Multi-scale spatio-temporal modeling: lifelines of microorganisms in bioreactors and tracking molecules in cells.

摘要: Agent-based models are rigorous tools for simulating the interactions of individual entities, such as organisms or molecules within cells and assessing their effects on dynamic behavior system a whole. In context with biopro- cess biosystems engineering there several interesting important appli- cations. This contribution aims at introducing this strategy aid two examples characterized by striking distinctions in scale entities mode interactions. first example structured-segregated model is applied to travel along lifelines single environment three-dimensional turbulent field stirred bioreactor. The modeling approach based an Euler-Lagrange formulation system. permits one account heterogeneity present real reactors both fluid cellular phases, respectively. response local variations extracellular concentrations pictured dynamically structured key reactions central metabolism. analysis space time. second application deals signal transduction pathways cells. Usually trans- duction networks portrayed being wired together spatially defined manner. Living circuitry, however, placed highly malleable internal architec- ture. Creating homogenous bag molecules, well-mixed system, which modeled set ordinary differential equations normally not valid. dynamics MAP kinase steroid hormone pathway serve illustrate how molecule tracking can be linked stochasticity biochemical reactions, where diffusion reaction occur probabilistic problem hindered caused macromo- lecular crowding also taken into account.