论文标题
模拟酶中的核和电子量子效应
Simulating nuclear and electronic quantum effects in enzymes
论文作者
论文摘要
对酶中化学反应增强的结构和动力学的准确处理需要明确处理电子和核量子效应。前者可以在从头算分子动力学（AIMD）模拟中捕获，而通过进行Ab Initio路径积分分子动力学（AI-PIMD）模拟可以包括后者。传统上，AIMD和AI-PIMD模拟对大型酶系统的计算过敏。现在，流媒体计算机体系结构和新算法加速路径积分模拟的最新发展使这些模拟对生物系统实用，从而使酶促反应以前所未有的细节阐明。在本章中，我们总结了这些最新的发展，并讨论了将AIMD和AI-PIMD模拟应用于酶的实际考虑因素。
An accurate treatment of the structures and dynamics that lead to enhanced chemical reactivity in enzymes requires explicit treatment of both electronic and nuclear quantum effects. The former can be captured in ab initio molecular dynamics (AIMD) simulations while the latter can be included by performing ab initio path integral molecular dynamics (AI-PIMD) simulations. Both AIMD and AI-PIMD simulations have traditionally been computationally prohibitive for large enzymatic systems. Recent developments in streaming computer architectures and new algorithms to accelerate path integral simulations now make these simulations practical for biological systems, allowing elucidation of enzymatic reactions in unprecedented detail. In this chapter, we summarize these recent developments and discuss practical considerations for applying AIMD and AI-PIMD simulations to enzymes.
