论文标题
从粗粒和全原子模型的DNA中的长度尺度依赖性弹性
Length scale dependent elasticity in DNA from coarse-grained and all-atom models
论文作者
论文摘要
DNA的机械性能通常由具有纯局部耦合（现场模型）的弹性理论描述。我们讨论并分析了粗粒（OxDNA）和全原子模拟，这表明在DNA中，远端位点耦合。因此，异地模型对双螺旋的机制提供了更现实的描述。我们表明，异地相互作用负责弹性的长度尺度依赖性，并且我们开发了一个分析框架，以估计包括这些相互作用在内的模型中的弯曲和扭转持久性长度。我们的模拟表明，在某些自由程度上，异地耦合特别强，而它们对他人来说非常虚弱。如果使用从DNA数据获得的刚度参数，该理论预测了扭转波动的长度依赖性效应，并且在弯曲波动中具有适度的效果，这与实验一致。
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are coupled. Hence, off-site models provide a more realistic description of the mechanics of the double helix. We show that off-site interactions are responsible for a length scale dependence of the elasticity, and we develop an analytical framework to estimate bending and torsional persistence lengths in models including these interactions. Our simulations indicate that off-site couplings are particularly strong for certain degrees of freedom, while they are very weak for others. If stiffness parameters obtained from DNA data are used, the theory predicts large length scale dependent effects for torsional fluctuations and a modest effect in bending fluctuations, which is in agreement with experiments.
