A Study of the Morphology, Dynamics, and Folding Pathways of Ring Polymers with Supramolecular Topological Constraints Using Molecular Simulation and Nonlinear Manifold Learning,Macromolecules

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A Study of the Morphology, Dynamics, and Folding Pathways of Ring Polymers with Supramolecular Topological Constraints Using Molecular Simulation and Nonlinear Manifold Learning
Macromolecules ( IF 5.1 ) Pub Date : 2018-01-09 00:00:00 , DOI: 10.1021/acs.macromol.7b01684
Jiang Wang ₁ , Andrew L. Ferguson ₁

Affiliation

Ring polymers are prevalent in natural and engineered systems, including circular bacterial DNA, crown ethers for cation chelation, and mechanical nanoswitches. The morphology and dynamics of ring polymers are governed by the chemistry and degree of polymerization of the ring and intramolecular and supramolecular topological constraints such as knots or mechanically interlocked rings. In this study, we perform molecular dynamics simulations of polyethylene ring polymers at two different degrees of polymerization and in different topological states, including a trefoil knot, catenane state (two interlocked rings), and Borromean state (three interlocked rings). We employ nonlinear manifold learning to extract the low-dimensional free energy surface to which the structure and dynamics of the polymer chain are effectively restrained. The free energy surfaces reveal how the degree of polymerization and topological constraints affect the thermally accessible conformations, chiral symmetry breaking, and folding and collapse pathways of the rings and present a means to rationally engineer ring size and topology to stabilize particular conformational states and folding pathways. We compute the rotational diffusion of the ring in these various states as a crucial property required for the design of engineered devices containing ring polymer components.

中文翻译：

利用分子模拟和非线性流形学习研究具有超分子拓扑约束的环状聚合物的形态，动力学和折叠途径

环状聚合物普遍存在于天然和工程系统中，包括环状细菌DNA，用于阳离子螯合的冠醚和机械纳米开关。环聚合物的形态和动力学受环的化学性质和聚合度以及分子内和超分子的拓扑约束（例如结或机械互锁的环）支配。在这项研究中，我们在两种不同的聚合度和不同的拓扑状态（包括三叶结，链烷状态（两个互锁环）和硼烷状态（三个互锁环））中进行聚乙烯环聚合物的分子动力学模拟。我们采用非线性流形学习来提取低维自由能表面，该表面有效地限制了聚合物链的结构和动力学。自由能表面揭示了聚合度和拓扑约束如何影响环的热可及构象，手性对称性断裂以及折叠和折叠路径，并提供了合理设计环大小和拓扑结构以稳定特定构象状态和折叠路径的方法。我们计算在这些不同状态下环的旋转扩散，这是设计包含环聚合物成分的工程设备所需的关键特性。

更新日期：2018-01-09

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