The parallel Green's Function Reaction Dynamics method enables whole signal transduction pathway simulations

2016 Fiscal Year Final Research Report

• Project/Area Number: 25711011
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Partial Multi-year Fund
• Research Field: Biophysics
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: Kouichi Takahashi 国立研究開発法人理化学研究所, 生命システム研究センター, チームリーダー (20514508)
• Project Period (FY): 2013-04-01 – 2017-03-31
• Keywords: 並列化 / シミュレーション / 細胞生物学

Outline of Final Research Achievements

Signal transduction pathways in eukaryotic cells are significant to understand cellular phenomena highly related to human life, e.g. cancer and cellular development and differentiation. In the field of computational biology, even though many algorithms have been developed, it is still difficult to simulate the signal transduction pathway at the single-molecule resolution, where only a few of molecules can affect the cellular fate. To overcome this difficulty, we have been developed a novel method named the enhanced Green's Function Reaction Dynamics (GFRD) method, which realizes fast and exact reaction-diffusion simulations in the single-particle level. In this study, we newly developed the parallelization algorithm of the GFRD method. This algorithm scales up simulations in time and space, and enables single-particle simulations of whole signal transduction pathways containing comprehensive structures such as cellular membrane, cell nucleus, and DNA.

Free Research Field

計算生物学