Physiological intracellular crowdedness is defined by the perimeter-to-area ratio of sub-cellular compartments

Noriko Hiroi, Takahiro Okuhara, Takeshi Kubojima, Keisuke Iba, Akito Tabira, Shuji Yamashita, Yasunori Okada, Tetsuya J. Kobayashi, Akira Funahashi

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)


The intracellular environment is known to be a crowded and inhomogeneous space. Such an in vivo environment differs from a well-diluted, homogeneous environment for bio-chemical reactions. However, the effects of both crowdedness and the inhomogeneity of environment on the behavior of a mobile particle have not yet been investigated sufficiently. As described in this paper, we constructed artificial reaction spaces with fractal models, which are assumed to be non-reactive solid obstacles in a reaction space with crevices that function as operating ranges for mobile particles threading the space. Because of the homogeneity of the structures of artificial reaction spaces, the models succeeded in reproducing the physiological fractal dimension of solid structures with a smaller number of non-reactive obstacles than in the physiological condition. This incomplete compatibility was mitigated when we chose a suitable condition of a perimeter-to-area ratio of the oper-ating range to our model. Our results also show that a simulation space is partitioned into convenient reaction compartments as an in vivo environment with the exact amount of solid structures estimated fromTEM images. The characteristics of these compartments engen-der larger mean square displacement of a mobile particle than that of particles in smaller compartments. Subsequently, the particles start to show confined particle-like behavior. These results are compatible with our previously presented results, which predicted that a physiological environment would produce quick response and slow exhaustion reactions.

Original languageEnglish
Article numberArticle 293
JournalFrontiers in Physiology
Volume3 JUL
Publication statusPublished - 2012


  • Fractal dimension
  • Mean square displacement
  • Molecular crowding
  • Percolation
  • Surface-to-volume ratio

ASJC Scopus subject areas

  • Physiology
  • Physiology (medical)


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