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
Artikel, Zweitveröffentlichung, Verlagsversion
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Kurzbeschreibung (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.
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2024 |
| Autor(en): | Klann, Michael ; Koeppl, Heinz |
| Art des Eintrags: | Zweitveröffentlichung |
| Titel: | Spatial Simulations in Systems Biology: From Molecules to Cells |
| Sprache: | Englisch |
| Publikationsjahr: | 30 April 2024 |
| Ort: | Darmstadt |
| Publikationsdatum der Erstveröffentlichung: | 2012 |
| Ort der Erstveröffentlichung: | Basel |
| Verlag: | MDPI |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | International Journal of Molecular Sciences |
| Jahrgang/Volume einer Zeitschrift: | 13 |
| (Heft-)Nummer: | 6 |
| DOI: | 10.26083/tuprints-00026923 |
| URL / URN: | https://tuprints.ulb.tu-darmstadt.de/26923 |
| Zugehörige Links: | |
| Herkunft: | Zweitveröffentlichungsservice |
| Kurzbeschreibung (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. |
| Freie Schlagworte: | Brownian dynamics, agent-based modeling, diffusion-controlled reactions, fractal kinetics, nonlinear diffusion, spatial-temporal dynamics |
| Status: | Verlagsversion |
| URN: | urn:nbn:de:tuda-tuprints-269230 |
| Zusätzliche Informationen: | This article belongs to the Special Issue Advances in Biomolecular Simulation |
| Sachgruppe der Dewey Dezimalklassifikatin (DDC): | 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie 600 Technik, Medizin, angewandte Wissenschaften > 621.3 Elektrotechnik, Elektronik |
| Hinterlegungsdatum: | 30 Apr 2024 09:25 |
| Letzte Änderung: | 13 Mai 2024 09:45 |
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| Suche nach Titel in: | TUfind oder in Google |
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- Spatial Simulations in Systems Biology: From Molecules to Cells. (deposited 30 Apr 2024 09:25) [Gegenwärtig angezeigt]
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