Atsushi Kajita, (firstname.lastname@example.org)
Masayuki Yamamura (email@example.com)
Yuji Kohara (firstname.lastname@example.org)
Genome Biology Laboratory, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Japan
Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan
The ultimate goal of bioinformatics is to reconstruct biological systems in a computer. Biological systems have a multi-scale and multi-level biological hierarchy. The cellular level of the hierarchy is appropriate and practicable for reconstructing biological systems by computer modeling. In our first application of computer modeling to development of the nematode C. elegans, we focus on the cellular arrangement in early embryos. This plays a very important role in cell fate determination by cell-cell interaction, which is largely restricted by physical conditions. We have already constructed a computer model of a C. elegans embryo, currently up to the 4-cell stage, using deformable and dividable geometric graphics. Modeling components of the embryo are based solely on cellular-level dynamics. Here, we modeled new physical phenomena of cell division, cell rounding and stiffening; we then combined them with already modeled phenomena, contractile ring contraction and cell elongation. We investigated effectiveness of the new model on cellular arrangement by computer simulations. We found that cell rounding and stiffening only during the period of cell division were effective to generate almost identical cellular arrangements to in real embryos. Since cells could be soft during the period between cell divisions, implementation of the new model resulted in cell shapes similar to real embryos. The nature of the model and its relationship to real embryos are discussed.