Inferring equilibrium transition rates from nonequilibrium protocols
Inferring equilibrium transition rates from nonequilibrium protocols
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从非平衡协议推断平衡转变率
DOI：
10.1016/j.bpj.2023.03.031
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发表时间：
2023
影响因子：
3.4
通讯作者：
Limmer, David T.
中科院分区：
文献类型：
--
作者：
Kuznets-Speck, Benjamin;Limmer, David T.
我们开发了一个理论推断平衡过渡率的轨迹驱动的时间依赖的力使用随机热力学的结果。应用川崎关系，用平衡态分布函数和超额耗散近似非平衡态分布函数，建立了非平衡态过渡态理论，估计了非平衡态协议对平衡态速率的增益.我们证明了我们的理论的效用在一个和两个维度，以及一个半柔性聚合物与反应性连接在三维的谐波捕获粒子的拉动的例子。我们希望我们的纯热力学方法将在分子模拟和力谱实验中找到使用。
We develop a theory for inferring equilibrium transition rates from trajectories driven by a time-dependent force using results from stochastic thermodynamics. Applying the Kawasaki relation to approximate the nonequilibrium distribution function in terms of the equilibrium distribution function and the excess dissipation, we formulate a nonequilibrium transition state theory to estimate the rate enhancement over the equilibrium rate due to the nonequilibrium protocol. We demonstrate the utility of our theory in examples of pulling of harmonically trapped particles in one and two dimensions, as well as a semiflexible polymer with a reactive linker in three dimensions. We expect our purely thermodynamic approach will find use in both molecular simulation and force spectroscopy experiments.