Large-Scale Modeling of the Extracellular Matrix on Hybrid Supercomputers Using Highly Parallel Stencil Computations

Modeling the crucial dynamic properties of tissue simulations is computationally expensive due to the complex interactions between cells and its surrounding extracellular matrix (ECM). This work extends the Cellular Potts Model (CPM) with a dynamic ECM model to simulate the viscoelastic mechanics. Our implementation leverages the NAStJA framework, a highly scalable system for distributed simulations. We assess the performance of our implementations on different HPC setups and analyze the scalability challenges of large-scale tissue simulations. GPU-accelerated simulations significantly reduce computation time but are limited by host-device communication.