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首页> 外文学位 >Electronic structure simulations of DNA base recognition and vibrational property analysis of polyanionic hydrides.
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Electronic structure simulations of DNA base recognition and vibrational property analysis of polyanionic hydrides.

机译：DNA碱基识别的电子结构模拟和聚阴离子氢化物的振动特性分析。

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摘要

This thesis presents electronic structure simulations of electron transport across DNA base-pairs for base recognition and analysis of vibrational properties for polyanionic hydrides.;The work on DNA base recognition is motivated by a recent experiment to sequence DNA by measuring tunnel conductance when a single stranded DNA molecule passes through a nanopore. An electric circuit is completed when a DNA base and the phosphate backbone form hydrogen bonds with the reader nucleobase and a guanidinium ion, respectively, tethered to either side of metal electrodes. The tunnel conductance has been obtained across DNA base-pairs, across nucleoside-base pairs, and for a complete circuit containing deoxycytidine-monophosphate (dCMP) by computing the complex bandstructure, Fermi level alignment, and current-voltage curve. The results indicate that a complete dCMP circuit has a very low conductance (on the order of fS) while the base-pair has a moderate conductance (on the order of tens of nS). An alternate base readout scheme, which uses a shorter tunneling path, is explored.;Electron transport through other organic single molecules is also examined. Examples include the effects of torsion angle between rings, oxidation states, and stretching on the electron transport properties of polyaniline molecules and the effects of molecule-metal contact geometries in alkanedithiol molecules.;Additionally, an analysis of vibrational properties is presented to understand the bonding of hydrogen in aluminum and gallium hydrides by computing phonon dispersion curve. Both Al-H and Ga-H stretching mode frequencies are found to be low compared to other hydrides. The weak Al(Ga)-H bond is balanced by Sr(Ba)-H interactions.;Finally, the electronic and the vibrational property changes are examined when superconducting MAlSi (M = Ca, Sr, Ba) absorbs hydrogen and forms semiconducting hydrides MAlSiH with hydrogen attached to Al exclusively. While only a minor rearrangement of the metal atoms occurs due to the hydrogenation, formation of Al-H bond causes a removal of partially occupied antibonding band responsible for metallic behavior and a stiffening of soft phonon mode pivotal for the superconducting properties of MAlSi. On the other hand, the Al-Si bond represented by Al-Si in-plane vibration is equally strong in the metals and semiconducting hydrides.
机译：本文提出了电子跨DNA碱基对的电子结构模拟，用于碱基识别和聚阴离子氢化物的振动特性分析。; DNA碱基识别的工作是受最近的一项实验的推动，该实验通过测量单链时的隧道电导来对DNA进行测序。 DNA分子穿过纳米孔。当DNA碱基和磷酸盐骨架与分别连接到金属电极两侧的读取器核碱基和胍离子形成氢键时，电路就完成了。通过计算复杂的能带结构，费米能级比对和电流-电压曲线，已在整个DNA碱基对，整个核苷碱基对以及包含脱氧胞苷一磷酸（dCMP）的完整电路中获得了隧道电导。结果表明，完整的dCMP电路具有非常低的电导率（约为fS），而碱基对具有中等的电导率（约为nS数十）。探索了使用更短隧穿路径的替代碱基读出方案。;还研究了电子通过其他有机单分子的传输。例子包括环之间的扭转角，氧化态和拉伸对聚苯胺分子的电子传输性质的影响以及链烷二酚分子中的分子-金属接触几何形状的影响。此外，还对振动性质进行了分析以了解键合计算声子弥散曲线分析氢化铝和氢化镓中的氢与其他氢化物相比，Al-H和Ga-H拉伸模式频率均较低。弱的Al（Ga）-H键通过Sr（Ba）-H相互作用来平衡。最后，当超导MAlSi（M = Ca，Sr，Ba）吸收氢并形成半导体氢化物时，检查电子和振动性质的变化MAlSiH的氢仅与Al相连。尽管由于氢化仅发生了金属原子的微小重排，但是Al-H键的形成导致负责金属行为的部分占据的反键带的去除以及对MAlSi超导性能至关重要的软声子模的增强。另一方面，以Al-Si面内振动为代表的Al-Si键在金属和半导体氢化物中同样强。

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  • 作者

    Lee, Myeong Hwa.;

  • 作者单位

    Arizona State University.;

  • 授予单位 Arizona State University.;
  • 学科 Physics Condensed Matter.;Physics Theory.
  • 学位 Ph.D.
  • 年度 2009
  • 页码 178 p.
  • 总页数 178
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 O49;
  • 关键词

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