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Spatial simulations in systems biology: from molecules to cells

Klann, M. and Koeppl, H. (2012):
Spatial simulations in systems biology: from molecules to cells.
In: International journal of molecular sciences, pp. 7798-7827, 13, (6), [Online-Edition: http://www.mdpi.com/1422-0067/13/6/7798],
[Article]

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.

Item Type: Article
Erschienen: 2012
Creators: Klann, M. and Koeppl, H.
Title: Spatial simulations in systems biology: from molecules to cells
Language: English
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.

Journal or Publication Title: International journal of molecular sciences
Volume: 13
Number: 6
Divisions: 18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications > Bioinspired Communication Systems
18 Department of Electrical Engineering and Information Technology
18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications
Date Deposited: 04 Apr 2014 12:50
Official URL: http://www.mdpi.com/1422-0067/13/6/7798
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