生体高分子の大変形を考慮した拘束系MDシミュレーション手法の開発(<特集>ライフサイエンス)

概要

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In this paper, novel schemes for molecular dynamics (MD) simulation are proposed to analyze the behavior of biomacromolecule with large deformation. In particular, well-known book keeping method is improved by simple algorithm for parallel computing, which is named as a double book keeping method. Double book keeping method saves the memory size and CPU time, and the effects become remarkable in huge molecular numbers. Second generation force field is also improved by mathematical and physical considerations for dynamical behavior of biomacromolecule with large deformation to prevent the divergence of the bond potential energy. MD simulation based on Gauss' principle of least constraint is developed to maintain the structure of biomacromolecule at high temperature. Numerical analysis for poly (dG)-poly (dC) DNA with 30 base pairs, which has received the attention because of the application to electron device in bionanotechnology, is performed to confirm the validity of the computational techniques introduced here. From 3D CG based on visualization technique, it is concluded that they are very effective from the viewpoint of stable and high performance computations.
日本シミュレーション学会の論文
2004-03-15