ECMSim: A high-performance web simulation of cardiac ECM remodeling through integrated ODE-based signaling and
Hasi Hays1, William Richardson1
1Department of Chemical Engineering, University of Arkansas, Fayetteville, AR 72701, USA.
Arxiv
|November 24, 2025
Summary
ECMSim is a new web application that simulates extracellular matrix (ECM) remodeling in real-time. This tool helps researchers investigate cardiac fibrosis and test potential drug effects by modeling complex cellular signaling networks.
Area of Science:
- Computational Biology
- Biophysics
- Biochemistry
Background:
- Extracellular matrix (ECM) remodeling is crucial in tissue health and disease.
- Predicting ECM remodeling is challenging due to complex, dynamic molecular networks.
- Cardiac fibrosis, a key aspect of heart failure, involves significant ECM remodeling.
Purpose of the Study:
- To introduce ECMSim, an interactive, real-time web application for simulating heterogeneous ECM remodeling.
- To model cardiac fibroblast signaling networks for simulating cardiac scar tissue.
- To provide a platform for investigating pathological conditions and potential therapeutic interventions.
Main Methods:
- Developed a large-scale model of cardiac fibroblast signaling network.
- Simulated over 1.3 million ordinary differential equations (ODEs) coupled with molecular diffusion.
- Utilized compiled C++ and WebAssembly for on-demand equation solving.
- Implemented interactive features including cell selection and parameter adjustment.
- Integrated real-time multi-scale visualizations of network dynamics.
Main Results:
- ECMSim simulates complex ECM remodeling processes in real-time.
- The application handles over 125 species and 200 edges per cell in a 10,000-cell spatial array.
- Simulations incorporate intracellular signaling, ECM production, feedback loops, and molecular diffusion.
- The platform enables dynamic adjustment of input conditions and parameters.
Conclusions:
- ECMSim provides a powerful, interactive tool for real-time ECM remodeling simulation.
- The application facilitates the investigation of cardiac fibrosis and other tissue remodeling processes.
- ECMSim supports the exploration of hypothetical scenarios and the testing of drug effects on targeted receptors.
