Maffeo C, Yoo J, Comer J, Wells D B, Luan B, Aksimentiev A
Department of Physics, University of Illinois, Urbana, IL, USA.
J Phys Condens Matter. 2014 Oct 15;26(41):413101. doi: 10.1088/0953-8984/26/41/413101. Epub 2014 Sep 19.
Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.
在过去十年中，全原子分子动力学方法在适用于它的系统和过程规模以及对实验系统行为进行定量预测的能力方面都有所发展。计算DNA研究领域也不例外，在原子分辨率模拟的系统规模、单个模拟的持续时间以及模拟结果的真实性方面都有显著增加。在这篇专题综述中，我们从全原子模拟的角度描述了DNA的标志性物理特性。我们展示了此类模拟揭示实验观测现象微观物理起源的惊人能力。我们还讨论了与当前原子力场的不完善和采样不足相关的令人沮丧的局限性。本综述聚焦于DNA的以下四个物理特性：有效电荷、对外界机械力的响应、与其他DNA分子的相互作用以及在外部电场中的行为。
