Biological System Modelling

Biological systems provide challenges in dynamic modelling and simulations. The limitations on the measurement technologies in molecular-level experiments and the spatial and stochastic natures of molecular interactions require various modelling and simulation tools to be appropriately used. We introduce a systematic perspective on how to use experimental data from cell cultures to identify common molecular circuits in cells. Using the multiple experimental data for Escherichia coli tryptophan reactions to three different cell types, we determine the unknown parameters in the model by solving a model fitting problem. Biological oscillation, one of the important mechanisms in all living life, of Dictyostelium is modelled. We introduce deterministic modelling and stochastic modelling, respectively. Deterministic modelling is sufficient at representing oscillations, but it fails in robustness tests. The fragility of the robustness in the modelling stems from the lack of stochastic noise. We study the importance of noise in biological oscillations through stochastic simulations.