标题： 染色质回收：组蛋白八聚体和染色质纤维的方向识别驱动自组装 显示英文标题

标题： ChromRec: Directional Recognition-Driven Self-Assembly of Histone Octamer and Chromatin Fiber

摘要： 理解跨多个时空尺度的染色质动态需要能够调和生物学特异性与基于物理的相互作用以及计算可处理性的模型。 我们提出了一种模块化、具有识别功能的超粗粒度（UCG）框架，该框架使用位点特异性、非中心的识别势能来捕捉组蛋白-DNA和组蛋白-组蛋白相互作用。 这些识别位点结合通用的吸引力和排斥力项，编码方向性和化学计量学准确的组装规则。 基准模拟表明，这种方案能够稳健地驱动几何正确的组蛋白八聚体的自组装，并实现稳定的核小体形成。 该模型还支持可调节的分辨率，可以根据生物问题简化八聚体内部、核小体或纤维级别的结构。 这种灵活性对于探索由表观遗传调控驱动的染色质重组特别有用。 虽然该框架是为染色质开发的，但它可以推广到由分子识别控制的其他多价组装。 显示英文摘要

摘要： Understanding chromatin dynamics across multiple spatiotemporal scales requires models that reconcile biological specificity with physics-based interactions and computational tractability. We present a modular, recognition-enabled ultra-coarse-grained (UCG) framework that captures both histone-DNA and histone-histone interactions using site-specific, off-center Recognition potentials. These recognition sites, combined with generic attractive and repulsive terms, encode directional and stoichiometrically faithful assembly rules. Benchmark simulations demonstrate that this scheme robustly drives the self-assembly of geometrically correct histone octamers and enables stable nucleosome formation. The model also supports tunable resolution, allowing simplification of intra-octamer, nucleosomal, or fiber-level structures depending on the biological question. This flexibility is especially useful for exploring chromatin reorganization driven by epigenetic regulation. While developed with chromatin in mind, our framework generalizes to other multivalent assemblies governed by molecular recognition.