13 Visual Cell Demo with 5 BioPhisics Engines

A multi-engine biophysical simulation of single-cell mechanobiology, rendered in real-time via Three.js. Five coupled Python ODE engines drive a persistent SSE stream that updates a fully parametric 3D cell geometry in the browser — no SDF, no C++ required, no internet connection. What this application is A standalone desktop application that simulates the biophysical state of a single cell in real time. The user adjusts substrate stiffness, prestress, morphogens, and oxygen tension via sliders; five coupled mathematical engines compute the resulting intracellular state; a Three.js renderer visualizes the cell's geometry, organelles, and cytoskeleton as they evolve. The application runs entirely offline after first install. It requires Python 3.10+ and a browser (opened automatically). There is no database, no cloud dependency, no C++ compiler needed. **What it is not:** a clinical tool, a drug simulator, a tissue-level model, or a validated diagnostic instrument. It is a research-grade computational demonstrator. Open Invite Research Project!

Authors

Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2026-05-11
DOI
https://doi.org/10.5281/zenodo.20114598
Primary Topic
Cell Image Analysis Techniques
Type
article
Field-Weighted Citation Impact
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article

13 Visual Cell Demo with 5 BioPhisics Engines

Ionut Alexandru Stefan
Zenodo (CERN European Organization for Nuclear Research)
Cell Image Analysis Techniques
article

13 Visual Cell Demo with 5 BioPhisics Engines

Ionut Alexandru Stefan
article en

Abstract

A multi-engine biophysical simulation of single-cell mechanobiology, rendered in real-time via Three.js. Five coupled Python ODE engines drive a persistent SSE stream that updates a fully parametric 3D cell geometry in the browser — no SDF, no C++ required, no internet connection. What this application is A standalone desktop application that simulates the biophysical state of a single cell in real time. The user adjusts substrate stiffness, prestress, morphogens, and oxygen tension via sliders; five coupled mathematical engines compute the resulting intracellular state; a Three.js renderer visualizes the cell's geometry, organelles, and cytoskeleton as they evolve. The application runs entirely offline after first install. It requires Python 3.10+ and a browser (opened automatically). There is no database, no cloud dependency, no C++ compiler needed. **What it is not:** a clinical tool, a drug simulator, a tissue-level model, or a validated diagnostic instrument. It is a research-grade computational demonstrator. Open Invite Research Project!

Zenodo (CERN European Organization for Nuclear Research)
Openalex Percentile: Top 6%
Cell Image Analysis Techniques
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