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

Authors:
Yoshiki Yamaguchi;Tsutomu Maruyama;Ryuzo Azuma;Moritoshi Yasunaga;Akihiko Konagaya
Affiliations:
Graduate Schoo of Systems and Information Engineering, University of Tsukuba, Tsukuba, Japan 305-8573 and RIKEN Genomic Sciences Center, Yokohama, Japan 230-0045;Graduate Schoo of Systems and Information Engineering, University of Tsukuba, Tsukuba, Japan 305-8573 and RIKEN Genomic Sciences Center, Yokohama, Japan 230-0045;RIKEN Genomic Sciences Center, Yokohama, Japan 230-0045;Graduate Schoo of Systems and Information Engineering, University of Tsukuba, Tsukuba, Japan 305-8573;RIKEN Genomic Sciences Center, Yokohama, Japan 230-0045 and Department of Mathematics and Computing Sciences, Tokyo Institute of Technology, Tokyo, Japan 152-8552
Venue:
Journal of VLSI Signal Processing Systems
Year:
2007

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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.