Multi-scale agent-based cell simulators sets daunting computational challenges in bioinformatics, only feasible by supercomputing resources. These simulators consider evolving microenvironmental conditions and cell interactions. By specifying rules at the cell level, researchers can explore complex tissue and organ systems, aiming to create Human Digital Twins (HDT) for personalized medicine. While significant milestones have been achieved, current systems are not able to model HDTs, only reaching real-sized tissue simulations of the order of 10⁶ cells while organs simulations are of the order of 10¹².

PhysiCell is a physics-based multi-scale cell simulator that facilitates the translation of intracellular mechanisms to tissue-level biomedical solutions. An analysis of PhysiCell and its distributed version, PhysiCell-X, reveals the diffusion time step as a critical bottleneck. BioFVM and BioFVM-X, using Finite Volume Methods, encounter scalability issues in modeling microenvironmental evolution. Enter BioFVM-B, a scalable library offering a lightweight data structure and an optimized Diffusion-decay 3D solver. BioFVM-B enables simulations of microenvironments that can contain real-sized tumors with reduced computing nodes and an efficient implementation for solving massive sets of tridiagonal equations that accelerates the Diffusion time-step with factors of up to ~200X.