DOI: 10.5061/dryad.51c59zwm6
title: Computational simulations show proof-of-concept for optogenetic suppression of ectopic activity in cardiac stem cell therapy

description: This dataset contains data required to reproduce computational simulations
 presented in the 2025 paper by Yang et al. This data set comprises (1)
 Geometric descriptions of the simulation domain (whole heart, tissue
 wedge, etc.), with point clouds interconnected by finite elements, each of
 which is associated with a vector encoding local myofiber orientation. (2)
 Parameter files describing functional cell- and tissue-scale properties of
 different tissue regions, perturbations to be applied to the model during
 the simulation (e.g., electrical stimuli), and numerical solver settings.
 (3) Initial condition state files describing the functional state of the
 model at the beginning of the simulation, if these conditions differ from
 the cell-scale default parameters. All of the above are stored in plain
 text or binary formats compatible with the openCARP framework, which is
 freely available for non-commercial use.
description: # Computational simulations show proof-of-concept for optogenetic
 suppression of ectopic activity in cardiac stem cell therapy 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](mailto: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](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](https://dx.doi.org/10.1007/s13239-025-00794-x)) #### Code/software information openCARP and meshalyzer information can be found at: [https://opencarp.org/](https://opencarp.org/)