Modelling biomacromolecular assemblies with continuum mechanics
Modelling biomacromolecular assemblies with continuum mechanics
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DOI：
10.1042/bst20140294
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发表时间：
2015-04-01
影响因子：
3.9
通讯作者：
Harris, Sarah
中科院分区：
文献类型：
--
作者：
Hanson, Benjamin;Richardson, Robin;Harris, Sarah
我们使用有限元算法建立了蛋白质的连续力学描述，该算法已被推广到包括热波动，因此被称为波动有限元分析(FFEA)。传统的分子动力学(MD)模拟提供了每个单个原子位置波动的轨迹，而FFEA轨迹显示了蛋白质的整体形状如何由于热搅拌而变化。我们描述了有限元分析的理论背景，它与更成熟的生物分子模拟方法的关系，并提供了它在分子马达动力蛋白的介观生物分子动力学中的应用实例。
We have developed a continuum mechanical description of proteins using a finite element algorithm which has been generalized to include thermal fluctuations and which is therefore known as fluctuating finite element analysis (FFEA). Whereas conventional molecular dynamics (MD) simulations provide a trajectory in which each individual atomic position fluctuates, a FFEA trajectory shows how the overall shape of the protein changes due to thermal agitation. We describe the theoretical background to FFEA, its relationship to more established biomolecular modelling methods and provide examples of its application to the mesoscale biomolecular dynamics of the molecular motor dynein.