CBMOS

CBMOS simulates center-based (cell-centered) models to numerically study multicellular dynamics in developmental biology.

Key Features:

• GPU Acceleration: Uses CuPy to leverage GPU computation, enabling simulation of large cell populations (reported up to 10,000 cells) in seconds.
• CPU Compatibility: Supports NumPy for CPU-based prototyping and smaller-scale simulations.
• Flexible API: Exposes multiple Ordinary Differential Equation (ODE) solvers and configurable force functions for center-based models.
• Numerical Method Evaluation: Includes comparative analysis of numerical integrators such as forward Euler and backward Euler, noting that backward Euler allows larger time steps for moderate accuracy but incurs additional computational cost due to its implicit nature.

Scientific Applications:

• Developmental Biology Simulations: Enables exploration of multicellular dynamics and cell population behavior under varying model assumptions and conditions.
• Numerical Analysis of Cell-Based Models: Facilitates assessment of solver accuracy and efficiency trade-offs in center-based model studies.

Methodology:

Implements simulations using CuPy for GPU execution and NumPy for CPU execution, provides multiple ODE solvers and force functions, and performs comparative evaluations of forward Euler versus backward Euler integration methods.