413.2 ms, freq = 2.420 Hz
Fig8A 2.6 cm +20% ERP -- last act. = 1499 ms; reentry: period = 430.1 ms, freq = 2.325 Hz
Fig8A 2.6 cm +40% ERP -- last act. = 849 ms [simulation terminated before 1000 ms post-stim]
Fig8A 2.8 cm Control -- last act. = 1464 ms; reentry: period = 422.1 ms, freq = 2.369 Hz
Fig8A 2.8 cm +20% ERP -- last act. = 1499 ms; reentry: period = 441.4 ms, freq = 2.266 Hz
Fig8A 2.8 cm +40% ERP -- last act. = 1499 ms; reentry: period = 464.1 ms, freq = 2.155 Hz

Data visualization -- tested using meshalyzer v5.2 on Ubuntu 22.04.5

The command below can be executed on a properly configure system to visualize the results of a particular simulation; modify the mesh name provided and the path to the relevant vm.igb file to visualize results of different simulations.

$ meshalyzer
mesh/ring_hemi_26mm.pts
ReproduceResults/Ring_26mm/1.00xIKrIKs/S2_374/vm.igb
mesh/ring_hemi_26mm_RenderVm.mshz;

The first line after the invocation of the visualization program is the path to the .pts file associated with the relevant mesh. The second line is the path to the vm.igb file containing membrane voltage over time. The third line is the path to a meshalyzer state file compatible with v5.2 of the software.

Sharing/access information

All files contained in this repository are published under the Creative Commons CC0 license. Future users are thus allowed and encouraged to distribute, remix, adapt, and build upon the material in any medium or format, with no conditions. Although CC0 does not require attribution, we encourage all parties who reuse
this dataset in any way to cite the paper with which it was published (Zenger et al. 2025).

Code/software information

• openCARP and meshalyzer information can be found at: https://opencarp.org/