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Int. J. Mol. Sci. 2012, 13(6), 7798-7827; doi:10.3390/ijms13067798

Spatial Simulations in Systems Biology: From Molecules to Cells

Automatic Control Laboratory, ETH Zurich, Physikstrasse 3, 8092 Zurich, Switzerland
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Received: 2 May 2012 / Revised: 8 June 2012 / Accepted: 12 June 2012 / Published: 21 June 2012
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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Abstract

Cells are highly organized objects containing millions of molecules. Each biomolecule has a specific shape in order to interact with others in the complex machinery. Spatial dynamics emerge in this system on length and time scales which can not yet be modeled with full atomic detail. This review gives an overview of methods which can be used to simulate the complete cell at least with molecular detail, especially Brownian dynamics simulations. Such simulations require correct implementation of the diffusion-controlled reaction scheme occurring on this level. Implementations and applications of spatial simulations are presented, and finally it is discussed how the atomic level can be included for instance in multi-scale simulation methods.
Keywords: Brownian dynamics; agent-based modeling; diffusion-controlled reactions; fractal kinetics; nonlinear diffusion; spatial-temporal dynamics Brownian dynamics; agent-based modeling; diffusion-controlled reactions; fractal kinetics; nonlinear diffusion; spatial-temporal dynamics
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Klann, M.; Koeppl, H. Spatial Simulations in Systems Biology: From Molecules to Cells. Int. J. Mol. Sci. 2012, 13, 7798-7827.

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