Heat conductivity of DNA double helix.
Heat conductivity of DNA double helix.
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DNA 双螺旋的热导率。
DOI：
10.1103/physrevb.83.245406
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发表时间：
2011
期刊：
影响因子：
--
通讯作者：
Onufriev,AlexeyV
中科院分区：
文献类型：
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作者：
Savin,AlexanderV;Mazo,MikhailA;Kikot,IrinaP;Manevitch,LeonidI;Onufriev,AlexeyV
分离的单分子DNA片段的热导率对于纳米技术很重要，但尚未通过实验测量。基于简化（1D）模型的理论估计预测了极高的热导率。为了研究单分子DNA的热性质，我们开发了一种3D粗粒度（CG）模型，该模型保留了完整原子描述的真实性，但效率明显更高。在所提出的模型中，每个核苷酸由六个粒子或颗粒表示;颗粒通过基于完善的全原子势函数从经典分子动力学（MD）轨迹推断的有效势相互作用。CG和相应的全原子模型之间的10 ns长的MD轨迹的比较显示出类似的均方根偏差从典型的B型DNA，和类似的结构波动。同时，CG模型的速度要快10到100倍，具体取决于模拟中DNA片段的长度。从CG模型得到的色散曲线的分析产生的纵向声速和扭转刚度与现有的实验密切一致。CG模型的计算效率使得计算单个DNA分子的热导率成为可能，而这在实验上还不可用。对于均质（polyG-polyC）DNA，估计的电导率系数为0.3W/mK，其是水的热导率值的一半。这一结果与预测异常（无限）热导率的简化的有效一维链（“弹簧上的珠子”）的热导率估计形成鲜明对比。因此，完整的3D字符的DNA双螺旋保留在所提出的模型似乎是必不可少的描述在单分子水平上的DNA的热性质。
Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal conductivity. To investigate thermal properties of single molecule DNA we have developed a 3D coarse-grained (CG) model that retains the realism of the full all-atom description, but is significantly more efficient. Within the proposed model each nucleotide is represented by six particles or grains; the grains interact via effective potentials inferred from classical molecular dynamics (MD) trajectories based on a well-established all-atom potential function. Comparisons of 10 ns long MD trajectories between the CG and the corresponding all-atom model show similar root-mean-square deviations from the canonical B-form DNA, and similar structural fluctuations. At the same time, the CG model is 10 to 100 times faster depending on the length of the DNA fragment in the simulation. Analysis of dispersion curves derived from the CG model yields longitudinal sound velocity and torsional stiffness in close agreement with existing experiments. The computational efficiency of the CG model makes it possible to calculate thermal conductivity of a single DNA molecule not yet available experimentally. For homogeneous (polyG-polyC) DNA, the estimated conductivity coefficient is 0.3 W/mK which is half the value of thermal conductivity for water. This result is in stark contrast with estimates of thermal conductivity for simplified, effectively 1D chains (“beads on a spring”) that predict anomalous (infinite) thermal conductivity. Thus, the full 3D character of DNA double-helix retained in the proposed model appears to be essential for describing thermal properties of DNA at a single molecule level.