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Mesoscopic-level Simulation of Dynamics and Interactions of Biological Molecules Using Monte Carlo Simulation

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Abstract

A mesoscopic-level method for clarifying living cell dynamics is described that uses Monte Carlo simulation of biological molecule interactions. The molecules are described as particles that take a random walk in 3-dimensional discrete space. Many kinds of molecules (including complex forms) are supported, so complex reactions with enzymes can be simulated. Also described is an field programmable gate array system with reconfigurable hardware that that will support complete modeling of an entire cell. Two-phase processing (migration and reaction) is used to simulate the complex reactions, so the method can be implemented in a limited amount of hardware. The migration and reaction circuits are deeply pipelined, resulting in high performance. Estimated performance is 30 times faster than with a 3.2-GHz Pentium 4 computer. This approach should make it possible to eventually simulate cell interactions involving one billion particles.

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Authors and Affiliations

  1. Graduate Schoo of Systems and Information Engineering, University of Tsukuba, 1-1-1 Tenoudai, Tsukuba, Ibaraki, 305-8573, Japan

    Yoshiki Yamaguchi, Tsutomu Maruyama & Moritoshi Yasunaga

  2. RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

    Yoshiki Yamaguchi, Tsutomu Maruyama, Ryuzo Azuma & Akihiko Konagaya

  3. Department of Mathematics and Computing Sciences, Tokyo Institute of Technology, 2-21-1 Ookayama, Meguro, Tokyo, 152-8552, Japan

    Akihiko Konagaya

Authors
  1. Yoshiki Yamaguchi
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  2. Tsutomu Maruyama
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  3. Ryuzo Azuma
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  4. Moritoshi Yasunaga
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  5. Akihiko Konagaya
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Correspondence to Yoshiki Yamaguchi.

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Yamaguchi, Y., Maruyama, T., Azuma, R. et al. Mesoscopic-level Simulation of Dynamics and Interactions of Biological Molecules Using Monte Carlo Simulation. J VLSI Sign Process Syst Sign Im 48, 287–299 (2007). https://doi.org/10.1007/s11265-007-0072-7

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  • DOI: https://doi.org/10.1007/s11265-007-0072-7

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