README

This repository contains source codes to produce:

• The results of the human atrial cell model reported in the article: Are SR Ca content fluctuations or SR refractoriness the key to atrial cardiac alternans?: insights from a human atrial model (DOI: 10.1152/ajpheart.00515.2013)

• The code to produce results in tissues by defining domains of alternating-non alternating cells and by coupling the membrane potential of each unit. Also, some scripts for creating python movies in one and two dimensions are provided.

SINGLE CELL VERSIONS.

It is composed by four files:

1. This file.
2. UPCATRIALMODEL.tar.gz: C version of the program.
3. A version of the gnu scientific library.
4. UPCATRIALMODELF.tar.gz: Fortran version of the program.

The gnu scientific library:

An updated version of the gsl library alongside installation instructions can be obtained at: http://www.gnu.org/software/gsl

Here it is only distributed for completeness, because the code heavily relies on the library, so it should be installed in your system.

The C version bundle: UPCATRIALMODEL.tar.gz

Once you have extracted the files in the compressed file you will find:

1. The source code itself, which is contained in the file UPCatrialCell.c
2. A folder called SAMPLEOUTPUT, which contains results obtained by running the code as it is packed in the bundle.
3. A shell script in a file called 'atriacompile'

The parameters chosen to produce the sample results are:

• Stimulus period Ts=400 ms.
• Recovery times of 200ms (healthy cell) and 700ms for the alternating cell.

All the output files consist of three columns which correspond to time, healthy cell and alternating cell signals respectively.

The codes does not starts writin outputs until a number of iterations are first calculated, so it only prints values closer or at the stationary state.

Compilation and Execution (Unix/Mac OS).

The script 'atriacompile' executes the line:

$cc -I/usr/local/include -o AtrialCell UPCatrialCell.c -L/usr/local/lib -lgsl -lgslcblas -lm

If the installation paths of the library are different they can be found by executing:

$gsl-config --libs --cflags

If the code links and compiles correctly it generates the file: AtrialCell, which should be run in a terminal as:

$ ./AtrialCell

Fortran Bundle: UPCATRIALMODELF.tar.gz

This contains a fortran source UPC-ATRIALCELL.f and a binary file check.dat.

Compilation and Execution (Unix/Mac OS)

To compile the code type in UNIX/MAC OS, type in a terminal:

$gfortran -o exfilename sourcefilename.f

then run:

$./exfilename

The binary file check.dat is read at the beginning of the execution and it contains the initial data obtained for Ts=1000 ms which are then evaluated for other pacing values (Tsvalue). Then, the outcomes are written in another binary file called output.dat.Tsvalue.

It also writes standard text files for the time evolution of the voltage and every Calcium concentration (volt.dat.Tsvalue) and a file with the action potential duration APD(DI) (rest0dss.dat).

TISSUE CODES AND MOVIES.

The tissues code provided is written in C only. This part of the project is contained in a folder called TISSUEMODEL. It contains:

• UPCatrialtissues.c
• atriacomplie
• anipy/Cai2d.py
• anipy/V2d.py
• anipy/domains.py

The first two files are the source code and the compilation script. Again it relies heavily on the GNU scientific library and it must be excecuted as:

$./atriacomiple

which executes:

$cc -I/opt/local/include/ -o AtrialTissue UPCatrialtissues.c -L/opt/local/lib -lgsl -lgslcblas -lm -fno-stack-protector

This creates the excecutable file AtrialTissue. The excecution of that file first runs the single cell version of the code for two cells, one alternating and one healthy, which states are copied into the predetermined domains established in the code (function inicond2()).

The default configuration is Lx=300 and Ly=250. and a circle centered at ix=110 and iy=74 of radius Ly-20. the cellular lengths are taken to be 0.025 micrometers.

The code stores pictures of the system at "snaps/tnCai.dat" and "snaps/tnVm.dat", so it is required to have a folder called 'snaps' in the excecution path. The code accepts random number seed environmental variables to create stochastic media (Some code is in the source commented).

The python scripts read configurations from "../snaps" and create movies, providing To and Tf, values for the initial and final times, this is discussed in more detail at my blog

Please do not hesitate to contact me for assistance.

Cheers!.