Grain Shape Dynamics for Molecular Simulations at the Mesoscale,Advanced Theory and Simulations

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Grain Shape Dynamics for Molecular Simulations at the Mesoscale
Advanced Theory and Simulations ( IF 2.9 ) Pub Date : 2020-08-16 , DOI: 10.1002/adts.202000124
Nicolas Martzel ₁ , Alain Dequidt ₂ , Julien Devémy ₂ , Ronald Blaak ₂ , Sebastien Garruchet ₁ , Benoit Latour ₁ , Florent Goujon ₂ , Etienne Munch ₁ , Patrice Malfreyt ₂

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Coarse‐graining routines are necessary for simulating systems involving large molecules. However, their accuracy is limited by excessive simplifications that are made during the upscaling procedure. The time autocorrelation of the shape anisotropy of grains in cis‐polybutadiene chains is computed, and it is concluded that the image of a grain as an undeformable object is no longer valid at high level of coarse‐graining. A model for the joint dynamics of the centers of mass and the shapes of grains, which are calculated from the positions of the atoms they represent, is introduced. The model reproduces the distribution and dynamics of the shape of a single‐grain oligomer in various solvents, opening a route to physical modeling of complex systems such as proteins, biological cells, or realistic polymer melts.

中文翻译：

中尺度分子模拟的晶粒形状动力学

粗粒度例程对于模拟涉及大分子的系统是必需的。但是，它们的精度受到升级过程中过度简化的限制。计算了顺-聚丁二烯链中晶粒形状各向异性的时间自相关，得出结论，作为高变形粗粒的晶粒作为不可变形物体的图像不再有效。引入了一个质心和晶粒形状的联合动力学模型，该模型是根据它们所代表的原子的位置计算出来的。该模型再现了单粒低聚物在各种溶剂中的分布和动力学，为复杂系统的物理建模（例如蛋白质，生物细胞或实际的聚合物熔体）开辟了道路。

更新日期：2020-09-23

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