In silico trials: Biventricular post-infarction geometries with Purkinje network and before and after cell delivery

This repository contains biventricular and Purkinje network files for computer simulations as described in Riebel et al., Sci Rep (2024), accompanying configuration files and monodomain solver code can be found in https://github.com/LLRiebel/MonoAlg3D_C-2023. Specifically, provided here are:

FullyGrown_LVRV : Purkinje network

FullyGrown_LVRV_PMJ : Purkinje-myocyte junctions

electrodeLocations_hex : Electrode locations

hex_300um_RVSeptumEPI_CellType_BaseToApex_FastEndo.fibres : Fibre, sheet and sheet normal fields

hex_300um_RVSeptumEPI_CellType_BaseToApex_FastEndo_largeScar, mediumScar, and smallScar : Three complex scar geometries before virtual cell injection

hex_300um_RVSeptumEPI_CellType_BaseToApex_FastEndo_[...]_homogeneous, moderately heterogeneous, and heterogeneous : Three complex scar geometries after virtual cell injection with varying heterogeneity (i.e. 100:0:0 %, 80:10:10 %, and 50:25:25 % of ventricular-like, atrial-like, and nodal-like human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs))

Files are in the format used by MonoAlg3D developped by Sachetto et al., Int J Numer Method Biomed Eng (2018) (the original solver is available at https://github.com/rsachetto/MonoAlg3D_C). Custom functions to read the mesh fields as provided here can be found at https://github.com/LLRiebel/MonoAlg3D_C-2023 and further detail is provided in Riebel et al., Sci Rep (2024). Briefly, the first field in the hexahedral biventricular mesh denotes the cell type (1: endocardial, 3: epicardial, 4: endocardial infarct centre, 6: epicardial infarct centre, 7: endocardial border zone, 9: epicardial border zone, 10: ventricular-like hPSC-CMs, 11: atrial-like hPSC-CMs, 12: nodal-like hPSC-CMs), the second field contains the apico-basal gradient (which is converted to an IKs scaling factor in the cellular model in the MonoAlg3D code), and finally, the third field encodes the fast endocardial layer (which is used to scale the conductance of the top endocardial layer - as a fully branched Purkinje tree was used here, this scaling was set to 1.0 in the MonoAlg3D assembly_matrix code and hence conduction was the same as in the rest of the adult ventricular tissue).

The healthy human biventricular mesh and ECG electrodes were derived from MRI data in Lyon et al., Front Physiol (2018) and Minchole et al., Front Physiol (2019) and can be found in https://zenodo.org/records/14046617 (referred to as Subject/Control 2 as in Camps et al., Med Image Anal (2024)).

Fibre fields were derived as in Doste et al., Int J Numer Method Biomed Eng (2019).

The Purkinje network and Purkinje-myocyte junctions were inferred in Camps et al., Med Image Anal (2024) and Berg et al., Sci Rep (2023). Original Purkinje mesh files can also be found in https://zenodo.org/records/14046617 (referred to as Subject/Control 2 as in Camps et al., Med Image Anal (2024)).

Three complex scar geometries were computationally created into the healthy biventricular geometry in Riebel et al., Sci Rep (2024) as described by Cardone-Noott et al., CinC (2014) and Hill et al., PLOS One (2016).

Virtual injection of homogeneous, moderately heterogeneous, and heterogeneous hPSC-CMs was computationally modelled as described in Riebel et al., Sci Rep (2024).