Biochemical Models Beyond the Perfect Mixing Assumption

Part of the Simulation Foundations, Methods and Applications book series (SFMA)


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.


Spatial Modeling Diffusion Constant External Concentration Spatial System Stochastic Simulation Algorithm 
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Copyright information

© Springer-Verlag London 2015

Authors and Affiliations

  1. 1.University of KentCanterburyUK

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