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The 2nd Biosupercomputing Symposium

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Research and Development of Cell Scale Simulation Team

Dr. Hideo Yokota
Cell Scale Team, Integrated Simulation of Living Matter Group,
Computational Science Research Program, RIKEN

Cells are the smallest life units, and the ultimate goal of the cell scale simulation team is to recreate intracellular and intercellular phenomena. However, intracellular phenomena have not, for the most part, been elucidated, and their clarification is a major objective in cell biology. It is currently impossible to develop a simulator that can recreate all complicated intracellular phenomena. Hence, the cell scale simulation team’s objective is to simulate intracellular and extracellular phenomena that have been sufficiently elucidated by past research and for which mathematical models have been established. In addition, using the computational power of next-generation 10-petaflop supercomputers that are scheduled to be completed in 2012, the team hopes to enable simulations that consider intracellular environments that heretofore could not have been calculated due to high computational costs. More concretely, intracellular spaces are viewed as grid coordinates with mesh-shaped positional information. In each grid, various intracellular phenomena are simulated to recreate intracellular environments, which are uneven environments containing spaces between organelles.

Future advances in cell biology, mathematical model construction, and simulation technologies should markedly expand the scope of cell simulation. In the hope of contributing to the future development of cell simulation, a cell simulation platform that can analyze coupled phenomena by linking simulators for multiple phenomena (RICS) was developed.

At cell scale simulation team, based on intracellular energy and oxygen metabolism simulation, research is being conducted to expand the scope of simulation to include the consideration of intracellular fields and model the presence of intracellular substances.

We set the target of the simulation to the hepatocyte. Concretely, the team is aiming at the achievement of the simulation of the hepatocyte and the hepatic lobule. The goal of cell phenomenon simulation developed by the team is to recreate actual intracellular phenomena, not merely running calculations inside a computer. Experiments have been performed concurrently to gather the necessary parameters for simulation and to verify simulation, in order to carry out simulation to discover unknown phenomena, not just recreating phenomena .

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