Multiscale simulations of transport in DNA and DNA-carbon nanotube systems

描述(申请人提供)：DNA序列的纳米级读数预计将在由一对纳米电极尖端定义的纳米间隙进行，因为DNA分子逐个碱基通过门。其基本原理是，四个不同的核苷酸碱基及其不同的序列，每个具有不同的化学成分和结构，应该与穿过两个末端的隧道电流的特定特征相关联。我们建议使用我们最近开发的多尺度方法来计算DNA和DNA-碳纳米管(DNA-CNT)杂化体系的原子、电子结构和输运性质。拟议工作的直接动机是在量子水平上洞察这些系统不同寻常的电子和传输特性，这些特性可能导致用于化学/生物应用的新型微型设备，如探测器和传感器以及DNA测序技术。这些研究将阐明在溶剂和反离子存在下电子结构和相关成键性质的变化对DNA和DNA-CNT本征电导性质的影响。计算将使用三种不同但相互补充的方法：1)自洽电荷密度泛函紧束缚(TB)方法；2)使用SIESTA和/或ONETEP方法的完全自洽从头计算；以及3)我们最近开发的多尺度方法，将从头计算和经验方案结合起来。与不能准确描述核酸相互作用的经验量子化学方法相比，这些方法在提供对原子间作用力和输运起关键作用的电子结构方面具有独特的洞察力。更具体地说，我们建议研究：(1)A、B、Lamda和过度伸展的带状结构的原子和电子结构以及(I)序列、(Ii)水和(Iii)反离子的影响；(2)结构和环境在输运性质中的作用；(3)带电环境(电子或空穴的存在)对可能引起与氧化损伤有关的DNA断裂的缺陷反应的影响；以及(4)碳纳米管直径/曲率对DNA-CNT杂化体系输运性质的影响。我们最近开发的非平衡传输TB方法也将被用来研究偏置的非线性效应。

DESCRIPTION (provided by applicant): The nanoscale reading of DNA sequences is envisioned to take place at a nanogap defined by a pair of nanoelectrode tips as a DNA molecule moves through the gate base by base. The rationale is that the four different nucleotide bases and their various sequences, each with a distinct chemical composition and structure, should be associated with a specific signature of tunneling current across the two tips. We propose to carry out calculations of the atomic and electronic structure and transport properties of DNA and DNA-carbon nanotube (DNA-CNT) hybrid systems, using a multiscale approach that we have recently developed. The immediate motivation for the proposed work is to gain insight at the quantum level of the unusual electronic and transport properties of these systems that could lead to new types of miniature devices for chemical/biological applications such as probes and sensors and DNA-sequencing technologies. The proposed studies will elucidate the effect of changes of the electronic structure and associated bonding properties in the presence of solvent and counter ions on the nature of the DNA and DNA-CNT intrinsic conductance. The calculations will employ three different but complementary methods: 1) the self-consistent charge density functional tight-binding (TB) method; 2) the fully self-consistent ab initio calculations using the SIESTA and/or ONETEP approach; and 3) our recently developed multiscale approach which couples ab initio and empirical schemes. These approaches are unique in providing insight into the electronic structure which plays a key role for the interatomic forces and the transport, in contrast to empirical quantum-chemical methods which do not allow an accurate description of nucleic acid interactions. More specifically, we propose to study: (1) The atomic and electronic structure of A, B, lamda, and overstretched ribbon-like structures and the effect of (i) sequence, (ii) water and (iii) counterions; (2) The role of structure and environment in the transport properties; (3) The effect of charged environment (presence of electrons or holes) on defect reactions which may give rise to DNA cleavage pertinent to oxidative damage; and (4) The effect of diameter/curvature of the CNT on the transport properties of DNA-CNT hybrid systems. Our recently developed non-equilibrium transport TB approach also will be used to study the non-linear effect of bias.