ChemChaste

ChemChaste extends the C++ computational biology library Chaste to simulate spatially inhomogeneous biochemical reaction-diffusion systems for modeling cell–environment interactions, cell fate specification during animal development, and multi-step metabolic processes within microbial communities.

Key Features:

• Spatial Simulation Capabilities: Simulates an arbitrary number of spatially diffusing chemicals to capture chemical dynamics across spatial scales.
• Heterogeneous Diffusion Coefficients: Supports spatially heterogeneous chemical diffusion coefficients to model environments with variable diffusion properties.
• Coupled Bulk and Intracellular Reactions: Facilitates inclusion and coupling of bulk (extracellular) and intracellular biochemical reactions.
• Discrete–Continuum Coupling: Integrates discrete cellular descriptions with continuum models of diffusing chemicals to enable multiscale interaction modeling.

Scientific Applications:

• Cell–Environment Interactions: Model and analyze feedback mechanisms between cells and their chemical environment.
• Developmental Cell Fate Specification: Simulate spatial processes underlying cell fate specification during animal development.
• Microbial Community Metabolism: Investigate multi-step metabolic processes within microbial communities combining intracellular and bulk biochemistry.
• Mechanistic Hypothesis Testing: Test and refine mechanistic hypotheses in spatially explicit models linking multicellular behavior and chemical fields.

Methodology:

Built on Chaste, ChemChaste implements spatially explicit simulations by modeling diffusion of chemicals in the surrounding medium while accounting for both intracellular and extracellular reactions.