论文标题

使用最陡峭的量子量子热力学框架预测聚合物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

论文作者

McDonald, Jared, von Spakovsky, Michael R., Reynolds Jr, William T.

论文摘要

副本交换Wang-Landau方法用于估计由使用HP蛋白模型组成的简单疏水和极性序列组成的聚合物的能量景观。使用最陡峭的量子量子热力学(SEAQT)框架的运动方程进行派生能量景观能量水平之间状态转变的计算。 SEAQT框架使从任意的准平衡或非平衡初始状态到稳定平衡的独特动力学路径成为可能。使用SEAQT进行的计算需要大大减少计算时间与可比的蒙特卡洛模拟,同时提供原本不可用的热力学和结构特性。状态平均结构参数的预期值用于产生基于状态的进化的代表性重建。结果表明,没有明显折叠阶段的状态之间的连续过渡。与沿准平衡路径相比,加热和冷却过程中链构象的变化更为剧烈。此外,将SEAQT衍生的动力学与实验得出的强度曲线进行了比较,这些强度谱图使用Rouse动态关系描述了细胞色素C蛋白的动力学。

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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