Framework for Computational Modelling of Cellular Diffusion Systems

2015Many biological processes are regulated by the presence and movement of cellular Ca²⁺ ions. The concentration of Ca²⁺ in a cellular environment is regulated by IP₃ sensitive channels that lie on the surface of a cell’s endoplasmic reticulum. Little is known about the macroscopic effects of intracellular Ca²⁺ activity, so these processes are of key interest to the field of experimental biophysics. Experiments that study macroscopic processes that result from intracellular Ca²⁺ action are difficult to conduct in a lab, so a computational simulation that accurately simulates ion diffusion within a multicellular system is a key tool for studying the large scale effects of intracellular Ca²⁺ fluctuations.\ud The product of this thesis is a computational framework for intracellular ion diffusion that will be used as the basis for modeling of multicellular systems in the future. This model generates a spatial boundary from a cell image and overlays a grid comprised of rectangular boxes suitable for discretized diffusion calculations on the cell space. Simulations of particle movement are performed by calculating the particle flux through the boundaries of each box in the grid using Fick’s laws of diffusion. An adaptive gridding method has been developed to increase the accuracy of the representation of cellular structures within the grid while greatly increasing calculation efficiency. Efficiency differences between simulations using the adaptive and non-adaptive gridding techniques have been analyzed