期刊
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
卷 13, 期 6, 页码 7798-7827出版社
MDPI
DOI: 10.3390/ijms13067798
关键词
Brownian dynamics; agent-based modeling; diffusion-controlled reactions; fractal kinetics; nonlinear diffusion; spatial-temporal dynamics
资金
- SystemsX.ch initiative
- Swiss Confederation's Commission for Technology and Innovation (CTI) [12532.1 PFLS-LS]
- Swiss National Science Foundation [PP00P2_128503]
- Swiss National Science Foundation (SNF) [PP00P2_128503] Funding Source: Swiss National Science Foundation (SNF)
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.
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