AMCS 300 Modelling and Simulation of Biosystems

Biological systems are distinguished by their enormous complexity and variability. That is why mathematical modelling and computational simulation of those systems is very difficult, in particular thinking of detailed models which are based on first principles. The difficulties start with geometric modelling which needs to extract basic structures from highly complex and variable phenotypes. Moreover, the models of the processes running on these geometries are not yet well established, since these are equally complex and often couple many scales in space and time. Thus, simulating such systems always means to put the whole frame to test, from modelling to the numerical methods and software tools used for simulation. We introduce the basic modelling and simulation concept and the numerical methods and apply them to a number of biological systems on different scales. Then, we treat the modelling of biological barrier membranes. In Chapter 3 we introduce a pathway to 3d modelling of electric signaling in neurons. Next, we introduce a model of Hepatitis C virus replication. We then turn to a macroscopic scale by introducing models for biomass fermentation, e.g. biogas production. Finally, we introduce models for infectious diseases.