Siretskiy Alexey, Elvingson Christer, Vorontsov-Velyaminov Pavel, Khan Malek O
Department of Physical and Analytical Chemistry, Uppsala University, Uppsala, Sweden.
Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jul;84(1 Pt 2):016702. doi: 10.1103/PhysRevE.84.016702. Epub 2011 Jul 7.
The sampling of compact configurations is crucial when investigating structural properties of semistiff polymers, like proteins and DNA, using Monte Carlo methods. A sampling scheme for a continuous model based on configuration biasing is introduced, tested, and compared with conventional methods. The proposed configuration biased Monte Carlo method, used together with the Wang-Landau sampling scheme, enables us to obtain any thermodynamic property within the statistical ensemble in use. Using the proposed method, it is possible to collect statistical data of interest for a wide range of compactions (from stretched up to several toroid loops) in a single computer experiment. A second-order-like stretched-toroid phase transition is observed for a semistiff polymer, and the critical temperature is estimated.
在使用蒙特卡罗方法研究半刚性聚合物（如蛋白质和DNA）的结构特性时，紧密构型的采样至关重要。本文介绍、测试了一种基于构型偏倚的连续模型采样方案，并将其与传统方法进行了比较。所提出的构型偏倚蒙特卡罗方法与王-兰道采样方案一起使用，使我们能够在所用的统计系综中获得任何热力学性质。使用所提出的方法，可以在单个计算机实验中收集广泛压实范围（从拉伸到几个环形环）内感兴趣的统计数据。观察到一种半刚性聚合物存在类似二阶的拉伸-环形相变，并估计了临界温度。
