The charge transfer via a double helix DNA

This paper reports a double helix model of charge transfer in DNA molecule. The calculated results show that the transmission characteristics of DNA are not only related to the longitudinal transfer but also to the helicity of molecule. It finds that there are four transmission bands centred at 0.92, 3.07, 7.75 and 8.87eV, also the width and intensity of bands corresponding to the helix direction are less than that of the longitudinal direction. With the increase of hopping energy, transmission bands become wide so that the transmission ability is enhanced.     

The effect of hydrogen bond breaking defect on charge transport in a DNA molecular device

The charge transport in a DNA molecular device is theoretically investigated based on the Lattice Green Function method and Landauer-Büttiker theory. The effect of a hydrogen bond defect at different sites is investigated. A defect at the end of the DNA molecule reduces the current through the molecule, but a defect in the middle region of the molecule will have relatively slight effect on the current through the molecule. The effect of defect on the wave function distribution at the ends of the DNA molecule plays an important role in the defect mediated transport properties.     

界面耦合对DNA分子电荷输运性质的影响

在三维紧束缚模型下,采用传递矩阵的方法研究了不同界面耦合对DNA分子电荷输运性质的影响.结果表明：界面耦合理想时,透射率和电子定域长度都很大,分子呈现出良好的导电性;反之,透射率和电子定域长度减小,分子呈现出较差的导电性.当分子与金属电极之间理想耦合时,从伏安特性上可以看出,poly(dG)-poly(dC) DNA分子的开启电压小于poly(dA)-poly(dT) DNA分子的开启电压,并且在相同的偏压下前者的电流值要大于后者.因此,poly(dG)-poly(dC) DNA分子的导电性优于poly( 关键词： 界面耦合 透射率 定域长度 导电性     

碱基对组分、电极位能及界面耦合对DNA分子I-V特性的影响

在紧束缚近似下,利用传输矩阵方法,计算研究了碱基对组分、金属电极位能及DNA分子与电极耦合强度对DNA分子I-V特征的影响.计算结果表明:由单一碱基对构成的DNA分子的饱和电流强度远大于由两种碱基对按一定组分随机分布的DNA分子的饱和电流强度,且当DNA分子中两种碱基对的含量相等时,其饱和电流强度最小.同时,富含C-G碱基对的DNA分子比富含A-T碱基对的DNA分子的电子输运能力大.金属电极位能对DNA分子电子输运的影响体现在两方面,当偏压较小时,电极位能具有阻碍电荷注入的效果,当偏压较大时     

Superexchange interaction enhancement of the quantum transport in a DNA-type molecule

We use the transfer matrix method and the Green function technique to theoretically study the quantum tunnelling through a DNA-type molecule. Ferromagnetic electrodes are used to produce the spin-polarized transmission probability and therefore the spin current. The distance-dependent crossover comes from the topological variation from the one-dimensional to the two-dimensional model transform as we switch on the interstrand coupling; a new base pair will present N-1 extrachannels for the charge and spin as N being the total base pairs. This will restrain the decay of the transmission and improve the stability of the quantum transport. The spin and charge transfer through the DNA-type molecule is consistent with the quantum tunneling barrier.     

Contemplating charge transport by modeling of DNA nucleobases based nano structures

Electrical charge transport through two basic strands Thymine and Adenine of DNA has been analyzed using jellium model approach. The FFT-2D computations have been performed for semi empirical Extended Huckel Theory using Atomistix Tool kit to contemplate the charge transport metrics like current and conductance. We have scrutinized the behavior of the devices in the range of -2 V–2 V for a step size of 0.2 V. A prominent observation is the drop in HLGs of Adenine and Thymine, when working as device as compared to their intrinsic values and this is comparative more visible in case of Adenine. The current in the thymine based device exhibit linear increase with voltage in spite of having low conductance. Further the broader transmission peaks represent the strong coupling of electrodes to the scattering molecule (Thymine). The NDR effect of Adenine based device for higher bias can be utilized in various future electronics applications.     

Effect of helix angles on polaron motion in poly-DNA

We investigate the effect of helix angles on polaron motion in poly-DNA in the framework of a tight binding model. A DNA molecule is supposed to have a uniform or a random distribution of the helix angles. It is found that a polaron moves faster along a DNA molecule with an overwinding helix than that with an unwinding one. In DNA molecule with randomly distributed helix angles, charge transport is suggested to be field-facilitated tunneling between spatial disordered potential wells.     

Transport properties of copper phthalocyanine based organic electronic devices

Ambipolar charge carrier transport in Copper phthalocyanine (CuPc) is studied experimentally in field-effect transistors and metal-insulator-semiconductor diodes at various temperatures. The electronic structure and the transport properties of CuPc attached to leads are calculated using density functional theory and scattering theory at the non-equilibrium Green’s function level. We discuss, in particular, the electronic structure of CuPc molecules attached to gold chains in different geometries to mimic the different experimental setups. The combined experimental and theoretical analysis explains the dependence of the mobility and the transmission coefficient on the charge carrier type (electrons or holes) and on the contact geometry. We demonstrate the correspondence between our experimental results on thick films and our theoretical studies of single molecule contacts. Preliminary results for fluorinated CuPc are discussed.     

Effects of cytosine methylation on DNA charge transport

The methylation of cytosine bases in DNA commonly takes place in the human genome and its abnormality can be used as a biomarker in the diagnosis of genetic diseases. In this paper we explore the effects of cytosine methylation on the conductance of DNA. Although the methyl group is a small chemical modification, and has a van der Waals radius of only 2 ?, its presence significantly changes the duplex stability, and as such may also affect the conductance properties of DNA. To determine if charge transport through the DNA stack is sensitive to this important biological modification we perform multiple conductance measurements on a methylated DNA molecule with an alternating G:C sequence and its non-methylated counterpart. From these studies we find a measurable difference in the conductance between the two types of molecules, and demonstrate that this difference is statistically significant. The conductance values of these molecules are also compared with a similar sequence that has been previously studied to help elucidate the charge transport mechanisms involved in direct DNA conductance measurements.     

Point-mutation effects on charge-transport properties of the tumor-suppressor gene p53

We report on a theoretical study of point mutations effects on charge transfer properties in the DNA sequence of the tumor-suppressor p53 gene. On the basis of effective tight-binding models which simulate hole propagation along the DNA, a statistical analysis of mutation-induced charge transfer modifications is performed. In contrast to noncancerous mutations, mutation hot spots tend to result in significantly weaker changes of transmission properties. This suggests that charge transport could play a significant role for DNA-repairing deficiency yielding carcinogenesis.     

Electron transport through asymmetric DNA molecules

We investigate quantum mechanical electron transport along the long axis of the DNA molecule using an effective tight-binding model. The overall contour plot of transmission, the current-voltage characteristics, and the differential conductance are examined for the variation of backbone onsite energy, the energy-dependent hopping strength, and the contact coupling between the leads and the DNA molecule. It is shown that as backbone asymmetry increases, the merging and collapse of the two mini-bands take place and an extra resonance peak in the transmission appears. In addition, we present the modulation of voltage threshold in the current-voltage curves and a double-peak structure in the differential conductance due to the disappearance of the merged mini-band. Finally, in the Coulomb blockade regime of asymmetric contact coupling, a distinct and under-unity resonance in the transmission appears due to the interference effects between the DNA molecular bands and the electronic structure of the leads at the DNA-lead interface.     

分子结电学特性的理论研究

在第一性原理的基础上，对共扼分子2-氨基-5-硝基-1，4-二乙炔基-4’，-苯硫醇基苯(2-amino-5-nitro-1,4-diethyny-4’-benzenethiol-benzene)与金表面形成的分子结的电学特性进行了理论研究.利用密度泛函理论计算了该分子及扩展分子的电子结构；讨论了分子与金表面的相互作用，定量地确定了耦合常数，求出了电子的迁移强度；利用弹性散射格林函数法研究了该分子结的伏—安特性.计算结果表明，当外加偏压小于0.9V时分子结存在电流禁区，随着偏压升高，分子结的电导出现平台特 关键词： 化学吸附 分子结 分子电子学     

First-principle studies of I-V properties of a molecular wire

The elastic scattering Green function method has been developed to describe the I-V characteristics of molecular wires. The molecular electronic structure and the interaction between the molecule and the gold surface are two key factors for the charge transport properties of molecular wires in the formulas. An ab initio calculation at the hybrid density functional theory level is carried out to obtain the electronic structure of 4-4′-dimercaptodibenzene molecule. The frontier orbit theory and the perturbation theory are employed to determine the constant of the interaction energy between molecule and surface quantitatively. The numerical results show that the bonding between the sulfur atom and the gold atoms corresponds mainly to the covalent bond. Some molecular orbits are extended over molecule and gold cluster that certainly give channels for the charge transport, other molecular orbits are localized and the charge transport can take place by tunnel mechanism. At zero bias region, there exists a current gap. With the increasing bias, the conductance of the wire takes a shape of plateaus.     

First-principle studies of I–V properties of a molecular wire

The elastic scattering Green function method has been developed to describe the I–V characteristics of molecular wires. The molecular electronic structure and the interaction between the molecule and the gold surface are two key factors for the charge transport properties of molecular wires in the formulas. Anab initio calculation at the hybrid density functional theory level is carried out to obtain the electronic structure of 4-4′-dimercaptodibenzene molecule. The frontier orbit theory and the perturbation theory are employed to determine the constant of the interaction energy between molecule and surface quantitatively. The numerical results show that the bonding between the sulfur atom and the gold atoms corresponds mainly to the covalent bond. Some molecular orbits are extended over molecule and gold cluster that certainly give channels for the charge transport, other molecular orbits are localized and the charge transport can take place by tunnel mechanism. At zero bias region, there exists a current gap. With the increasing bias, the conductance of the wire takes a shape of plateaus.     

Itinerant electron model and conductance of DNA

DNA (Deoxyribonucleic acid) has recently caught the attention of chemists and physicists. A major reason for this interest is DNA’s potential use in nanoelectronic devices, both as a template for assembling nanocircuits and as an element of such circuits. However, the electronic properties of the DNA molecule remain very controversial. Charge-transfer reactions and conductivity measurements show a large variety of possible electronic behavior, ranging from Anderson and band-gap insulators to effective molecular wires and induced superconductors. In this review article, we summarize the wide-ranging experimental and theoretical results of charge transport in DNA. An itinerant electron model is suggested and the effect of the density of itinerant electrons on the conductivity of DNA is studied. Calculations show that a DNA molecule may show conductivity from insulating to metallic, which explains the controversial and profuse electric characteristics of DNA to some extent.      

单分子器件与电极间耦合界面对电子传输的影响

利用自恰tight-binding 理论，对由phenalenyl分子构成的全对称三电极纳米单分子器件的电子传导特性进行了理论研究. 通过改变电极与分子界面上的耦合，得出了分子与原子线电极间耦合强度变化对电子传输的影响. 结果显示电子通过phenalenyl分子器件的概率随着分子与电极的耦合强度变弱而减小. 当耦合强度变大时，不仅电子通过phenalenyl分子器件的概率变大，而且在较宽的能带内电子都可以通过phenalenyl分子. 所得结果还揭示出在特定的能区，对称三电极phenalenyl分子可以构成一个无源正负能量开关器件的新特性.     

Optical properties and component composition of layers of cyanine dyes on dielectric supports: influence of asymmetry of the molecular electron density distribution

The component composition of molecular layers of dicarbocyanine dyes of cationic type on glass is determined by the absorption spectroscopy methods. For symmetric and asymmetric molecules the component composition depends on the chemical structure of a molecule and its interaction with the substrate, which are responsible for the electron density distribution in a molecule. The interaction with the substrate depends on the thickness of a layer and the orientation of a layer molecule on the substrate. The increase in the separation between the molecule and the substrate in thicker layers decreases the interaction with the substrate and the asymmetry of a molecule. In symmetric and slightly asymmetric dyes the value of the charge difference on the end groups decreases with increasing layer thickness, whereas in dyes with a large asymmetry, both the value and the sign of the charge difference change. The above results are confirmed by data on the computer simulation of the charge distribution in a dicarbocyanine cation upon its interaction with the oxygen anion on the substrate.     

A renormalization approach to describe charge transport in quasiperiodic dangling backbone ladder (DBL)-DNA molecules

We study the charge transport properties of a dangling backbone ladder (DBL)-DNA molecule focusing on a quasiperiodic arrangement of its constituent nucleotides forming a Rudin-Shapiro (RS) and Fibonacci (FB) Poly (CG) sequences, as well as a natural DNA sequence (Ch22) for the sake of comparison. Making use of a one-step renormalization process, the DBL-DNA molecule is modeled in terms of a one-dimensional tight-binding Hamiltonian to investigate its transmissivity and current-voltage (I-V) profiles. Beyond the semiconductor I-V characteristics, a striking similarity between the electronic transport properties of the RS quasiperiodic structure and the natural DNA sequence was found.     

六取代三环喹唑啉电荷传输性质的理论研究

六取代三环喹唑啉分子可以作为液晶半导体材料。使用电子传输的半经典模型和密度泛函理论方法在B3LYP/6-31G**水平上对六取代三环喹唑啉分子的电荷传输性质进行理论研究。结果显示,该分子的正电荷传输速率为负电荷传输速率的30倍。与苯并菲和六氮杂苯并菲比较,该分子更有利于正电荷传输。     

Electronic Transport in Single-Stranded DNA Molecule Related to Huntington’s Disease

We report a numerical analysis of the electronic transport in single chain DNA molecule consisting of 182 nucleotides. The DNA chains studied were extracted from a segment of the human chromosome 4p16.3, which were modified by expansion of CAG (cytosine-adenine-guanine) triplet repeats to mimics Huntington’s disease. The mutated DNA chains were connected between two platinum electrodes to analyze the relationship between charge propagation in the molecule and Huntington’s disease. The computations were performed within a tight-binding model, together with a transfer matrix technique, to investigate the current-voltage (I–V) of 23 types of DNA sequence and compare them with the distributions of the related CAG repeat numbers with the disease. All DNA sequences studied have a characteristic behavior of a semiconductor. In addition, the results showed a direct correlation between the current-voltage curves and the distributions of the CAG repeat numbers, suggesting possible applications in the development of DNA-based biosensors for molecular diagnostics.