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摘要翻译：
文献中可用的统计DNA模型通常是只考虑碱基对状态（未断裂或断裂）的有效模型。由于断键或气泡序列的有效弯曲刚度比双链态降低了30倍，因此需要在更一般的介观模型中包含分子构象自由度。在本文中，我们提出了一个描述内部碱基对状态的一维Ising模型，耦合到描述链构型的离散蠕虫链模型[J.Palmeri,M.Manghi,N.Destainville,Phys.Rev.Lett.99，088103(2007)]。这种耦合模型的精确求解采用传输矩阵技术，它类似于量子二态双原子分子的路径积分处理。当链涨落积分后，变性转变温度和宽度自然地表现为一个明确定义的哈密顿量模型参数的显函数，揭示了转变是由气泡和双链段之间弯曲（熵主导）自由能的差异驱动的。计算得到的熔化曲线（开碱基对的分数）与实验得到的PolyDA-PolyDT的熔化曲线符合得很好。预测的均方半径随温度的变化为实验观察到的热粘度转变提供了一个相干的新解释。最后，详细研究了DNA链长度的影响，强调了有限尺寸效应的重要性，即使对于几千个碱基对组成的DNA也是如此。
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英文标题：
《Thermal denaturation of fluctuating finite DNA chains: the role of
bending rigidity in bubble nucleation》
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作者：
John Palmeri, Manoel Manghi and Nicolas Destainville
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最新提交年份：
2007
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分类信息：
一级分类：Physics 物理学
二级分类：Soft Condensed Matter 软凝聚态物质
分类描述：Membranes, polymers, liquid crystals, glasses, colloids, granular matter
膜，聚合物，液晶，玻璃，胶体，颗粒物质
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一级分类：Physics 物理学
二级分类：Statistical Mechanics 统计力学
分类描述：Phase transitions, thermodynamics, field theory, non-equilibrium phenomena, renormalization group and scaling, integrable models, turbulence
相变，热力学，场论，非平衡现象，重整化群和标度，可积模型，湍流
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英文摘要：
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of broken bonds, or bubble, compared to the double stranded state, the inclusion of the molecular conformational degrees of freedom in a more general mesoscopic model is needed. In this paper we do so by presenting a 1D Ising model, which describes the internal base pair states, coupled to a discrete worm like chain model describing the chain configurations [J. Palmeri, M. Manghi, and N. Destainville, Phys. Rev. Lett. 99, 088103 (2007)]. This coupled model is exactly solved using a transfer matrix technique that presents an analogy with the path integral treatment of a quantum two-state diatomic molecule. When the chain fluctuations are integrated out, the denaturation transition temperature and width emerge naturally as an explicit function of the model parameters of a well defined Hamiltonian, revealing that the transition is driven by the difference in bending (entropy dominated) free energy between bubble and double-stranded segments. The calculated melting curve (fraction of open base pairs) is in good agreement with the experimental melting profile of polydA-polydT. The predicted variation of the mean-square-radius as a function of temperature leads to a coherent novel explanation for the experimentally observed thermal viscosity transition. Finally, the influence of the DNA strand length is studied in detail, underlining the importance of finite size effects, even for DNA made of several thousand base pairs.
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PDF链接：
https://arxiv.org/pdf/709.2843
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