粗粒化分子动力学模拟的价键限制修正势
Valency-bounding correction potential for coarse-grained molecular dynamics simulations
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中文总结 AI 辅助
本文提出价键限制修正（VBC），一种多体修正的通用短程成对势，无需角度自由度即可限制配位数，成本低，适用于GPU，可重现RNA重入聚集并修复热力学不稳定性。
中文摘要 AI 辅助
软物质和生命物质中的许多系统通过每个粒子的有限数量的键结合：蛋白质通过离散的表面斑块关联，核酸形成一对一接触，多价生物分子的相行为由其携带的结合位点数量控制。在模拟中，价键限制通常通过斑块粒子来强制执行，其各向异性势需要积分转动自由度，并将硬核与窄斑块结合，这迫使使用小时间步长，并将模型固定于通常未知、柔性或可移动的结合位点几何结构。我们引入了价键限制修正（VBC），这是一种对通用短程成对势的多体修正，当任一相互作用粒子的邻居数超过规定价键时，平滑地抑制吸引力。该修正不携带角度自由度，适用于软排斥核之上，并在邻居列表上通过两次遍历评估，成本与标准成对势相当。VBC将配位数驱动到规定价键，误差较低，而其团簇统计通过不受限制的环形成偏离Wertheim和Flory-Stockmayer预测。一个调整后的变体通过普通分子动力学交换键合伙伴，在高饱和度下将键寿命降低一个数量级。在GPU上，该修正的成本几乎与价键无关，相比斑块粒子参考实现达到近十倍的优势。我们通过重现重复扩增RNA的重入聚集来说明大规模应用，并表明VBC还修复了软核势与吸引的Fisher-Ruelle热力学不稳定性。VBC可作为HOOMD-blue的开源GPU插件获得。
英文摘要
Many systems in soft and living matter bind through a limited number of bonds per particle: proteins associate via discrete surface patches, nucleic acids form one-to-one contacts, and the phase behaviour of multivalent biomolecules is governed by the number of binding sites they carry. In simulations, valency limits are typically enforced with patchy particles, whose anisotropic potentials require integration of rotational degrees of freedom and combine hard cores with narrow patches, which forces small timesteps and commits the model to a fixed binding-site geometry that is often unknown, flexible or mobile. We introduce the valency-bounding correction (VBC), a many-body modification of generic short-range pairwise potentials that smoothly suppresses attraction once the neighbour count of either interacting particle exceeds a prescribed valency. The correction carries no angular degrees of freedom, applies on top of soft repulsive cores and evaluates in two passes over the neighbour list at the cost of a standard pairwise potential. The VBC drives the coordination number to the prescribed valency with low error, while its cluster statistics depart from Wertheim and Flory-Stockmayer predictions through unrestricted ring formation. A tuned variant exchanges bonded partners through ordinary molecular dynamics, reducing bond lifetimes at high saturation by an order of magnitude. On GPUs the cost of the correction is nearly independent of valency, reaching an almost tenfold advantage over a patchy-particle reference. We illustrate large-scale applications by reproducing the reentrant aggregation of repeat-expanded RNA, and show that the VBC also remedies the Fisher-Ruelle thermodynamic instability of soft-core potentials with attraction. The VBC is available as an open-source GPU plugin for HOOMD-blue.
