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Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel

机译:多尺度方法构建基于聚乙二醇的水凝胶的平衡全原子模型

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摘要

A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications.
机译:提出了一种多尺度建模方法,可使用全原子聚合物一致力场(PCFF)有效构建交联的聚乙二醇(PEG)基水凝胶的平衡全原子模型。最终的平衡全原子模型是使用系统仿真工具集构建的,该工具集由三个连续的部分组成:(1)使用基于蒙特卡洛法的格子上Monte Carlo方法,以实验确定的交联密度构建全局交联PEG链网络。键波动模型;(2)通过从晶格模型过渡到PCFF参数化的非晶格粗粒(CG)模型来恢复网络的局部分子结构,然后使用高性能分子动力学方法进行平衡,并且( 3)通过从平衡的CG结构进行反向映射来恢复网络的原子结构,用明确表示的水将结构水化,然后使用PCFF参数化进行最终平衡。发达的三阶段建模方法已应用于多种其他复杂的大分子水凝胶系统,包括将肽,蛋白质和/或药物分子作为侧链整合在水凝胶网络中,以整合生物活性用于组织工程,再生医学和药物输送应用。

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