Li Wenjin, Ma Ao
Department of Bioengineering, the University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA.
J Chem Phys. 2016 Apr 7;144(13):134104. doi: 10.1063/1.4945337.
The molecular mechanism of a reaction is embedded in its transition path ensemble, the complete collection of reactive trajectories. Utilizing the information in the transition path ensemble alone, we developed a novel metric, which we termed the emergent potential energy, for distinguishing reaction coordinates from the bath modes. The emergent potential energy can be understood as the average energy cost for making a displacement of a coordinate in the transition path ensemble. Where displacing a bath mode invokes essentially no cost, it costs significantly to move the reaction coordinate. Based on some general assumptions of the behaviors of reaction and bath coordinates in the transition path ensemble, we proved theoretically with statistical mechanics that the emergent potential energy could serve as a benchmark of reaction coordinates and demonstrated its effectiveness by applying it to a prototypical system of biomolecular dynamics. Using the emergent potential energy as guidance, we developed a committor-free and intuition-independent method for identifying reaction coordinates in complex systems. We expect this method to be applicable to a wide range of reaction processes in complex biomolecular systems.
反应的分子机制蕴含于其过渡路径系综之中，即所有反应轨迹的完整集合。仅利用过渡路径系综中的信息，我们开发了一种新的度量，称之为“涌现势能”，用于区分反应坐标与浴模。涌现势能可理解为在过渡路径系综中使一个坐标发生位移的平均能量成本。其中，使浴模发生位移基本不产生成本，而移动反应坐标则成本显著。基于过渡路径系综中反应坐标和浴模行为的一些一般假设，我们用统计力学从理论上证明了涌现势能可作为反应坐标的基准，并通过将其应用于一个生物分子动力学的典型系统来证明其有效性。以涌现势能为指导，我们开发了一种无需反应进度参量且不依赖直觉的方法，用于识别复杂系统中的反应坐标。我们期望该方法适用于复杂生物分子系统中的广泛反应过程。
