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

DNA 和 DNA-碳纳米管系统中传输的多尺度模拟

• 批准号: 7499202
• 负责人: NICHOLAS G KIOUSSIS
• 金额: $ 10.73万
• 依托单位: CALIFORNIA STATE UNIVERSITY NORTHRIDGE
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2012-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7499202
• 关键词: Adenine; Aging; Appendix; Base Sequence; Binding; Biological; Buffers; Caliber; Capillary Electrophoresis; Carbon; Charge; Chemicals; Classification; Consensus; Couples; Coupling; DNA; DNA Modification Process; DNA Repair; DNA Sequence; Defect; Deoxyribose; Detection; Development; Devices; Electric Conductivity; Electrodes; Electron Transport; Electronics; Electrons; Electrostatics; Environment; Equilibrium; Generations; Genetic; Guanine; Hybrids; Ions; Laboratories; Lasers; Lead; Malignant Neoplasms; Manuscripts; Methods; Molecular; Motivation; Mutation; Nature; Nucleic Acids; Nucleotides; Numbers; Object Attachment; Play; Polymers; Positioning Attribute; Process; Property; Protocols documentation; Protons; Radiation Induced DNA Damage; Reaction; Reading; Relative (related person); Role; Scheme; Screening procedure; Solutions; Solvents; Structure; Sugar Phosphates; System; Techniques; Technology; Temperature; Theoretical Studies; Thymine; Time; Vertebral column; Water; Work; base; concept; density; inorganic phosphate; insight; molecular dynamics; nanoscale; nanoscience; neglect; quantum; sensor; simulation; size; theories; voltage

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.

描述（由申请人提供）：DNA序列的纳米级阅读被设想为当DNA分子逐碱基移动通过门时在由一对纳米电极尖端限定的纳米间隙处发生。基本原理是，四种不同的核苷酸碱基及其各种序列，每一种都具有不同的化学组成和结构，应该与穿过两个尖端的隧道电流的特定特征相关联。我们建议进行计算的DNA和DNA-碳纳米管（DNA-CNT）的混合系统的原子和电子结构和输运性质，使用多尺度的方法，我们最近开发的。拟议工作的直接动机是在量子水平上深入了解这些系统的不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，如探针和传感器以及DNA测序技术。拟议的研究将阐明的电子结构的变化和相关的键合性质的溶剂和反离子的存在下的DNA和DNA-CNT的固有电导的性质的影响。计算将采用三种不同但互补的方法：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; 3）我们最近开发的耦合从头计算和经验方案的多尺度方法。这些方法是独特的，在提供洞察电子结构中起着关键作用的原子间的力量和运输，在相反的经验量子化学方法，不允许一个准确的描述核酸相互作用。具体地说，我们打算研究：（1）A、B、λ和超拉伸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）带电环境的影响（电子或空穴的存在）缺陷反应，这可能会导致与氧化损伤有关的DNA切割;（4）碳纳米管的直径/曲率对DNA-CNT杂化体系输运性质的影响。我们最近发展的非平衡输运TB方法也将被用来研究非线性效应的偏见。