Simulating 3-D bone tissue growth using repast HPC: initial simulation design and performance results

Bone is one of the most implanted tissues worldwide. Bone tissue engineering deals with the replacement and regeneration of bone tissue; outcomes are determined by complex biological interactions, making it difficult to design an optimal tissue growth environment. Agent-Based Modeling (ABM) is a powerful tool to simulate such a system. We present a simulation of engineered bone tissue growth using the Repast HPC toolkit, an ABM tool for high-performance computing environments. We use this example to provide preliminary performance tests on new features (not yet publicly released) of Repast HPC that accommodate operations common to biological modeling: 3-Dimensional parallelized spatial simulation and diffusion in 3 dimensions. Repast HPC is a general ABM toolkit, and the performance documented here should be representative of performance on other simulations. Using the baseline Repast HPC tools provides flexibility for continued model development and improvement.