Efficient Methods to Calculate Partial Sphere Surface Areas for a Higher Resolution Finite Volume Method for Diffusion-Reaction Systems in Biological Modeling

Abstract

Computational models for multicellular biological systems, in both in vitro and in vivo environments, require solving systems of differential equations to incorporate molecular transport and their reactions such as release, uptake, or decay. Examples can be found from drugs, growth nutrients, and signaling factors. The systems of differential equations frequently fall into the category of the diffusion-reaction system due to the nature of the spatial and temporal change. Due to the complexity of equations and complexity of the modeled systems, an analytical solution for the systems of the differential equations is not possible. Therefore, numerical calculation schemes are required and have been used for multicellular biological systems such as bacterial population dynamics or cancer cell dynamics. Finite volume methods in conjunction with agent-based models have been popular choices to simulate such reaction-diffusion systems. In such implementations, the reaction occurs within each finite volume and finite volumes interact with one another following the law of diffusion. The characteristic of the reaction can be determined by the agents in the finite volume. In the case of cancer cell growth dynamics, it is observed that cell behavior can be different by a matter of a few cell size distances because of the chemical gradient. Therefore, in the modeling of such systems, the spatial resolution must be comparable to the cell size. Such spatial resolution poses an extra challenge in the development and execution of the computational model due to the agents sitting over multiple finite volumes. In this article, a few computational methods for cell surface-based reaction for the finite volume method will be introduced and tested for their performance in terms of accuracy and computation speed.