title: Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico.
abstract: How cells utilize intracellular spatial features to optimize their signaling characteristics is still not clearly understood. The physical distance between the cell-surface receptor and the gene expression machinery, fast reactions, and slow protein diffusion coefficients are some of the properties that contribute to their intricacy. This article reviews computational frameworks that can help biologists to elucidate the implications of space in signaling pathways. We argue that intracellular macromolecular crowding is an important modeling issue, and describe how recent simulation methods can reproduce this phenomenon in either implicit, semi-explicit or fully explicit representation.
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan. shafi@e-cell.org
authors.forename: Kouichi
authors.initials: K
authors.lastname: Takahashi
authors.forename: Satya Nanda Vel
authors.initials: SN
authors.lastname: Arjunan
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D003198:Computer Simulation; D006801:Humans; D042541:Intracellular Space / Q000502:physiology*; D008962:Models, Theoretical; D015398:Signal Transduction; D013269:Stochastic Processes