Data from: Systematic computational assessment of atrial function impairment due to fibrotic remodeling in electromechanical properties
Data files
Nov 07, 2025 version files 195.47 MB
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cv_calibration.sh
3.06 KB
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geometries.zip
67.76 MB
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parameters_OFAT_FFD.csv
3.75 KB
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pv_loops_all_simulations.zip
126.75 MB
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README.md
5.42 KB
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sensitivity_analysis_scripts.zip
928.14 KB
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unloading_scripts.zip
18.38 KB
Abstract
This dataset supports our study “Systematic computational assessment of atrial function impairment due to fibrotic remodeling in electromechanical properties,” which explores the impact of electromechanical remodeling in the fibrotic left atrium. It contains deidentified, patient-specific left atrial geometries; complete parameter sets for baseline and fibrotic combinations; scripts used to perform the simulations; and the resulting output files.
Each geometry includes fibrosis patterns, fiber orientations, region tags, and pacing sites. Parameter files specify alterations in nine fibrosis-associated properties—conduction velocities, ion channel conductances, active tension scaling, myofilament kinetics, and tissue stiffness—across one-factor-at-a-time and fractional factorial sensitivity analysis setups. Simulation and preprocessing scripts are provided for reproducibility and can be executed using the Carpentry software framework (Numericor).
Output data, provided in CSV format, include left atrial pressure–volume (PV) loop recordings and hemodynamic variables from the coupled 3D electromechanical–0D circulatory model for all simulated conditions. These data quantify atrial work and contractile performance under varied remodeling scenarios.
The dataset is structured to enable replication of the published results and to support further investigations into the biophysical determinants of atrial dysfunction and stroke risk.
Dataset DOI: 10.5061/dryad.g79cnp62q
Description of the data and file structure
This data set contains deidentified patient LA geometries, parameters and scripts used to run electromechanical simumulations for these in two sensitivity analysis setups, and resulting output PV loop data.
Files and variables
File: geometries.zip
Description: vtk files for all LA geometries, with fiber orientations and tags (tag file attached in main folder) + vtx files for pacing areas for each patient. Structured in folders for Patient 1, Patient 2, and Patient 3; for original and extended fibrosis levels.
File: parameters_OFAT_FFD.csv
Description: parameter changes imposed in fibrotic regions in geometries above in the various sensitivity analysis simulations (baseline; 9 one-factor-at-a-time simulations, and 32 fractional factorial analysis simulations)
Variables
- Simulation: Given sensitivity analysis combination this parameter combination was applied for
- CV_L (P1): Longitudinal conduction velocity (CV) for Patient 1
- CV_T (P1): Transverse CV for Patient 1 (cm/s)
- CV_L (P2): Longitudinal CV for Patient 2 (cm/s)
- CV_T (P2): Transverse CV for Patient 2 (cm/s)
- CV_L (P3): Longitudinal CV for Patient 3 (cm/s)
- CV_T (P3): Transverse CV for Patient 3 (cm/s)
- GK1: Conductance for IK1 (mS/cm^2)
- GCaL: Conductance for ICaL (mS/cm^2)
- GNa: Conductance for INa (mS/cm^2)
- Ta: Active tension scaling factor (kPa)
- mu: Myofilament binding rate (-)
- a: Isotropic stiffness parameter (kPa)
- af: Additional fiber direction stiffness parameter (kPa)
File: pv_loops_all_simulations.zip
Description: pv_loops_all_simulations.zip – output files for LA measurements from the coupled biomechanical-0D circulatory model; for all sensitivity analysis combinations; also this per patient and per fibrosis level
Each txt file contains these variables:
- Time: Time step for simulated values; note that it starts with 50 "minus" steps which corresponds to the unloading procedure. 10 cycles with 2000 steps in each; pacing happens at 30 ms (ms).
- Pressure: Recorded LA pressure in the coupled biomechanical - 0D circulatory model (mmHg)
- Volume: Recorded LA volume in the coupled biomechanical - 0D circulatory model (mL)
- State: descriptive state; load (for preloading), eject (for active contraction), or fill (for passive blood filling)
- P_out (mmHg), Q_out (mL/s), D_P_out (mmHg), P_in (mmHg), Q_in (mL/s), D_P_in (mmHg) – additional parameters tracked by the coupled biomechanical-0D circulatory model (see details in Augustin et al., 2021, Comput. Methods Appl. Mech. Eng.)
File: sensitivity_analysis_scripts.zip
Description: bash scripts used to run all the sensitivity analysis simulations; for all 3 patients and both fibrosis levels (note: in these Patient 1=AF2, Patient 2=AF4, and Patient 3=AF5). These can be run with Carpentry software (Numericor; https://numericor.at/rlb/wordpress/), or opened as txt files to see specific parameter assignments.
File: unloading_scripts.zip
Description: bash scripts used to run the unloading/reloading procedure, producing pre-systolic inflated volumes with a constant pressure of 10 mmHg; these were run prior to the organ-level simulations, for all 4 possible stiffness parameter combinations, for all 3 patients and both fibrosis levels. These can be run with Carpentry software (Numericor; https://numericor.at/rlb/wordpress/), or opened as txt files to see specific parameter assignments.
File: cv_calibration.sh
Description: Bash script used to calculate all CV value combinations. It can be run in the terminal with a Patient ID string (e.g., "P1") and target longitudinal CV as parameters, and outputs all fibrotic value combinations for that patient/value. Builds on OpenCarp's tuneCV functionality.
Code/software
Geometries (vtk files; https://vtk.org/) files can be opened by a number of softwares; e.g. Paraview.
Parameter documentation and pv loop output data come as csv files (text files). Scripts used to analyze and plot results are published here: https://github.com/aashildte/sensitivity_analysis_pvloops.
Scripts are bash scripts used to run simulations on the University of Washington Hyak supercomputer cluster, with Carpentry (commercial software from https://numericor.at/) installed.
The cv calibration script can be used with the open-source OpenCarp installed (see https://opencarp.org/documentation/examples/02_ep_tissue/03a_study_prep_tunecv for documentation and examples on how to use tuneCV).
Human subjects data
This repository contains computational meshes of human left atria segmented from late gadolinium enhanced cardiac magnetic resonance imaging. These meshes support the replication of our findings while protecting confidential patient information. This study was approved by the University of Washington Institutional Review Board. All participants provided written informed consent.