Large-Scale Parallel Simulations of 3D Cell Colony Dynamics: The Cellular Environment

The authors present a large-scale, hybrid 3D model for simulating dynamics of cell colonies growing in and interacting with a variable environment. For this purpose, they extended an earlier mathematical and computational formulation of a cell colony model to incorporate the cellular environment modeled in a continuous manner. A mathematical description based on partial differential equations is formulated for selected important components of the environment. Such extension is necessary to deal with complex biological processes such as cancer growth, where a number of scales need to be considered (subcellular, cellular, and tissue). The authors show how a continuous model can be efficiently solved on a massively parallel processing system. They also present computational methods that couple discrete and continuous descriptions while maintaining high scalability of the resulting application.