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国防科技大学戴佳钰教授团队和中科院半导体所汪林望教授团队针对上述假说开展合作研究，利用一种新颖的实时含时密度泛函理论方法——自然轨道分支方法，该方法可以有效考虑细致平衡，量子退相干以及化学反应随机轨迹等效应，研究了有机样品受到电子束辐照后的动力学过程。他们首先用自然轨道分支方法研究了不同温度下分子解离过程，发现分子受到电子束辐照后电离导致分子断裂并不受温度的影响，并且还发现分子碎裂模式和电子跃迁之间存在一定联系，相似的电子跃迁路径会导致相似的断键情况，在不同温度下的结论也是相似的。然后他们用从头算分子动力学对分子裂解产生的碎片动力学过程进行模拟，发现该阶段的动力学过程是低温保护机制的关键，在不同温度条件下碎片运动情况大相径庭；低温下水分子会形成“牢笼”，将碎片困住，碎片之间则会发生重组；而室温下碎片会四处扩散，很难发生重组。该研究为低温防护机制中的“笼”效应提供了直接的支持，为辐射防护提供了一定的见解。

 Figure 1 Conceptual diagram of the cage effect

论文近期发表于npj Computational Materials 10:115 (2024)，英文标题与摘要如下，点击左下角“阅读原文”可以自由获取论文PDF。

The cage effect of electron beam irradiation damage in cryo-electron microscopy 

Yi Li, Dong-Dong Kang, Jia-Yu Dai & Lin-Wang Wang

Electron beam irradiation can cause damage to biological and organic samples, as determined via transmission electron microscopy (TEM). Cryo-electron microscopy (cryo-EM) significantly reduces such damage by quickly freezing the environmental water around organic molecules. However, there are multiple hypotheses about the mechanism of cryo-protection in cryo-EM. A lower temperature can cause less molecular dissociation in the first stage, or frozen water can have a “cage” effect by preventing the dissociated fragments from flying away. In this work, we use real-time time-dependent density functional theory molecular dynamics(rt-TDDFT-MD) simulations to study the related dynamics. We use our recently developed natural orbital branching (NOB) algorithm to describe the molecular dissociation process after the molecule is ionized. We find that despite the difference in surrounding water molecules at different temperatures, the initial dissociation process is similar. On the other hand, the dissociated fragments fly away at room temperature, while they remain in the same cage when frozen water is used. Our results provide direct support for the cage effect mechanism.