用扩散模型先验采样过渡态,无需初始猜测即可发现多条反应路径。
A Priori Sampling of Transition States with Guided Diffusion
- 训练扩散模型学习稳定构象,通过条件分数引导采样到势能面分界处。
- 在2D势场和生物分子系统上精确找到过渡态,可发现多条反应路径。
- 适合研究复杂反应机理的科研人员,尤其适用于无先验知识的场景。
过渡态是势能面上的一阶鞍点,决定化学反应与构象变化的动力学与机理。定位过渡态困难,因反应路径拓扑复杂且存在多种可能路径。现有方法依赖对路径或反应坐标的启发式假设,当缺乏良好初始猜测或猜测限制了其他潜在路径时,适用性受限。本文提出ASTRA(A Priori Sampling of TRAnsition States with Guided Diffusion),将过渡态搜索重构为生成模型推理阶段的缩放问题。ASTRA在已知亚稳态构象上训练基于得分的扩散模型,通过条件得分的合理组合,引导推理至分隔亚稳态盆地的等密度面。随后,通过得分对齐上升(SAA)过程,从条件得分差中近似反应坐标,并结合物理力驱动收敛至一阶过渡态。在二维势场、生物分子构象变化及化学反应等基准测试中,ASTRA以高精度定位过渡态并发现多条反应路径,支持复杂分子系统的机理研究。
原文摘要 · Abstract (English)
Transition states, the first-order saddle points on the potential energy surfaces, govern the kinetics and mechanisms of chemical reactions and conformational changes. Locating them is challenging because transition pathways are topologically complex and can proceed via an ensemble of diverse routes. Existing methods address these challenges by introducing heuristic assumptions about the pathway or reaction coordinates, which limits their applicability when a good initial guess is unavailable or when the guess precludes alternative, potentially relevant pathways. We propose to bypass such heuristic limitations by introducing ASTRA, A Priori Sampling of TRAnsition States with Guided Diffusion, which reframes the transition state search as an inference-time scaling problem for generative models. ASTRA trains a score-based diffusion model on configurations from known metastable states. Then, ASTRA guides inference toward the isodensity surface separating the basins of metastable states via a principled composition of conditional scores. A Score-Aligned Ascent (SAA) process then approximates a reaction coordinate from the difference between conditioned scores and combines it with physical forces to drive convergence onto first-order transition states. Validated on benchmarks ranging from 2D potentials to biomolecular conformational changes and a chemical reaction, ASTRA locates transition states with high precision and discovers multiple reaction pathways, enabling mechanistic studies of complex molecular systems.
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