从非平衡实验方案推断平衡转变速率。
Inferring equilibrium transition rates from nonequilibrium protocols.
机构信息
Biophysics Graduate Group, University of California, Berkeley, Berkeley, California.
Chemistry Department, University of California, Berkeley, Berkeley, California; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California; Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California; Kavli Energy NanoSciences Institute, University of California, Berkeley, Berkeley, California.
出版信息
Biophys J. 2023 May 2;122(9):1659-1664. doi: 10.1016/j.bpj.2023.03.031. Epub 2023 Mar 24.
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.
我们应用随机热力学的研究成果，提出了一种理论，用于从时变力驱动的轨迹中推断平衡跃迁速率。我们利用 Kawasaki 关系，将非平衡分布函数用平衡分布函数和过剩耗散来近似，从而构建了一个非平衡过渡态理论，来估算由于非平衡协议而导致的相对于平衡速率的速率增强。我们在一维和二维的谐波囚禁粒子的牵引以及三维的带有反应性连接体的半柔性聚合物的示例中展示了我们理论的有效性。我们预计我们的纯热力学方法将在分子模拟和力谱实验中都有应用。
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