Emerging methods for multiscale simulation of biomolecular systems
Emerging methods for multiscale simulation of biomolecular systems
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DOI：
10.1080/00268970701256696
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发表时间：
2007-01-01
影响因子：
1.7
通讯作者：
Voth, G. A.
中科院分区：
文献类型：
--
作者：
Chu, J. -W.;Ayton, G. S.;Voth, G. A.
生物分子系统的三个多尺度计算方法进行了描述：直接从原子模拟开发粗粒度模型的力匹配方法;在介观尺度上模拟场论表示的准粒子方法;以及在飞行中介观和原子尺度之间直接信息传递的多尺度耦合方法。每种方法的统计力学背景进行了全面的描述，以突出其理论基础。这些方法来模拟不同的生物物理过程的各种应用的例子。结合原子级MD模拟，这三种方法构成了一个强大的工具，用于桥接和跨越多个空间和时间域，存在于许多生物组件。最后讨论了该方法的发展方向。
Three multiscale computational methodologies for biomolecular systems are described: the force-matching method for developing coarse-grained models directly from atomistic simulations; the quasi-particle approach of simulating field theory representations at the mesoscopic scale; and the multiscale-coupling method for direct information transfer between mesoscopic and atomistic scales on the fly. The statistical mechanical background for each of the methods is described in a comprehensive manner in order to highlight their theoretical foundations. Examples of various applications of these methods to model different biophysical processes are given. Combining with atomistic-level MD simulations, these three methods compose a powerful tool for bridging and spanning the multiple spatial and temporal domains that are present in many biological assemblies. Future directions of the methodology developments are also discussed.