C++ code for Zhang et al. three-dimensional model of human atrial myocyte coupling electrophysiology and calcium signaling, with replicated transversal-axial tubular system.

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Contents:

• ReadMe.md: this file

• Makefile: the default make file

• build: folder of object files

• run.slurm: the command file in slurm-managed system

• pace_2.cpp: the main function with inputs: basic-cycle-length in ms, number of pacing beats, input file of tubular structure

• lib_cell: folder with all the functions

• pool_tubule: folder of input fles of tubular structures

• global_result: folder of output files (whole-cell averaged ion concentrations and ion currents)

• BinaryFiles: folder of output binary files (local CRU calcium concentration)

• steady_state_init: folder of files with initial steady state variables

• steady_state_output: folder of files with varible values at the end of pacing period

• tubule_generator: folder of files with the tubule generator

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Sample command in the terminal command line:

make
mkdir -p global_result # create folders for data ouput
mkdir -p BinaryFiles
mkdir -p steady_state_output
./pace_2 1000 28 "pool_tubule/tub_input_ver2_10.txt"

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References:

Zhang, Xianwei, Haibo Ni, Stefano Morotti, Charlotte E. R. Smith, Daisuke Sato, William E. Louch, Andrew G. Edwards, and Eleonora Grandi. Mechanisms of Spontaneous Ca2+ Release-Mediated Arrhythmia in a Novel 3D Human Atrial Myocyte Model: I. Transverse-Axial Tubule Variation. The Journal of Physiology. https://doi.org/10.1113/JP283363.

Zhang, Xianwei, Charlotte E. R. Smith, Stefano Morotti, Andrew G. Edwards, Daisuke Sato, William E. Louch, Haibo Ni, and Eleonora Grandi. Mechanisms of Spontaneous Ca2+ Release-Mediated Arrhythmia in a Novel 3D Human Atrial Myocyte Model: II. Ca2+-Handling Protein Variation. The Journal of Physiology. https://doi.org/10.1113/JP283602.

Please cite the above papers when using this model.