This dataset contains data required to reproduce computational simulations presented in the 2025 CVET paper by Yang et al (DOI: 10.1007/s13239-025-00794-x)

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

Description of the data and file structure

Raw data for Figures 3,5 and 6 can be found in Raw_Figure_Data_V2.xlsx. This can be opened in Microsoft Excel.

Figure 3 sheet contains raw values of spontaneous beating frequency of the cell-scale hPSC-CM for the different irradiances and opsins tested.

Figure 5 sheet contains the percentage of simulations where GHE was observed when different irradiances were applied for the three geometries.

Figure 6 sheet contains the minimum, first quartile (Q1), median (Q2), third quartile (Q3), and maximum for values calculated for geometry.

For all simulations run, the raw APD value for each geometry can be found in Geometry1_apd.dat, Geometry2_apd.dat, or Geometry3_apd.dat.

Simulations_rev2.zip is a compressed archive containing an example model with all files needed to rerun and visualize simulations in openCARP and Meshalyzer.

Simulations_rev2.zip contains the following:

• • IWiChR_like.model
  • Kernik2019_ModifiedByGibbs2023.model
  • Kernik2019_ModifiedByGibbs2023_Spont-60-beats_MDP-SaveTime-30909ms_TotalTime-31500ms_WICHR.sv
  • Meshes
  • README.md
  • RunExampleSimulation.sh
  • SimulationResults
  • TT2_60-beats-BCL-910ms_SaveTime-54000ms_TotalTime-54600ms.sv
  • vm.mshz
  • WiChR_like_sims.par
• ./Meshes:
  • Geometry2_Split0.875_N10_BlueLightAtten593.adj
  • Geometry2_Split0.875_N10_CloseToEndo_250.vtx
  • Geometry2_Split0.875_N10.elem
  • Geometry2_Split0.875_N10.lon
  • Geometry2_Split0.875_N10.pts
• ./SimulationResults:

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

The file .par provides the example parameters used to run simulations in this study. The file RunExampleSimulation.sh is a driver script to run two examples in openCARP. When no irradiance is applied (Irradiance = 0), ectopic activity will be observed. When an irradiance of 0.001 is applied, the ectopic activity is successfully suppressed. When an irradiance of 0.0001 is applied, the ectopic activity still occurs, but the onset of wavefront propagation is slightly later compared to the first example. In all three cases, a test endocardial electrical stimulus is delivered at 800 ms to determine whether the tissue remains excitable despite optogenetic stimulation.

The file Kernik2019_ModifedByGibbs2023.model comes from our previous repository, accessible via DOI: https://doi.org/10.5061/dryad.63xsj3v75.

Specific finite element mesh file types found in the Meshes Folder:

• .pts: points in Cartesian coordinates (spatial unit: microns)
• .elem: description of how nodes (zero-indexed) are interconnected by elements
• .lon: fiber orientations for each element
• .mshz: state files for model visualization
• .adj: file contains the light intensity adjustment factors used in the modeling of light attenuation through tissue
• .vtx: vertex points for stimulus electrode

Rerunning the driver script will produce all of the files shown in SimulationResults/Irradiance_X, where X = 0.0000 or 0.0010: 

• electrics.log: information about the ODE/PDE solvers used
• par_stats.dat: information about the parabolic solver
• parameters.par: default options universal to all simulations
• petsc_err_log.txt: errors encountered by the PETSc solver.
• protocol.trc: information about electrical stimuli applied
• vm_act-thresh.dat: activation nodes and times in temporal sequence, measured via threshold crossing (-40 mV)
• vm.igb: voltage over time data; can be visualized in meshalyzer
• SimResults.tgz: archive containing a downsampled version of the unified mesh and the voltage over time data, provided for reference purposes in a more accessible format (VTK)

Example usage – tested using openCARP v8.2 on Ubuntu 18.04.6 and Ubuntu 22.04.5 LTS

The command below (text following $) can be executed on a properly configured system.

$ bash -u RunExampleSimulation.sh:
Data visualization – tested using meshalyzer v5.2 on Ubuntu 18.04.6

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

$ meshalyzer Meshes/Geometry2_Split0.875_N10.pts SimulationResults/Irradiance_0.0000/vm.igb vm.mshz

$ meshalyzer Meshes/Geometry2_Split0.875_N10.pts SimulationResults/Irradiance_0.0001/vm.igb vm.mshz

$ meshalyzer Meshes/Geometry2_Split0.875_N10.pts SimulationResults/Irradiance_0.0010/vm.igb vm.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 the 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.

We encourage to cite the paper with which it was published (Yang, Ochs, Gibbs, and Boyle. Cardiovasc Eng Technol. 2025. DOI: 10.1007/s13239-025-00794-x)

Code/software information

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