Roles of boundary conditions in DNA simulations: analysis of ion distributions with the finite-difference Poisson-Boltzmann method.
Roles of boundary conditions in DNA simulations: analysis of ion distributions with the finite-difference Poisson-Boltzmann method.
复制标题
DNA 模拟中边界条件的作用：使用有限差分泊松-玻尔兹曼方法分析离子分布。
DOI：
10.1016/j.bpj.2009.05.012
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发表时间：
2009
影响因子：
3.4
通讯作者：
Luo,Ray
中科院分区：
文献类型：
--
作者：
Ye,Xiang;Cai,Qin;Yang,Wei;Luo,Ray
晶格和策略在生物分子模拟中的广泛应用引发了许多关于这些策略中潜在伪影的问题。一个有趣的问题是高电荷态系统反离子分布中的伪迹。在高电荷态体系中，周期边界条件下的库仑相互作用可能明显偏离自由边界条件下的库仑相互作用，从而显著影响它们的反离子分布。另一方面，水分子和可移动离子的静电屏蔽可以有效地抑制库仑相互作用中可能出现的周期性扭曲。因此，在没有详细分析的情况下，反离子分布中周期性引起的伪影的大小是不容易剖析的。在这项研究中，我们发展了一种移动离子的显式反离子/隐式盐混合表示法来解决这个问题。我们选择了一个经过充分研究的DNA，以便于验证最小杂化离子表示。然而，我们对连续离子分布、显式离子分布、径向反离子分布函数和序列相关反离子分布的详细分析表明，周期性伪影在被测DNA表面并不明显。然而，边界条件的影响确实从第二溶剂化壳层开始，并在晶胞边界变得明显。
The wide use of lattice-sum strategies in biomolecular simulations has raised many questions on potential artifacts in these strategies. One interesting question is the artifacts in the counterion distributions of highly charged systems. As one would anticipate, Coulombic interactions under the periodic boundary condition may deviate noticeably from those under the free boundary condition in the highly charged systems, significantly influencing their counterion distributions. On the other hand, the electrostatic screening due to water molecules and mobile ions may effectively damp the possible periodic distortions in Coulombic interactions. Therefore, the magnitude of periodicity-induced artifacts in counterion distributions is not straightforward to dissect without detailed analyses. In this study, we have developed a hybrid explicit counterion/implicit salt representation of mobile ions to address this question. We have chosen a well-studied DNA for easy validation of the minimal hybrid ion representation. Our detailed analysis of continuum ion distributions, explicit ion distributions, radial counterion distribution functions, and sequence-dependent counterion distributions, however, indicates that periodicity artifacts are not apparent at the surface of the tested DNA. Nevertheless, influence of boundary conditions does show up starting at the second solvation shell and becomes apparent at the cell boundary.