BioFVM

BioFVM solves partial differential equations (PDEs) that model the release, uptake, decay, and diffusion of multiple substrates in three-dimensional biological domains.

Key Features:

• Multi-substrate simulation: Simultaneously simulates numerous substrates diffusing and interacting within large three-dimensional domains.
• Reaction terms: Explicitly models release, uptake, and decay processes for substrates.
• Temporal and spatial accuracy: Achieves first-order accuracy in time and second-order accuracy in space.
• Stability with large time steps: Employs computational techniques that maintain stability even with relatively large time steps.
• Computational scaling: Exhibits linear computational cost scaling with problem size.
• Parallelization: Parallelized with OpenMP for multi-core performance.
• Implementation: Implemented in C++.

Scientific Applications:

• Multicellular systems modeling: Simulates substrate diffusion and interactions within multicellular environments.
• Pharmacology and drug delivery: Models diffusion and interaction of drugs in three-dimensional tissue domains.
• Signaling and nutrient distribution: Studies spatial dynamics of growth substrates and signaling factors in tissues.

Methodology:

Solves PDEs for diffusion with terms for release, uptake, and decay in 3D domains; implemented in C++, first-order accurate in time, second-order accurate in space, parallelized with OpenMP, and demonstrating linear computational cost scaling.