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Arne T Bittig, Matthias Jeschke, and Adelinde M Uhrmacher (2010)

Towards Modelling and Simulation of Crowded Environments in Cell Biology

In: AIP Conference Proceedings, ed. by Theodore E. Simos, George Psihoyios, Ch. Tsitouras, vol. 1821, pp. 1326-1329.

In modelling and simulation of cell biological processes, spatial homogeneity in the distribution of components is a common but not always valid assumption. Spatial simulation methods differ in computational effort and accuracy, and usually rely on tool-specific input formats for model specification. A clear separation between modelling and simulation allows a declarative model specification thereby facilitating reuse of models and exploiting  different simulators. We outline a modelling formalism covering both stochastic spatial simulation at the population level and simulation of individual entities moving in continuous space as well as the combination thereof. A multi-level spatial simulator is presented that combines populations of small particles simulated according to the Next Subvolume Method with individually represented large particles following Brownian motion. This approach entails several challenges that need to be overcome, but nicely balances between calculation effort and required levels of detail.

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