AI 中文总结
本文提出一种用归一化替代边界条件的变分原理，仅需少量输入即可高效估计高维反应坐标与速率，成功应用于多种蛋白质的相关计算。
AI 中文摘要
反应坐标是稀有转变过程的最优描述，可确定过渡态并计算反应速率，涵盖蛋白质折叠、晶体成核等过程。它最小化狄利克雷能量，最小值对应反应通量，要求试探函数在反应物态取0、产物态取1。高维场景下这类试探空间难以构建，本文重写变分原理，用边界可观测量保真度的归一化替代边界条件，允许任何试探函数，包括无法满足边界值的函数。基于此，仅利用已有的平衡或重加权构型、扩散常数估计及两个态的定义，从投影坐标的一维分布估计高维反应坐标与反应速率，最优解为闭式形式，计算成本低。本文在全扭转空间中得到AIB9和villin HP-35的反应坐标，仅用伞形采样得到chignolin的折叠与去折叠速率。
英文摘要
The committor is the optimal reaction coordinate for a rare transition: it pinpoints the transition state and fixes the rate, and it governs events from protein folding to crystal nucleation. It minimises a Dirichlet energy, whose value at the minimum is the reactive flux, over functions that vanish on the reactant state and equal one on the product state. In high dimensions such a trial space is very hard to build. Here we rewrite the variational principle so that the boundary conditions are replaced by a normalisation of one boundary observable, the fidelity. Any trial function is then admissible, including functions that cannot satisfy the boundary values at all. On this basis we estimate the high-dimensional committor and rates from one-dimensional profiles along projected coordinates, taking as input only pre-existing equilibrium or reweighted configurations, a diffusion constant estimate, and the two state definitions. The optimum has a closed form that is cheap to evaluate. We obtain committors for AIB9 and villin HP-35 in full torsion space, and folding and unfolding rates for chignolin from umbrella sampling alone.
