Theory of DNA melting based on the Peyrard-Bishop model
Theory of DNA melting based on the Peyrard-Bishop model
复制标题
基于 Peyard-Bishop 模型的 DNA 熔解理论
DOI：
10.1103/physreve.56.7100
复制
发表时间：
1997
影响因子：
2.4
通讯作者：
Yu Zong Chen
中科院分区：
文献类型：
--
作者：
Yong;Wei;Jixing Liu;Yu Zong Chen
系统地研究了基于Peyrard-Bishop（PB）模型的DNA解链。研究了PB模型转移积分方程的本征值和本征向量，指出本征向量由两类组成：构成DNA分子内部态的离散束缚态和代表DNA分子解离态的连续非束缚态.另一个过程控制DNA的熔化-双链体和单链DNA之间的解离平衡的介绍，这导致了一个扩展的模型适用于现实的DNA链与有限数量的碱基对。在核展开的基础上，将系统热力学量的计算归结为矩阵级数的乘法运算。对模型块DNA的计算表明，该方法比分子动力学模拟更有效，并且具有足够高的精度来处理具有任意序列的天然DNA的解链。在高斯模型的基础上，讨论了模型的离散性效应和非线性效应。本文用传递积分方法计算了单胞内含有两个和三个碱基对的周期DNA的解链曲线，并考虑了边界效应。
The DNA melting based on the Peyrard-Bishop (PB) model is systematically investigated. Our study on the eigenvalues and eigenvectors of the transfer integral equation for the original PB model points out that the eigenvectors are composed of two kinds: discrete bound states that constitute the internal states of a DNA molecule and the continuous unbound states that represent its dissociated states. Another process controlling the melting of DNA-the dissociation equilibrium between duplex and single-stranded DNAs-is introduced, which leads to an extended model applicable for a realistic DNA chain with a finite number of base pairs. Based on the expansion of kernels, the calculations of the thermodynamic quantities of the system are reduced to multiplication of matrix series. Calculations on model block DNAs show the method is much more efficient than molecular dynamic simulation and has enough high precision to handle the melting of a natural DNA with arbitrary sequence. The discreteness effect and nonlinear effect of the model are discussed based on the Gaussian model. Rigorous melting curves for periodic DNA with two and three base pairs in a unit cell and boundary effects are presented by the transfer integral approach.