纳米星的平面性调节DNA水凝胶的弹性
Nanostars planarity modulates the elasticity of DNA hydrogels
AI总结：
本研究通过oxDNA模型和元动力学模拟，构建了可自组装成三维渗透网络的DNA纳米星粗粒化模型，揭示了平面与非平面纳米星设计会导致截然不同的水凝胶弹性与流变特性。
摘要：
类似于网络和框架的经典刚度问题，由DNA纳米星（DNAns）制成的水凝胶的弹性特性预计强烈依赖于其构建单元的精确几何形状。然而，目前无法通过实验确定DNAns的形状。能够保留DNA纳米星正确几何形状并解释近期实验中观察到的体相特性的计算粗粒化模型，可以提供缺失的见解。在本研究中，我们执行元动力学模拟，以获得使用oxDNA模型模拟的三臂DNA纳米星的优选构型。基于这些结果，我们引入了一个纳米星粗粒化计算模型，该模型可以自组装成复杂的三维渗透网络。我们比较了两种不同设计的系统，分别使用平面或非平面纳米星。结构和网络分析揭示了两种情况完全不同的特征，导致两种截然不同的弹性特性。在非平面情况下，分子的迁移率更大，这与从平衡态Green-Kubo模拟中测量到的较低粘度相一致。据我们所知，这是第一项将DNAns几何形状与DNA水凝胶体相流变特性联系起来的工作，并可能为未来基于DNA的材料设计提供参考。
英文摘要：
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently not possible to determine DNAns shape experimentally. Computational coarse-grained models that can retain the correct geometry of DNA nanostars and account for the bulk properties observed in recent experiments could provide missing insights. In this study, we perform metadynamics simulations to obtain the preferred configuration of three-armed DNA nanostars simulated with the oxDNA model. Based on these results we introduce a coarse-grained computational model of nanostars that can self assemble into complex three dimensional percolating networks. We compare two systems with different designs, in which either planar or non-planar nanostars are used. Structural and network analysis reveal completely different features for the two cases, leading to two contrasting elastic properties. The mobility of molecules is larger in the non-planar case, which is consistent with a lower viscosity measured from Green-Kubo simulations in equilibrium. To the best of our knowledge, this is the first work connecting the geometry of DNAns with the bulk rheological properties of DNA hydrogels and may inform the design of future DNA based materials.
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