用最速熵升量子热力学框架预测Polymer链的非平衡折叠行为
Predicting Non-Equilibrium Folding Behavior of Polymer Chains using the Steepest-Entropy-Ascent Quantum Thermodynamic Framework
摘要：
使用HP蛋白质模型，使用能量交换Wang-Landau方法来估计由简单疏水和极性序列组成的聚合物的能量景观。使用最陡熵上升量子热力学（SEAQT）框架的运动方程的计算的能量景观的能级之间的状态转换。SEAQT框架使得确定从任意准平衡或非平衡初始状态到稳定平衡的唯一动力学路径成为可能。与可比较的蒙特卡罗模拟相比，使用SEAQT进行的计算需要显著减少的计算时间，同时提供否则不可用的热力学和结构性质。状态平均结构参数的预期值用于产生计算的基于状态的演化的代表性重建。结果表明，状态之间的连续过渡，没有明显的折叠阶段。在加热和冷却过程中，链构象的变化沿非平衡路径比沿准平衡路径更剧烈。此外，SEAQT衍生的动力学进行比较，实验得出的强度曲线描述的细胞色素c蛋白质的动力学，使用劳斯动态关系。
英文摘要：
The Replica Exchange Wang-Landau Method is used to estimate the energy landscape of a polymer composed of a simple hydrophobic and polar sequence using the HP protein model. Calculations of state transitions between the energy levels of the derived energy landscape are made using an equation of motion from the steepest-entropy-ascent quantum thermodynamic (SEAQT) framework. The SEAQT framework makes it possible to determine the unique kinetic paths from an arbitrary quasi-equilibrium or non-equilibrium initial state to stable equilibrium. Calculations performed with SEAQT require significantly reduced computational time versus comparable Monte Carlo simulations while providing otherwise unavailable thermodynamic and structural properties. Expected values for state averaged structural parameters are used to produce representative reconstructions of the calculated state-based evolution. Results show continuous transitions between states with no distinct folding phases. Changes in chain conformations during heating and cooling are more drastic along non-equilibrium paths than along quasi-equilibrium paths. In addition, SEAQT-derived kinetics are compared to experimentally derived intensity profiles describing the kinetics of the cytochrome c protein using Rouse dynamic relations.
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