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Matthias Jeschke and Adelinde M Uhrmacher (2008)

Multi-resolution Spatial Simulation For Molecular Crowding

In: Proceedings of the Winter Simulation Conference, ed. by S.J. Mason, R.R. Hill, L. Moench, O. Rose, pp. 1384-1392, IEEE Computer Society.

Spatial phenomena attract increasingly interest in computational biology. Molecular crowding, i.e. a dense population of macromolecules, is known to have a significant impact on the kinetics of molecules. However, an in-detail inspection of cell behavior in time and space is extremely costly. To balance between cost and accuracy, multi-resolution approaches offer one solution. Particularly, a combination of individual and lattice-population based algorithms promise an adequate treatment of phenomena like macromolecular crowding. In realizing such an approach, central questions are how to specify and synchronize the interaction between population and individual spatial level, and to decide what is best treated at a specific level, respectively. Based on an algorithm which combines the Next Subvolume Method and a simple, individual-based spatial approach, we will present possible answers to these questions, and will discuss first experimental results.                               

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