碱基对序列对B-DNA热导率的影响
Effect of base-pair sequence on B-DNA thermal conductivity
摘要：
采用经典的分子动力学（MD）模拟方法对双链（ds）B-DNA的热导率进行了系统的研究。改变碱基对对双链DNA的热导率的影响，需要在分子水平上进行研究。因此，在这项工作中，首先分析了四个序列，即poly（A），poly（G），poly（CG）和poly（AT）。首先，在300 K下，这些序列的长度在4-40个碱基对（bp）之间变化，并计算相应的热导率（$\mathrmκ$）。其次，在100 - 400 K之间的温度依赖的热导率在50 K的步骤中在28 bp长度获得。本文采用Müller-Plathe逆非平衡分子动力学（RNEMD）方法，通过设定温度梯度，得到了所有导热系数。此外，基于AT和CG序列的混合序列，即$\mathrm{A(CG)_{n}T}$（n=3-7）、$\mathrm{ACGC(AT)_{m}GCGT}$（m=0-5）和$\mathrm{ACGC(AT)_{n}AGCGT}$（n=1-4）可以是更好的热电性的假设，研究了这些序列。1-三维晶格被认为在较长的长度上具有发散的热导率，这违反了傅立叶定律。这些都遵循幂律，其中$\mathrm{κ\propto\ L^β}$。在较长的长度上，指数$\mathrmβ$需要满足发散热导率的条件$\mathrmβ>1/3$。我们发现没有这样的显着的傅立叶定律违反通过发散的热导率在80 bp的长度或40 bp的长度。此外，在第二研究的情况下，CG序列内短（m $\le$ 2）包封AT序列的存在显示出增加的趋势。这些重要的结果对于设计基于DNA的热器件是重要的。
英文摘要：
The thermal conductivity of double-stranded (ds) B-DNA was systematically investigated using classical molecular dynamics (MD) simulations. The effect of changing base-pairs on the thermal conductivity of dsDNA, needed investigation at a molecular level. Hence, four sequences, viz. poly(A), poly(G), poly(CG) and poly(AT) were initially analysed in this work. Firstly, length of these sequences was varied from 4-40 base-pairs (bp) at 300 K and the respective thermal conductivity ($\mathrmκ$) was computed. Secondly, the temperature dependent thermal conductivities between 100 K and 400 K were obtained in 50 K steps at 28 bp length. The Müller-Plathe reverse non-equilibrium molecular dynamics (RNEMD) was employed to set a thermal gradient and obtain all thermal conductivities in this work. Moreover, mixed sequences using AT and CG sequencces, namely $\mathrm{A(CG)_{n}T}$ (n=3-7), $\mathrm{ACGC(AT)_{m}GCGT}$ (m=0-5) and $\mathrm{ACGC(AT)_{n}AGCGT}$ (n=1-4) were investigated based on the hypothesis that these sequences could be better thermoelectrics. 1-dimensional lattices are said to have diverging thermal conductivities at longer lengths, which violate Fourier law. These follow power law, where $\mathrm{κ\propto\ L^β}$. At longer lengths, the exponent $\mathrmβ$ need to satisfy the condition $\mathrmβ>1/3$ for divergent thermal conductivity. We find no such significant Fourier law violation through divergence of thermal conductivities at 80 bp lengths or 40 bp lengths. Also, in the case of second study, the presence of short (m$\le$2) encapsulated AT sequences within CG sequences show an increasing trend. These significant results are important for engineering DNA based thermal devices.
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