PhysiMeSS - a new physiCell addon for extracellular matrix modelling

Area of Science:

• Computational Biology
• Cancer Research
• Biophysics

Background:

• The extracellular matrix (ECM) provides structural support and influences cancer metastasis.
• Existing agent-based frameworks like PhysiCell model cells as simple shapes, limiting ECM representation.
• Accurate modeling of the ECM fiber network is crucial for understanding tumor microenvironment dynamics.

Purpose of the Study:

• To introduce a novel agent type for representing extracellular matrix fibers in agent-based simulations.
• To develop an extension for PhysiCell, named PhysiMeSS, enabling the simulation of fiber-cell and fiber-fiber interactions.
• To provide a computational tool for investigating diseases related to ECM dysregulation and cancer metastasis.

Main Methods:

• Developed PhysiMeSS as an addon to the PhysiCell framework.
• Introduced a new agent type representing line segments (2D) or cylinders (3D) for ECM fibers.
• Implemented physical interactions between fiber agents, cell agents, and other fiber agents.

Main Results:

• PhysiMeSS successfully extends PhysiCell to model the extracellular matrix as a network of fibers.
• The framework allows for the simulation of physical interactions between cells and ECM fibers.
• Demonstrated the utility of PhysiMeSS through examples showcasing its capabilities.

Conclusions:

• PhysiMeSS provides a novel computational approach to model the extracellular matrix in agent-based simulations.
• This tool enhances the study of complex biological processes, including cancer cell invasion and ECM-related pathologies.
• PhysiMeSS facilitates research into diseases linked to extracellular matrix dysregulation and cancer metastasis.