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Spatial stochastic simulation software tools | Mathematical modeling

Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems.

Source text:
(Hepburn et al., 2012) STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies. BMC Syst Biol.

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