ChemChaste: Simulating spatially inhomogeneous biochemical reaction-diffusion systems for modeling cell-environment...

Area of Science:

• Computational Biology
• Systems Biology
• Biophysics

Background:

• Spatial organization is crucial for biological system function, from development to microbial communities.
• Spatially explicit computational models are valuable for studying these systems.
• Existing models often lack concurrent bulk and intracellular biochemical reaction modeling.

Purpose of the Study:

• To introduce ChemChaste, an extension for the Chaste computational biology library.
• To enable spatial simulation of multicellular and bulk biochemistry.
• To facilitate modeling of coupled bulk and intracellular biochemical reactions.

Main Methods:

• Developed ChemChaste as an extension to the open-source C++ library Chaste.
• Implemented simulation of arbitrary numbers of diffusing chemicals.
• Enabled spatially heterogeneous diffusion coefficients and coupled biochemical reactions.
• Introduced a file-based interface for parameter definition.

Main Results:

• ChemChaste allows for simulation of multiple diffusing chemicals with heterogeneous coefficients.
• The tool integrates bulk and intracellular biochemical reactions and their coupling.
• Demonstrated functionality with chemical and biochemical exemplars.

Conclusions:

• ChemChaste enhances computational biology by enabling detailed spatial modeling of complex biochemical systems.
• The library provides a user-friendly interface for defining simulation parameters.
• It offers increased capability for modeling coupled bulk and intracellular reactions.