Center for Cell and Virus Theory, Indiana University, Bloomington, Indiana 47405, USA.
J Chem Phys. 2011 Jan 28;134(4):044104. doi: 10.1063/1.3524532.
Order parameters (OPs) characterizing the nanoscale features of macromolecules are presented. They are generated in a general fashion so that they do not need to be redesigned with each new application. They evolve on time scales much longer than 10(-14) s typical for individual atomic collisions/vibrations. The list of OPs can be automatically increased, and completeness can be determined via a correlation analysis. They serve as the basis of a multiscale analysis that starts with the N-atom Liouville equation and yields rigorous Smoluchowski/Langevin equations of stochastic OP dynamics. Such OPs and the multiscale analysis imply computational algorithms that we demonstrate in an application to ribonucleic acid structural dynamics for 50 ns.
本文提出了用于描述生物大分子纳米级特征的序参量（order parameters，OPs）。这些序参量是通过通用方式生成的，因此不需要针对每个新应用重新设计。它们的演化时间尺度比单个原子碰撞/振动的典型时间尺度 10(-14) s 长得多。OP 的列表可以自动增加，并且可以通过相关分析来确定其完整性。这些序参量是多尺度分析的基础，该分析从 N 原子刘维尔方程开始，得出了严格的随机 OP 动力学斯莫卢霍夫斯基/朗之万方程。这些序参量和多尺度分析意味着我们在应用于 RNA 结构动力学的 50 ns 中展示的计算算法。
