MonoAlg3D

The MonoAlg3D is a program for solving the 3D monodomain equation by applying the Finite Volume Method.

Pre-Requisites

• Linux-based operating system
• Nvidia Driver
• CUDA library

Setting the enviroment

Ubuntu: Refer to the ubuntu guide

Fedora: Refer to the fedora guide

Windows: Refer to the windows guide

Compile

$ ./build.sh

The binary files will be saved in the bin folder.

Running examples

$ bin/MonoAlg3D -c example_configs/cuboid_ohara.ini 

The output will be saved in the VTK format. In order to see the results you can use Paraview (https://www.paraview.org/) or the compiled visualization tool in bin/MonoAlg3D_visualizer. You can also set the output to plain text, by changing the section save_result in example_configs/cuboid_ohara.ini to:

[save_result]
print_rate=250
output_dir=./outputs/tmp_cube
main_function=save_as_text_or_binary
binary=false

In the plain text format we have:

• Each line represents a Volume
• Each volume is represented by its center point (X, Y, and Z), the value of half of its side length on x, y and z and the calculated V

Example file:

850,850,950,50,50,50, -85
850,950,950,50,50,50, -85
850,950,850,50,50,50, -85

This file represents 3 volumes with 100 micrometer of side. The first volume is centered at at 850,850,950 and the calculated V is -85 mV.

Contributors:

@rsachetto Rafael Sachetto Oliveira

@bergolho Lucas Arantes Berg

@Rodrigo-Weber-dos-Santos Rodrigo Weber dos Santos

Among others.

How to cite:

Oliveira RS, Rocha BM, Burgarelli D, Meira Jr W, Constantinides C, dos Santos RW. Performance evaluation of GPU parallelization, space‐time adaptive algorithms, and their combination for simulating cardiac electrophysiology. Int J Numer Meth Biomed Engng. 2018;34:e2913. https://doi.org/10.1002/cnm.2913

Credits

Heart icons created by phatplus - Flaticon

Of course. Here is the appendix formatted as a Markdown file with the title, authors, and a link for each publication.

Research utilizing MonoAlg3D (not all, not sorted)

In Silico TRials guide optimal stratification of ATrIal FIbrillation patients to Catheter Ablation and pharmacological medicaTION: the i-STRATIFICATION study

• Authors: Albert Dasí, Claudia Nagel, Michael T B Pope, Rohan S Wijesurendra, Timothy R Betts, Rafael Sachetto, Axel Loewe, Alfonso Bueno-Orovio, Blanca Rodriguez
• Link: https://doi.org/10.1093/europace/euae150

Mechanisms of ischaemia-induced arrhythmias in hypertrophic cardiomyopathy: a large-scale computational study

• Authors: James A Coleman, Ruben Doste, Zakariye Ashkir, Raffaele Coppini, Rafael Sachetto, Hugh Watkins, Betty Raman, Alfonso Bueno-Orovio
• Link: https://doi.org/10.1093/cvr/cvae086

Uncovering Arrhythmic Substrate in a Heart Failure Patient Using Digital Twins

• Authors: Thaís de J. Soares, Guilherme M. Couto, Yan B. Werneck, Daniel K. Almeida, Daniel M. P. Leme, João P. B. Pereira, Filipe L. Namorato, Matheus C. Faesy, Tiago D. Franco, Fabricio J. M. Santos, Raul P. Barra, Marcelle C. S. B. Vasconcelos, Thaiz R. Schmal, Thiago G. S. Souza, Rafael S. Oliveira, Joventino O. Campos, and Rodrigo W. dos Santos
• Link: https://cinc.org/2025/Program/accepted/301_Preprint.pdf

Variability in electrophysiological properties and conducting obstacles controls re-entry risk in heterogeneous ischaemic tissue

• Authors: Brodie A. J. Lawson, Rafael S. Oliveira, Lucas A. Berg, Pedro A. A. Silva, Kevin Burrage, Rodrigo Weber dos Santos
• Link: https://doi.org/10.1098/rsta.2019.0341

Ectopic beats arise from micro-reentries near infarct regions in simulations of a patient-specific heart model

• Authors: Rafael Sachetto Oliveira, Sergio Alonso, Fernando Otaviano Campos, Bernardo Martins Rocha, João Filipe Fernandes, Titus Kuehne, Rodrigo Weber Dos Santos
• Link: https://doi.org/10.1038/s41598-018-34304-y

Killing many birds with two stones: hypoxia and fibrosis can generate ectopic beats in a human ventricular model

• Authors: Rafael Sachetto, Sergio Alonso, Rodrigo Weber dos Santos
• Link: https://doi.org/10.3389/fphys.2018.00764

Digital twinning of the human ventricular activation sequence to Clinical 12-lead ECGs and magnetic resonance imaging using realistic Purkinje networks for in silico clinical trials

• Authors: J. Camps, L.A. Berg, Z.J. Wang, R. Sebastian, L.L. Riebel, R. Doste, X. Zhou, et al.
• Link: https://doi.org/10.1016/j.media.2024.103108

Development of a Three-Dimensional Computational Pipeline in Python for Personalized Heart Modeling

• Authors: Filipe L Namorato, Daniel M P Leme, Thaıs J Soares, Rafael S Oliveira, Thaiz R Schmal, Rodrigo W dos Santos, Joventino O Campos
• Link: https://cinc.org/2025/Program/accepted/329_Preprint.pdf

In-silico drug trials for precision medicine in atrial fibrillation: From ionic mechanisms to electrocardiogram-based predictions in structurally-healthy human atria

• Authors: A. Dasí, A. Roy, R. Sachetto, J. Camps, A. Bueno-Orovio, B. Rodriguez
• Link: https://doi.org/10.3389/fphys.2022.966046

Benchmarking Open Cardiac Electrophysiology Simulators: MonoAlg3D and OpenCARP

• Authors: de Lima, Lucas MR and Oliveira, Rafael S and Campos, Fernando O and Berg, Lucas A and Campos, Joventino O and dos Santos, Rodrigo W
• Link: https://cinc.org/2025/Program/accepted/376.html [17]

ECG analysis of ventricular fibrillation dynamics reflects ischaemic progression subject to variability in patient anatomy and electrode location

• Authors: Hector Martinez-Navarro, Ambre Bertrand, Ruben Doste, Hannah Smith, Jakub Tomek, Giuseppe Ristagno, Rafael S. Oliveira, Rodrigo Weber dos Santos, and Blanca Rodriguez
• Link: https://www.frontiersin.org/journals/cardiovascular-medicine/articles/10.3389/fcvm.2024.1408822/full

Creating Digital Twins for Cardiac Electrophysiology in Patients with Non-Ischemic Dilated Cardiomyopathy

• Authors: Thais de Jesus Soares, Tiago Dutra Franco, Fabricio Junio Mendes Santos, Thaiz Ruberti Schmal, Thiago Goncalves Schroder e Souza, Rafael Sachetto Oliveira, Joventino de Oliveira Campos, Rodrigo Weber dos Santos
• Link: https://doi.org/10.1007/978-3-031-94921-0_64

Electrophysiological mechanisms underlying T wave pseudonormalisation on stress ECGs in hypertrophic cardiomyopathy

• Authors: J. Coleman, R. Doste, M. Beltrami, I. Olivotto, B. Raman, A. Bueno Orovio
• Link: https://doi.org/10.1016/j.compbiomed.2023.107829

A Multi-Scale Computational Framework for Human-Based Modelling and Simulation of Adverse Cardiac Remodelling in Type 2 Diabetes

• Authors: Ambre Bertrand, Lucas Arantes-Berg, Ruben Doste, Jakub Tomek, Albert Dasi, Abhirup Banerjee, Julia Camps, Vicente Grau, Blanca Rodriguez
• Link: https://cinc.org/2025/Program/accepted/418.pdf