URDME

URDME simulates stochastic reaction-diffusion processes on unstructured triangular and tetrahedral meshes to model spatial molecular systems biology using the Reaction-Diffusion Master Equation formalism.

Key Features:

• Modularity: Modular architecture supports extension with new stochastic simulation algorithms and method development.
• Unstructured meshes: Uses unstructured triangular and tetrahedral meshes to resolve complex geometries and curved boundaries.
• Reaction-Diffusion Master Equation: Employs the Reaction-Diffusion Master Equation formalism to model spatial stochastic reaction-diffusion processes.
• High-performance implementation: Core simulation routines are implemented in low-level languages to optimize computational performance for fast reaction and diffusion events.

Scientific Applications:

• Molecular systems biology: Enables in silico experiments using spatial stochastic reaction-diffusion models to study molecular processes and complex spatial phenomena.

Methodology:

URDME uses unstructured triangular and tetrahedral meshes; applies the Reaction-Diffusion Master Equation formalism for stochastic process modeling; and implements core simulation routines in low-level languages for computational efficiency.