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 publication2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013
Pages2716-2719
Number of pages4
DOIs
Publication statusPublished - 2013 Oct 31
Event2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013 - Osaka, Japan
Duration: 2013 Jul 32013 Jul 7

Publication series

NameProceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
ISSN (Print)1557-170X

Other

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

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ASJC Scopus subject areas

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

Cite this

Hiroi, N., Iba, K., Tabira, A., Okuhara, T., Kubojima, T., Hiraiwa, T., Kobayashi, T. J., Oka, K., & Funahashi, A. (2013). In vivo oriented modeling with consideration of intracellular crowding. In 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013 (pp. 2716-2719). [6610101] (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS). https://doi.org/10.1109/EMBC.2013.6610101