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From microscopy data to in silico environments for in vivo-oriented simulations

Hiroi, Noriko ; Klann, Michael ; Iba, Keisuke ; Heras Ciechomski, Pablo de ; Yamashita, Shuji ; Tabira, Akito ; Okuhara, Takahiro ; Kubojima, Takeshi ; Okada, Yasunori ; Oka, Kotaro ; Mange, Robin ; Unger, Michael ; Funahashi, Akira ; Koeppl, Heinz (2024)
From microscopy data to in silico environments for in vivo-oriented simulations.
In: EURASIP Journal on Bioinformatics and Systems Biology, 2012, 1 (7)
doi: 10.26083/tuprints-00026938
Article, Secondary publication, Publisher's Version

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Item Type: Article
Type of entry: Secondary publication
Title: From microscopy data to in silico environments for in vivo-oriented simulations
Language: English
Date: 30 April 2024
Place of Publication: Darmstadt
Year of primary publication: 2012
Place of primary publication: Heidelberg
Publisher: Springer
Journal or Publication Title: EURASIP Journal on Bioinformatics and Systems Biology
Volume of the journal: 1
Issue Number: 7
Collation: 11 Seiten
DOI: 10.26083/tuprints-00026938
Corresponding Links:
Origin: Secondary publication service

In our previous study, we introduced a combination methodology of Fluorescence Correlation Spectroscopy (FCS) and Transmission Electron Microscopy (TEM), which is powerful to investigate the effect of intracellular environment to biochemical reaction processes. Now, we developed a reconstruction method of realistic simulation spaces based on our TEM images. Interactive raytracing visualization of this space allows the perception of the overall 3D structure, which is not directly accessible from 2D TEM images. Simulation results show that the diffusion in such generated structures strongly depends on image post-processing. Frayed structures corresponding to noisy images hinder the diffusion much stronger than smooth surfaces from denoised images. This means that the correct identification of noise or structure is significant to reconstruct appropriate reaction environment in silico in order to estimate realistic behaviors of reactants in vivo. Static structures lead to anomalous diffusion due to the partial confinement. In contrast, mobile crowding agents do not lead to anomalous diffusion at moderate crowding levels. By varying the mobility of these non-reactive obstacles (NRO), we estimated the relationship between NRO diffusion coefficient (Dnro) and the anomaly in the tracer diffusion (α). For Dnro=21.96 to 44.49 μ m²/s, the simulation results match the anomaly obtained from FCS measurements. This range of the diffusion coefficient from simulations is compatible with the range of the diffusion coefficient of structural proteins in the cytoplasm. In addition, we investigated the relationship between the radius of NRO and anomalous diffusion coefficient of tracers by the comparison between different simulations. The radius of NRO has to be 58 nm when the polymer moves with the same diffusion speed as a reactant, which is close to the radius of functional protein complexes in a cell.

Uncontrolled Keywords: Transmission Electron Microscopy Image; Mean Square Displacement; Fluorescence Correlation Spectroscopy; Anomalous Diffusion; Reaction Space
Identification Number: Artikel-ID: 7
Status: Publisher's Version
URN: urn:nbn:de:tuda-tuprints-269388
Additional Information:

Supplements sind auf der Verlagsseite erhältlich: https://bsb-eurasipjournals.springeropen.com/articles/10.1186/1687-4153-2012-7#Sec21

Classification DDC: 000 Generalities, computers, information > 004 Computer science
500 Science and mathematics > 570 Life sciences, biology
600 Technology, medicine, applied sciences > 621.3 Electrical engineering, electronics
Date Deposited: 30 Apr 2024 09:28
Last Modified: 30 Apr 2024 09:28
URI: https://tuprints.ulb.tu-darmstadt.de/id/eprint/26938
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