用于软物质与生物模拟的纯FENE键势：理论、HOOMD-blue实现及在聚合物、胶体和膜系统中的应用
Pure FENE Bond Potential for Soft Matter and Biological Simulations: Theory, HOOMD-blue Implementation, and Applications to Polymer, Colloidal, and Membrane Systems
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中文总结 AI 辅助
该研究在HOOMD-blue中实现了独立的纯FENE键势，将键可伸长性与非键合相互作用解耦，可与多种对相互作用组合，在聚合物、胶体、膜模拟中实现对键力学与结构组织的独立控制。
中文摘要 AI 辅助
有限可伸长非线性弹性（FENE）势被广泛用作聚合物、软物质、胶体和生物系统粗粒化模拟中的键合相互作用。在经典的Kremer--Grest框架中，FENE键合与短程的Weeks--Chandler--Andersen（WCA）相互作用相结合，以提供有限的键可伸长性以及排除体积排斥。尽管这种组合非常成功，但它本质上将键合弹性与非键合相互作用耦合在一起，限制了独立控制这两个贡献的能力。在此，我们在HOOMD-blue中引入了一种独立的FENE键势，其中有限的键可伸长性独立于非键合相互作用的选择来实现。这种表述允许相同的FENE键势与WCA、Lennard--Jones或其他对相互作用组合，而无需修改键合相互作用本身。我们在粗粒化聚合物链、胶体网络和基于网格的生物膜模型中展示了这种独立表述的实用性。在这些系统中，没有短程排除体积稳定的纯FENE键合会产生明显的结构收缩，而添加WCA排斥则会抑制这种塌陷并保留有限的、空间延展的结构。这些结果表明，将有限的键可伸长性与空间位阻相互作用分离，可实现对局部键力学和集体结构组织的独立控制。因此，独立的FENE表述为粗粒化模拟提供了一个模块化框架，其中分子连接性和非键合相互作用代表了不同的物理机制。
英文摘要
The finitely extensible nonlinear elastic (FENE) potential is widely used as a bonded interaction in coarse-grained simulations of polymers, soft matter, colloids, and biological systems. In the classical Kremer--Grest framework, FENE bonding is combined with a short-range Weeks--Chandler--Andersen (WCA) interaction to provide finite bond extensibility together with excluded-volume repulsion. Although this combination is highly successful, it intrinsically couples bonded elasticity to the nonbonded interaction, limiting the ability to independently control these two contributions. Here, we introduce a standalone FENE bond potential in HOOMD-blue in which finite bond extensibility is implemented independently of the choice of nonbonded interaction. This formulation allows the same FENE bond potential to be combined with WCA, Lennard--Jones, or other pair interactions without modifying the bonded interaction itself. We demonstrate the utility of the standalone formulation in coarse-grained polymer chains, colloidal networks, and mesh-based biological membrane models. Across these systems, Pure FENE bonding without short-range excluded-volume stabilization produces pronounced structural contraction, whereas the addition of WCA repulsion suppresses this collapse and preserves finite, spatially extended structures. These results demonstrate that separating finite bond extensibility from steric interactions provides independent control over local bond mechanics and collective structural organization. The standalone FENE formulation therefore provides a modular framework for coarse-grained simulations in which molecular connectivity and nonbonded interactions represent distinct physical mechanisms.
