Biochemical Models Beyond the Perfect Mixing Assumption
This chapter looks at modeling of biochemical systems when the assumption of perfect mixing is relaxed and spatial configurations of molecules need to be taken into account. Spatial simulations not only introduce additional degrees of freedom in the system, but demand a somewhat different way of thinking about the model. This chapter introduces the reader conceptually to spatial modeling but also contains two walk-through examples. It uses the widely respected Smoldyn simulation software to illustrate the modeling process in spatial systems. The case study in this model is a biochemical change detector.
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