论文标题
Radonpy:使用全原子经典分子动力学模拟聚合物信息学的自动化物理属性计算
RadonPy: Automated Physical Property Calculation using All-atom Classical Molecular Dynamics Simulations for Polymer Informatics
论文作者
论文摘要
数据驱动材料研究的快速增长使得有必要开发系统设计的材料特性的开放数据库。但是,与其他材料系统(例如无机晶体)相比,聚合物材料的开放数据库很少。为此,我们开发了radonpy,这是世界上第一个开源Python库,用于完全自动化的全原子经典分子动力学(MD)模拟。对于给定的聚合物重复单元,可以完全自动进行分子建模,平衡和非平衡MD计算以及属性计算的整个过程。在这项研究中,计算了1,000多个独特的无定形聚合物,计算了15种不同的特性,包括热导率,密度,比热容量,热膨胀系数和折射率。比较计算出的特性并系统地与Polyinfo的实验值进行了系统的验证。在高通量数据生产过程中,鉴定出八个具有极高热导率(超过0.4 w/mk)的无定形聚合物,其中包括六个未报告的导热率的聚合物。发现这些聚合物具有高密度的氢键单元或刚性骨架。对热传导进行的分解分析,该分析揭示了产生无定形聚合物的高热电导率的潜在机制:通过氢键通过氢键之间的氢键和偶极 - 偶极相互作用与氢键之间的偶极链之间的相互作用或通过其氢键通过高较大的聚合物键的氢键转移。使用Radypy创建大量计算属性数据将有助于聚合物信息学的发展,类似于对无机晶体的第一原理计算数据库的出现如何具有明显的高级材料信息学信息。
The rapid growth of data-driven materials research has made it necessary to develop systematically designed, open databases of material properties. However, there are few open databases for polymeric materials compared to other material systems such as inorganic crystals. To this end, we developed RadonPy, the world-first open-source Python library for fully automated all-atom classical molecular dynamics (MD) simulations. For a given polymer repeating unit, the entire process of molecular modeling, equilibrium and nonequilibrium MD calculations, and property calculations can be conducted fully automatically. In this study, 15 different properties, including the thermal conductivity, density, specific heat capacity, thermal expansion coefficients, and refractive index, were calculated for more than 1,000 unique amorphous polymers. The calculated properties were compared and validated systematically with experimental values from PoLyInfo. During the high-throughput data production, eight amorphous polymers with extremely high thermal conductivities, exceeding 0.4 W/mK, were identified, including six polymers with unreported thermal conductivities. These polymers were found to have a high density of hydrogen bonding units or rigid backbones. A decomposition analysis of the heat conduction, which is implemented in RadonPy, revealed the underlying mechanisms that yield a high thermal conductivity of the amorphous polymers: heat transfer via hydrogen bonds and dipole-dipole interactions between the polymer chains with their hydrogen bonding units or via the covalent bonds of the polymer backbone with high rigidity. The creation of massive amounts of computational property data using RadonPy will facilitate the development of polymer informatics, similar to how the emergence of the first-principles computational database for inorganic crystals had significantly advanced materials informatics.