SCI: Multiscale Modeling To Develop A Cyberinfrastructure For The Dynamics Of Flexible And Stiff Entangled Macromolecules

采用理论和实验相结合的方法预测了在浓缩环境中柔性和半柔性大分子链的动力学和迁移率。聚合物的动力学涵盖了大范围的长度和时间尺度，因此它们不能直接适用于分子动力学研究。相反，我们实现了一种多尺度、粗粒度的方法，利用滑动链接来模拟介观水平上的纠缠。该方法具有鲁棒性，可以考虑轻度交联的弹性网络，凝胶中的半柔性迁移率，纠缠链的线性粘弹性，或线性和星形大分子的非线性流变学。模型的介观水平参数可以通过蒙特卡罗（MC）和分子动力学（MD）模拟来确定，尽管最小特征时间尺度（_e）更容易从现象学上处理。这种方法允许对从原子到数百秒的时间尺度进行建模。由此产生的计算工具代表了软凝聚态物理的重大进步，特别是对于生物材料，并显着增强了研究，建模和利用此类系统所需的共享网络基础设施。该研究的实验部分利用了最近获得的关于支链蛋白生物合成的知识，生成了具有确定结构和分子量的星形蛋白的系统集合。这些蛋白质的行为在不同水平的纠缠与一个固定的矩阵是通过表征他们的迁移在电泳期间探索。支链多肽的生物学特性是人们非常感兴趣的主题，但在大多数分析技术中，它们的异常行为阻碍了它们的分析。

A combined theoretical and experimental project is used to predict the dynamics and mobility of flexible, and semi-flexible macromolecular chains in a concentrated environment. The dynamics of polymers cover a large range of length and timescales, so they are not directly amenable to molecular dynamics studies. Instead, we implement a multiscale, coarse-graining approach utilizing slip-links to model entanglements on the mesoscopic level. The approach is robust, allowing consideration of lightly crosslinked elastic networks, semi-flexible mobility in gels, linear viscoelasticity of entangled chains, or nonlinear rheology of linear and star-shaped macromolecules. Mesoscopic-level parameters for the model may be determined by Monte Carlo (MC) and Molecular Dynamics (MD) simulations, although the smallest characteristic time scale (_e) is more easily treated phenomenologically. The approach allows modeling of time scales from the atomic up to hundreds of seconds. The resulting computational tools represent a major advance in soft-condensed matter physics, in particular for biological materials, and significantly enhances the shared cyberinfrastructure necessary to study, model and exploit such systems.The experimental component of the study takes advantage of recently acquired knowledge about the biosynthesis of branched proteins to generate a systematic collection of star-shaped proteins of defined architecture and molecular weight. The behavior of these proteins at various levels of entanglement with an immobile matrix are explored by characterizing their mobility during electrophoresis. The biological properties of branched polypeptides are the subject of intense interest but their analysis has been hampered by their anomalous behavior in most analytical techniques.