计算稀有事件的跃迁率：当Kramers理论遇到自由能景观时
Computing Transition Rates for Rare Event: When Kramers Theory meets Free Energy Landscape
摘要：
计算与稀有事件动力学相关的反应轨迹和自由能（FE）景观是理解复杂系统动力学的关键。分析FE表面上发生的基本动力学已成为中央计算过渡率。在生物物理学和软凝聚态物质中最常遇到的过阻尼极限中，Kramers理论（KT）已被证明在恢复正确的动力学方面相当成功。然而，在构型熵与能量竞争的复杂系统中获得速率常数的额外计算在概念上和计算上仍然具有挑战性。建立在KT和metadadenics框架，速率表示在沿最小FE路径测量的FE障碍的高度和配置熵的辅助措施。我们适用于两个不同的问题，我们的方法与模拟和实验表现出良好的一致性，并可以提出显着的改进标准KT。
英文摘要：
Computing reactive trajectories and free energy (FE) landscapes associated to rare event kinetics is key to understanding the dynamics of complex systems. The analysis of the FE surface on which the underlying dynamics takes place has become central to compute transition rates. In the overdamped limit, most often encountered in biophysics and soft condensed matter, the Kramers' Theory (KT) has proved to be quite successful in recovering correct kinetics. However, the additional calculation to obtain rate constants in complex systems where configurational entropy is competing with energy is still challenging conceptually and computationally. Building on KT and the metadynamics framework, the rate is expressed in terms of the height of the FE barrier measured along the minimum FE path and an auxiliary measure of the configurational entropy. We apply the formalism to two different problems where our approach shows good agreement with simulations and experiments and can present significant improvement over the standard KT.
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