论文标题
瞬时结合快速链接器的粗粒动力学
Coarse-grained dynamics of transiently-bound fast linkers
论文作者
论文摘要
快速接头和较慢的颗粒之间的瞬态键在物理和生物系统中广泛存在。尽管它们的结构和功能各不相同，但一个共同点是，与与与其结合的粒子的整体运动相比，接头在时间尺度上的扩散速度要快得多。这限制了需要高精度来解决这些不同时间尺度的数值和理论方法。因此，许多模型诉诸于有效但临时的动态，其中仅在绑定时才考虑接头运动。本文为这种粗粒的动力学提供了数学上的理由，该动态可在平衡下保持详细的平衡。我们的推导基于多尺度平均技术，并且广泛适用。我们通过对快速接头与慢速粒子结合的最小模型进行模拟来验证我们的结果。我们展示了如何将我们的框架应用于各种系统，包括具有多个接头的系统，绑定后的链接器加强链接或具有力依赖性解框的滑动键。重要的是，详细平衡的保存仅设置了结合与未连接速率的比率，但它不会限制结合动力学的详细表达。我们通过讨论各种结合动力学的选择如何影响宏观动力学来得出结论。
Transient bonds between fast linkers and slower particles are widespread in physical and biological systems. In spite of their diverse structure and function, a commonality is that the linkers diffuse on timescales much faster compared to the overall motion of the particles they bind to. This limits numerical and theoretical approaches that need to resolve these diverse timescales with high accuracy. Many models, therefore, resort to effective, yet ad-hoc, dynamics, where linker motion is only accounted for when bound. This paper provides a mathematical justification for such coarse-grained dynamics that preserves detailed balance at equilibrium. Our derivation is based on multiscale averaging techniques and is broadly applicable. We verify our results with simulations on a minimal model of fast linker binding to a slow particle. We show how our framework can be applied to various systems, including those with multiple linkers, stiffening linkers upon binding, or slip bonds with force-dependent unbinding. Importantly, the preservation of detailed balance only sets the ratio of the binding to the unbinding rates, but it does not constrain the detailed expression of binding kinetics. We conclude by discussing how various choices of binding kinetics may affect macroscopic dynamics.
