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Theory of DNA melting based on the Peyrard-Bishop model
Zhang, YL; Zheng, WM; Liu, JX; Chen, YZ; Zhang, YL , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China.
1997
发表期刊PHYSICAL REVIEW E
ISSN1063-651X
卷号56期号:6页码:7100-7115
摘要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.
部门归属Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China; Purdue Univ, Dept Phys, W Lafayette, IN 47907 USA
关键词Statistical-mechanics Nonlinear Model Thermal-denaturation Phase-transition Dynamics
学科领域Physics
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收录类别SCI
WOS记录号WOS:000071043500107
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文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/12403
专题理论物理所SCI论文
通讯作者Zhang, YL , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China.
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Zhang, YL,Zheng, WM,Liu, JX,et al. Theory of DNA melting based on the Peyrard-Bishop model[J]. PHYSICAL REVIEW E,1997,56(6):7100-7115.
APA Zhang, YL,Zheng, WM,Liu, JX,Chen, YZ,&Zhang, YL , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China..(1997).Theory of DNA melting based on the Peyrard-Bishop model.PHYSICAL REVIEW E,56(6),7100-7115.
MLA Zhang, YL,et al."Theory of DNA melting based on the Peyrard-Bishop model".PHYSICAL REVIEW E 56.6(1997):7100-7115.
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