Intracellular molecular signalling plays a crucial role in modulating ion channel dynamics, synaptic plasticity and, ultimately, the behaviour of the whole cell. In this chapter, we investigate ways of modelling intracellular signalling systems. We focus on calcium, as it plays an extensive role in many cell functions. Included are models of intracellular buffering systems, ionic pumps and calcium-dependent processes. This leads us to outline other intracellular signalling pathways involving more complex enzymatic reactions and cascades. We introduce the well-mixed approach to modelling these pathways and explore its limitations. Rule-based modelling can be used when full specification of a signalling network is infeasible. When small numbers of molecules are involved, stochastic approaches are necessary and we consider both population-based and particle-based methods for stochastic modelling. Movement of molecules through diffusion must be considered in spatially inhomogeneous systems.
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