McDonald Jared, von Spakovsky Michael R, Reynolds William T
Materials Science and Engineering Department, Virginia Tech, Blacksburg, Virginia 24061, USA.
Mechanical Engineering Department, Virginia Tech, Blacksburg, Virginia 24061, USA.
J Chem Phys. 2023 Mar 14;158(10):104904. doi: 10.1063/5.0137444.
The steepest-entropy-ascent quantum thermodynamic (SEAQT) framework is used to explore the influence of heating and cooling on polymer chain folding kinetics. The framework predicts how a chain moves from an initial non-equilibrium state to stable equilibrium along a unique thermodynamic path. The thermodynamic state is expressed by occupation probabilities corresponding to the levels of a discrete energy landscape. The landscape is generated using the Replica Exchange Wang-Landau method applied to a polymer chain represented by a sequence of hydrophobic and polar monomers with a simple hydrophobic-polar amino acid model. The chain conformation evolves as energy shifts among the levels of the energy landscape according to the principle of steepest entropy ascent. This principle is implemented via the SEAQT equation of motion. The SEAQT framework has the benefit of providing insight into structural properties under non-equilibrium conditions. Chain conformations during heating and cooling change continuously without sharp transitions in morphology. The changes are more drastic along non-equilibrium paths than along quasi-equilibrium paths. The SEAQT-predicted kinetics are fitted to rates associated with the experimental intensity profiles of cytochrome c protein folding with Rouse dynamics.
采用最大熵上升量子热力学（SEAQT）框架来探究加热和冷却对聚合物链折叠动力学的影响。该框架预测了一条链如何沿着一条独特的热力学路径从初始非平衡态转变为稳定平衡态。热力学状态由对应于离散能量景观各能级的占据概率来表示。该景观是通过将复制交换王-朗道方法应用于由具有简单疏水-极性氨基酸模型的疏水和极性单体序列表示的聚合物链而生成的。根据最大熵上升原理，链构象随着能量在能量景观各能级之间的转移而演化。这一原理通过SEAQT运动方程得以实现。SEAQT框架的优点在于能够深入了解非平衡条件下的结构特性。加热和冷却过程中的链构象持续变化，形态上没有明显的转变。与准平衡路径相比，沿着非平衡路径的变化更为剧烈。将SEAQT预测的动力学与细胞色素c蛋白折叠的实验强度分布相关的速率进行拟合，采用了Rouse动力学。
