揭示分子动力学中罕见事件的原子机制
Jakob J Kresse1, Alexander Sikorski1,2, Vikram Sunkara1
1Computational Molecular Design, Zuse Institut Berlin, Berlin 14195, Germany.
Journal of chemical theory and computation
|February 23, 2026
概括
分子动力学罕见事件的原子机制 (AMORE-MD) 框架揭示了分子转换的原子细节. 它增强了深度学习的解释性,以便在没有先前路径知识的情况下理解罕见事件.
科学领域:
- 计算化学的计算化学
- 分子动力学模拟模型
- 生物物理学的生物物理.
背景情况:
- 了解分子动力学中罕见的构造转变至关重要.
- 可解释的反应坐标对于分析这些事件至关重要.
- 当前的方法往往需要先前了解路径或终点.
研究的目的:
- 引入分子动力学 (AMORE-MD) 框架中罕见事件的原子机制.
- 通过将它们与原子化机制联系起来,提高深度学习反应坐标的解释性.
- 能够在没有对集体变量,途径或终点的先验知识的情况下进行分析.
主要方法:
- AMORE-MD使用ISOKANN算法来学习代表缓慢过程的神经成员函数.
- 过渡路径被重建为与已学习函数的梯度对齐的最小能量路径.
- 原子贡献量化使用梯度基于灵敏度分析.
- 代增强采样改善了罕见事件的覆盖范围.
主要成果:
- 该框架成功地恢复了对基准系统的已知机制.
- 在过渡过程中确定了可化学解释的原子重组.
- 该方法在Müller-Brown潜力,氨酸二和VGVAPG六上得到了验证.
结论:
- AMORE-MD提供了一种强大的工具,用于揭示分子动力学中罕见事件的原子化机制.
- 该框架提高了用于分子模拟的深度学习模型的可解释性.
- 它提供了一种数据驱动的方法来研究没有预定义变量的复杂构造变化.
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