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Matthias Jeschke and Adelinde M Uhrmacher (2008)

Multi-Resolution Spatial Simulation

Poster, , The 6th Conference on Computational Methods in Systems Biology (CMSB).

Recent findings emphasize the central role space plays in inter- and intracellular dynamics, for example that molecular crowding, i.e. a dense population of macromolecules, alters diffusion, hydration, and other properties of individual molecules. The simulation of this type of phenomena is rather costly. To reduce the effort required in simulation, different approaches are already exploited in computational biology. One is to trade accuracy for efficiency. Among other approaches, this can be done by a combination of different simulation algorithms, e.g. a numerical integration algorithm and a stochastic discrete event approach. In both cases temporal resolution forms the basis. The principal idea of this multi-resolution simulation can be adopted for the spatial variant. However, in this case time and space has to be taken into account. When simulating macromolecular crowding it makes sense to simulate the larger molecules individually and the smaller ones with less detail, i.e. at population level. This combination of population, i.e. concentration-based, and individual-based approaches leads us to multi-level modeling and simulation.

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