基于非平稳局域投影分布导出的GLE中的蛋白质折叠位置依赖摩擦
Position-dependent friction in protein folding from a GLE derived with a non-stationary localized projection distribution
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中文总结 AI 辅助
本文利用非平稳投影分布导出新型广义朗之万方程，揭示蛋白质折叠中摩擦依赖可观测值，并在绒毛蛋白和α-螺旋聚丙氨酸中证实折叠态摩擦更高。
中文摘要 AI 辅助
广义朗之万方程（GLE）是多体系统一般可观测量的积分微分运动方程，可通过投影算子形式严格推导。在标准推导中，投影使用平稳的典范相空间分布。本文使用非平稳投影分布导出一类新型GLE，该分布将初始系综约束在相空间中可观测值固定为$A_0$的超曲面上。因此，所有GLE参数，特别是记忆摩擦核，都依赖于$A_0$，并且可以从不采样整个相空间的短时模拟中提取。将该非平稳GLE应用于蛋白质折叠轨迹，我们发现对于绒毛蛋白和$α$-螺旋聚丙氨酸片段，折叠态的总摩擦更高。这些结果表明，可观测值依赖的摩擦效应不可忽略，并且可以通过约束投影方案导出的非平稳GLE加以考虑。
英文摘要
The Generalized Langevin Equation (GLE) is an integro-differential equation of motion for a general observable of a many-body system and is rigorously derived using the projection operator formalism. In the standard derivation, a stationary canonical phase space distribution is used for the projection. Here, we derive a novel class of GLEs using a non-stationary projection distribution that constrains the initial ensemble to a hypersurface in phase space on which the observable has a fixed value $A_0$. As a result, all GLE parameters, and in particular the memory friction kernel, depend on $A_0$ and can be extracted from short simulations that do not sample the entire phase space. Applying this non-stationary GLE to protein folding trajectories, we find for villin and an $α$-helical poly-alanine segment that the total friction is higher in the folded state. These results demonstrate that observable-dependent friction effects are non-negligible and can be accounted for using non-stationary GLEs derived by constrained projection schemes.
发表机构
- Freie Universität Berlin（柏林自由大学）
- Cairo University（开罗大学）
机构由 AI 辅助整理，请以论文原文为准。
