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: 7933124
• 负责人: NICHOLAS G KIOUSSIS
• 金额: $ 14.99万
• 依托单位: CALIFORNIA STATE UNIVERSITY NORTHRIDGE
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2011-09-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7933124
• 关键词: Adenine; Aging; 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; 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; density; electronic structure; inorganic phosphate; insight; molecular dynamics; nanoscale; nanoscience; neglect; oxidative damage; quantum; sensor; simulation; 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序列的纳米级读取设想发生在由一对纳米电极尖端定义的纳米间隙中，当DNA分子一个碱基一个碱基地通过门时。其基本原理是，四种不同的核苷酸碱基及其不同的序列，每种碱基都有不同的化学成分和结构，应该与穿越两个尖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）混合系统的原子和电子结构和传输性质。提出这项工作的直接动机是在量子水平上深入了解这些系统的不同寻常的电子和输运特性，这可能会导致用于化学/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。提出的研究将阐明在溶剂和反离子存在下电子结构和相关键性质的变化对DNA和DNA-碳纳米管固有电导性质的影响。计算将采用三种不同但互补的方法：1)自洽电荷密度功能紧密结合（TB）方法；2)使用SIESTA和/或ONETEP方法的完全自洽从头计算；3)我们最近开发的结合从头算和经验方案的多尺度方法。与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的洞察方面是独一无二的，而经验量子化学方法不允许准确描述核酸相互作用。更具体地说，我们建议研究：(1)A， B， lamda和过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)结构和环境对输运性质的影响；(3)带电环境（电子或空穴的存在）对缺陷反应的影响，缺陷反应可能导致与氧化损伤相关的DNA分裂；(4)纳米碳纳米管直径/曲率对dna -纳米碳纳米管混合体系输运特性的影响。我们最近开发的非平衡输运TB方法也将用于研究偏差的非线性效应。