Laboratory for Biochemical Simulation

Cellular biochemical reaction networks give rise to all living organisms on the earth. Modeling and simulation of biochemical pathways is a key technology towards the next generation of life sciences. Our Team has been developing computational methods for cellular simulations including Green's function reaction dynamics and microscopic lattice reaction-diffusion method, and a software platform called the E-Cell System. We are trying to give answers to such fundamental questions as how cells take advantage of distinct characteristics of its intracellular space including fluctuation, localization and crowding of macromolecules to optimize their information-processing functions through realistic simulations of intracellular signaling pathways at the molecular resolution.

Research Subjects

• Biochemical reaction network simulation algorithms
• Spatio-temporal architectures of intracellular signaling pathways
• Enzyme kinetics in intracellular environments
• E-Cell cell simulation software platform

Publications

1. S. Hihara, C. G. Pac,K. Kaizu, T. Tani,T. Hanafusa, T. Nozaki,S. Takemoto,T. Yoshimi, H. Yokota, N. Imamoto,Y. Sako,M. Kinjo,K. Takahashi,T. Nagai,K. Maeshima:
   "Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells"
   Cell Reports 2 1645-1656 (2012)
2. A. Mugler, A. G. Bailey, K. Takahashi, P.R. ten Wolde:
   "Membrane Clustering and the Role of Rebinding in Biochemical Signaling"
   Biophys. J. 102:5 1069-1078 (2012)
3. K. Takahashi, S. Tanase-Nicola, P.R. ten Wolde:
   "Spatio-temporal correlations can drastically change the response of a MAPK pathway"
   Proc. Natl Acad. Sci. USA, 107 2473-2478 (2010)
4. S. N. V. Arjunan and M. Tomita:
   "A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation"
   Syst. Synth. Biol., 4 35-53 (2010)
5. K. Takahashi, S.N.V. Arjunan, M. Tomita:
   "Space in Systems Biology of Signaling Pathways - towards intracellular molecular crowding in silico"
   FEBS Lett., 579 1783-1788 (2005)
6. K. Takahashi, K. Kaizu, B. Hu, M. Tomita:
   "A multi-algorithm, multi-timescale method for cell simulation"
   Bioinformatics 20, 538-546 (2004)