In vivo oriented modeling with consideration of intracellular crowding

Noriko Hiroi, Keisuke Iba, Akito Tabira, Takahiro Okuhara, Takeshi Kubojima, Takumi Hiraiwa, Tetsuya J. Kobayashi, Kotaro Oka, Akira Funahashi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

In vivo reaction space is constrained by complex structures which are made of entwined cytoskeletons and organelles; this create the difference between in vivo and in vitro in respect of molecular mobility, and it may affect reaction processes. Our motivation is to reveal the background mechanisms of the properties of molecular behaviors in vivo by numerical approach. For this object, we reassembled a pseudo-intracellular environment in 3D lattice space, and executed Monte Carlo simulation. By changing the relative amount of non-reactive obstacles in the simulation space, we tested the effect of the level of crowdedness to the molecular mobility and reaction processes. Our results showed that molecules demonstrated anomalous diffusion correlating to the restriction level of the reaction space. Reaction processes also showed distinct characteristics, that is increase of reaction rate at the beginning of reactions, with the decrease of the reaction rate at later time frame of reactions. Our results suggested that the anomalous behaviors at singe molecule level in vivo could bring an essential difference to the reaction processes and the results.

Original languageEnglish
Title of host publicationProceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
Pages2716-2719
Number of pages4
DOIs
Publication statusPublished - 2013
Event2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013 - Osaka, Japan
Duration: 2013 Jul 32013 Jul 7

Other

Other2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013
CountryJapan
CityOsaka
Period13/7/313/7/7

Fingerprint

Space Simulation
Cytoskeleton
Organelles
Reaction rates
Molecules
In Vitro Techniques
Monte Carlo simulation

ASJC Scopus subject areas

  • Computer Vision and Pattern Recognition
  • Signal Processing
  • Biomedical Engineering
  • Health Informatics

Cite this

Hiroi, N., Iba, K., Tabira, A., Okuhara, T., Kubojima, T., Hiraiwa, T., ... Funahashi, A. (2013). In vivo oriented modeling with consideration of intracellular crowding. In Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS (pp. 2716-2719). [6610101] https://doi.org/10.1109/EMBC.2013.6610101

In vivo oriented modeling with consideration of intracellular crowding. / Hiroi, Noriko; Iba, Keisuke; Tabira, Akito; Okuhara, Takahiro; Kubojima, Takeshi; Hiraiwa, Takumi; Kobayashi, Tetsuya J.; Oka, Kotaro; Funahashi, Akira.

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. 2013. p. 2716-2719 6610101.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hiroi, N, Iba, K, Tabira, A, Okuhara, T, Kubojima, T, Hiraiwa, T, Kobayashi, TJ, Oka, K & Funahashi, A 2013, In vivo oriented modeling with consideration of intracellular crowding. in Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS., 6610101, pp. 2716-2719, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013, Osaka, Japan, 13/7/3. https://doi.org/10.1109/EMBC.2013.6610101
Hiroi N, Iba K, Tabira A, Okuhara T, Kubojima T, Hiraiwa T et al. In vivo oriented modeling with consideration of intracellular crowding. In Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. 2013. p. 2716-2719. 6610101 https://doi.org/10.1109/EMBC.2013.6610101
Hiroi, Noriko ; Iba, Keisuke ; Tabira, Akito ; Okuhara, Takahiro ; Kubojima, Takeshi ; Hiraiwa, Takumi ; Kobayashi, Tetsuya J. ; Oka, Kotaro ; Funahashi, Akira. / In vivo oriented modeling with consideration of intracellular crowding. Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. 2013. pp. 2716-2719
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