SimuCell3D: three-dimensional simulation of tissue mechanics with cell polarization

Area of Science:

• Biophysics
• Computational Biology
• Tissue Engineering

Background:

• The 3D organization of cells is crucial for tissue function, changing significantly during development and disease.
• Cell-based simulations are vital for understanding tissue mechanics, but often limited by computational cost, restricting them to simplified geometries or small tissue sizes.

Purpose of the Study:

• To introduce SimuCell3D, an efficient open-source program for simulating large-scale 3D tissues with subcellular resolution.
• To enable detailed in silico studies of tissue organization, incorporating features like growth, proliferation, extracellular matrix, and non-uniform mechanical properties.

Main Methods:

• Development of SimuCell3D, an efficient open-source computational program.
• Simulation of various tissue geometries (spheroids, vesicles, sheets, tubes) imported from microscopy images.
• Incorporation of subcellular resolution, growth, proliferation, extracellular matrix, and non-uniform mechanical properties.

Main Results:

• SimuCell3D allows for the simulation of large tissues in three dimensions with subcellular resolution.
• The program can model complex tissue features including growth, proliferation, extracellular matrix, and fluid cavities.
• Analysis of layered and pseudostratified epithelia revealed that 3D cell shapes are governed by surface tension and intercellular adhesion.

Conclusions:

• SimuCell3D provides an efficient platform for large-scale in silico studies of 3D tissue organization.
• The software facilitates the investigation of biomechanical parameters and their influence on tissue structure.
• This tool enhances our understanding of tissue development and disease mechanisms through detailed computational modeling.