Spatiotemporal simulation of a single living cell

In the field of biology, many relationships among biological molecules have been unraveled during this decade by a number of experiments, which observe macroscopic temporal quantity changes of biological molecules in cells. Recent advances in experiments make it also possible to track the spatial movement of a single molecule in a living cell by adding fluorescent substance to the molecule. These progresses in experiments have pulled the trigger of demands for a spatiotemporal dynamic analysis in a living cell. However, the spatiotemporal analysis by biological experiments is still very difficult, and the powers of previous simulation systems are not enough for its simulation. In this paper, we propose an approach for the high-speed simulation, and a specialized system with one FPGA. In this system, biological molecules are described as particles which take random walk in three-dimensional discrete space, and two phase processing by reconfiguration is used in order to realize complex reactions among the molecules. The performance of the system is about 30 times of Pentium 4 3.2GHz.