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Spatial Simulations in Systems Biology: From Molecules to Cells

Klann, Michael ; Koeppl, Heinz (2024)
Spatial Simulations in Systems Biology: From Molecules to Cells.
In: International Journal of Molecular Sciences, 2012, 13 (6)
doi: 10.26083/tuprints-00026923
Article, Secondary publication, Publisher's Version

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Item Type: Article
Type of entry: Secondary publication
Title: Spatial Simulations in Systems Biology: From Molecules to Cells
Language: English
Date: 30 April 2024
Place of Publication: Darmstadt
Year of primary publication: 2012
Place of primary publication: Basel
Publisher: MDPI
Journal or Publication Title: International Journal of Molecular Sciences
Volume of the journal: 13
Issue Number: 6
DOI: 10.26083/tuprints-00026923
Corresponding Links:
Origin: Secondary publication service

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.

Uncontrolled Keywords: Brownian dynamics, agent-based modeling, diffusion-controlled reactions, fractal kinetics, nonlinear diffusion, spatial-temporal dynamics
Status: Publisher's Version
URN: urn:nbn:de:tuda-tuprints-269230
Additional Information:

This article belongs to the Special Issue Advances in Biomolecular Simulation

Classification DDC: 500 Science and mathematics > 570 Life sciences, biology
600 Technology, medicine, applied sciences > 621.3 Electrical engineering, electronics
Date Deposited: 30 Apr 2024 09:25
Last Modified: 30 Apr 2024 09:25
URI: https://tuprints.ulb.tu-darmstadt.de/id/eprint/26923
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