Computer simulation

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Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. Here, we developed the first building toolkit named as “HBP Builder” for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user’s specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Based on it, we have disclosed the formation mechanisms of the self-assembly of micelles and vesicles from HMCs and the effects of the degree of branching (DB), pH, and different solvents on the self-assembly of HMCs by using DPD simulation. Very recently, the group is more focused on the structures and transport dynamics of water and salt ions in polyamide reverse osmosis membranes. We developed a universal toolkit for constructing polyamide reverse osmosis membranes, named as MembrFactory, which combines flexibility of force field and membrane compositions. Based on it, much of the work is going on.

1. Yu, C. Y.; Ma, L.; Li, S. L.; Tan, H. N.; Zhou, Y. F*; Yan, D. Y., “HBP Builder: A Tool to Generate Hyperbranched Polymers and Hyperbranched Multi-Arm Copolymers for Coarse-grained and Fully Atomistic Molecular Simulations”, Sci. Rep., 2016, 6, 26264.

2. Yu, C. Y.; Ma, L.; Li, K.; Li, S. L.; Liu, Y. N.; Zhou, Y. F.*; Yan, D. Y., “Molecular Dynamics Simulation Studies of Hyperbranched Polyglycerols and Their Encapsulation Behaviors of Small Drug Molecules”, Phys. Chem. Chem. Phys., 2016, 18, 22446.

3. Wang, Y. L.; Li, B.; Zhou, Y. F.*; Lu, Z. Y.*; Yan, D. Y., “Dissipative particle dynamics simulation study on the mechanisms of self-assembly of large multimolecular micelles from amphiphilic dendritic multiarm copolymers”, Soft Matter, 2013, 9, 3293.

4. Li, K.; Li, S. L.; Huang W.; Yu, C. Y.*; Zhou, Y. F.*, MembrFactory: A Force Field and Composition Double Independent Universal Tool for Constructing Polyamide Reverse Osmosis Membranes, J. Coumput. Chem., 2019, DOI:10.1002/jcc.26015.

5. Li, S. L.; Yu, C. Y.; Zhou, Y. F.*, “Phase diagrams, mechanisms and unique characteristics of alternating-structured polymer self-assembly via simulations”, Sci. China Chem., 2019, 62, 226. 

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