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Carsten Maus, Matthias Jeschke, and Adelinde M Uhrmacher (2009)

Spatial Multi-Level Modelling and Simulation for Systems Biology

Poster, Bologna, Italy, Computational Methods in Systems Biology (CMSB).

Spatial constraints influence the dynamics of various biological processes, e.g. cytoplasmic molecular crowding or membrane lipid rafts, just to mention a few of them. With advanced experimental laboratory techniques like high-resolution microscopy, spatial methods gain increasing importance in computational Systems Biology as well. Simulation methods taking space into account have been developed for different levels of detail, i.e. spatial and temporal resolutions. They vary from microscopic to mesoscopic and finally macroscopic scales each representing different abstraction levels. However, simulations at levels of high detail are rather costly and at higher abstraction levels some processes may be represented insufficiently detailed for the simulation study objective. Here, multi-level approaches come into play combining different abstraction levels and thus supporting details on demand while reducing computational costs. One example is the combination of an abstract population-based level, i.e. particles of the same species type are indistinguishable from each other, and a more detailed individual level where each particle has its own identity showing individual behaviour.

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