Adlayer Structures of DL-Homocysteine and L-Homocysteine Thiolactone on Au(111) Surface: an in situ STM Study

The adsorption Of DL-homocysteine (Hcy) and L-homocysteine thiolactone (HTL) on Au(1 1 1) electrode was investigated in 0.1 M HClO4 by cyclic voltammetry and in situ scanning tunneling microscopy (STM). Hcy and HTL molecules formed highly ordered adlayers on Au(1 1 1) surface. High-resolution STM images revealed the orientation and packing arrangement in the ordered adlayers. Hcy molecules formed (2root3 x 3root3)R30degrees adlayer structure and H-bonds between carboxyl groups were assumed to be responsible for the origin of tail-to-tail or head-to-head molecular arrangement, while HTL molecules formed (4 x 6) adlayer structure, and two different orientations and appearances in the ordered adlayer were found. Structural models were proposed for the two adlayers.

Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Molecular dynamics (MD) simulations are performed to study the interaction of His-tagged peptide with three different metal surfaces in explicit water. The equilibrium properties are analyzed by using pair correlation functions (PCF) to give an insight into the behavior of the peptide adsorption to metal surfaces in water solvent. The intermolecular interactions between peptide residues and the metal surfaces are evaluated. By pulling the peptide away from the peptide in the presence of solvent water, peeling forces are obtained and reveal the binding strength of peptide adsorption on nickel, copper and gold. From the analysis of the dynamics properties of the peptide interaction with the metal surfaces, it is shown that the affinity of peptide to Ni surface is the strongest, while on Cu and An the affinity is a little weaker. In MD simulations including metals, the His-tagged region interacts with the substrate to an extent greater than the other regions. The work presented here reveals various interactions between His-tagged peptide and Ni/Cu/Au surfaces. The interesting affinities and dynamical properties of the peptide are also derived. The results give predictions for the structure of His-tagged peptide adsorbing on three different metal surfaces and show the different affinities between them, which assist the understanding of how peptides behave on metal surfaces and of how designers select amino sequences in molecule devices design. (c) 2007 Elsevier Ltd. All rights reserved.

Structure and properties of amorphous thin film for optical data storage

In this paper the magnetic and magneto-optical properties of amorphous rare earth-transition metal (RE-TM) alloys as well as the magnetic coupling in the multi-layer thin films for high density optical data storage are presented. Using magnetic effect in scanning tunneling microscopy the clusters structure of amorphous RE-TM thin films has been observed and the perpendicular magnetic anisotropy in amorphous RE-TM thin films has been interpreted. Experimental results of quick phase transformation under short pulse laser irradiation of amorphous semiconductor and metallic alloy thin films for phase change optical recording are reported. A step-by-step phase transformation process through metastable states has been observed. The waveform of crystallization propagation in micro-size spot during laser recording in amorphous semiconductor thin films is characterized and quick recording and erasing mechanism for optical data storage with high performance are discussed. The nonlinear optical effects in amorphous alloy thin films have been studied. By photo-thermal effect or third order optical nonlinearity, the optical self-focusing is observed in amorphous mask thin films. The application of amorphous thin films with super-resolution near field structure for high-density optical data storage is performed. (c) 2007 Elsevier B.V. All rights reserved.

Theoretical studies on conformation comparison of braid-like and triplex DNA

Based on the experimental data of scanning tunneling microscopy (STM), models of three-stranded braid-like DNAs composed by three kinds of base triplets AAA, TAT and GCA were constructed. We investigated the braid-like DNAs and their comparative tripler DNAs using a molecular mechanics method. The three strands of braid-like DNAs are proven equivalent, while those of tripler DNAs are not. The conformational energies for braid-like DNAs were found to be higher than that for tripler DNAs. Each period in one strand of braid-like DNA has 18 nucleotides, half of which are right-handed, while the other half are left-handed. Additional discussions concerning sugar puckering modes and the H-bonds are also included. (C) 1999 Elsevier Science B.V. All rights reserved.

Effects of seed dot layer and thin GaAs spacer layer on the structure and optical properties of upper In(Ga)As quantum dots

The structure and optical properties of In(Ga)As with the introduction of InGaAlAs or InAlAs seed dot layers are investigated. The area density and size homogeneity of the upper InGaAs dots are efficiently improved by the introduction of a buried layer of high-density dots. Our explanation for the realization of high density and size homogeneity dots is presented. When the GaAs spacer layer is too thin to cover the seed dots, the upper dots exhibit some optical properties like those of a quantum well. By analyzing the growth dynamics, we refer to this kind of dot as an empty-core dot. (C) 2003 American Institute of Physics.

Structure and optical properties of upper In(Ga)As quantum dots on a different seed layer with a thin GaAs spacer layer

The structure and optical properties of In(Ga)As grown with the introduction of InGaAlAs or InAlAs seed dots layers are investigated. The area density and size homogeneity of the upper InGaAs dots are efficiently improved with the introduction of a layer of high-density buried dots. When the GaAs spacer layer is too thin to cover the seed dots, the upper dots exhibit the characterization of a quantum well. By analyzing the growth dynamics, we refer to it as an empty-core structure dot. (C) 2002 Elsevier Science B.V. All rights reserved.

Growth mode and strain evolution during InN growth on GaN(0001) by molecular-beam epitaxy

Epitaxial growth of InN on GaN(0001) by plasma-assisted molecular-beam epitaxy is investigated over a range of growth parameters including source flux and substrate temperature. Combining reflection high-energy electron diffraction (RHEED) and scanning tunneling microscopy (STM), we establish a relationship between film growth mode and the deposition condition. Both two-dimensional (2D) and three-dimensional (3D) growth modes of the film are observed. For 2D growth, sustained RHEED intensity oscillations are recorded while STM reveals 2D nucleation islands. For 3D growth, less than three oscillation periods are observed indicating the Stranski-Krastanov (SK) growth mode of the film. Simultaneous measurements of (reciprocal) lattice constant by RHEED suggest a gradual relaxation of the strain in film, which commences during the first bilayer (BL) deposition and almost completes after 2-4 BLs. For SK growth, 3D islanding initiates after the strain has mostly been relieved, presumably by dislocations, so the islands are likely strain free. (C) 2002 American Institute of Physics.

Growth and structural properties of GaN films on flat and vicinal SiC(0001) substrates

Initial stage GaN growth by molecular-beam epitaxy (MBE) on SiC(0001) substrate is followed by in situ scanning tunneling microscopy. Comparison is made between growth on nominally flat and vicinal substrate surfaces and the results reveal characteristic differences between the two. Ex situ transmission electron microscopy (TEM) and X-ray diffraction (XRD) rocking curve measurements of the films show lower density of defects and better structural quality of the vicinal film. We suggest the improved structural quality of the vicinal film is related to the characteristic difference in its initial stage nucleation and coalescence proccsses than that of the flat film.

Electrical transport through individual DNA molecules

A theoretical model is presented to describe electrical transport through individual DNA molecules. By contacting the proposed model with the experimentally measured data, a variety of valuable quantities are identified. The partially decoherent nature on the guanine-cytosine (GC) pairs of DNA is also elaborated in contrast to the completely incoherent hopping mechanism discussed in the context of charge transfer experiments. (C) 2001 American Institute of Physics.

Observation of "ghost" islands and surfactant effect of surface gallium atoms during GaN growth by molecular beam epitaxy

We observe "ghost" islands formed on terraces during homoepitaxial nucleation of GaN. We attribute the ghost islands to intermediate nucleation states, which can be driven into "normal" islands by scanning tunneling microscopy. The formation of ghost islands is related to excess Ga atoms on the surface. The excess Ga also affect island number density: by increasing Ga coverage, the island density first decreases, reaching a minimum at about 1 monolayer (ML) Ga and then increases rapidly for coverages above 1 ML. This nonmonotonic behavior points to a surfactant effect of the Ga atoms.

Photoluminescence study of InAs/GaAs self-organized quantum dots with bimodal size distribution

We have investigated the temperature dependence of the photoluminescence (PL) spectrum of self-organized InAs/GaAs quantum dots. A distinctive double-peak feature of the PL spectra from quantum dots has been observed, and a bimodal distribution of dot sizes has also been confirmed by scanning tunneling microscopy image for uncapped sample. The power-dependent PL study demonstrates that the distinctive PL emission peaks are associated with the ground-state emission of islands in different size branches. The temperature-dependent PL study shows that the PL quenching temperature for different dot families is different. Due to lacking of the couple between quantum dots, an unusual temperature dependence of the linewidth and peak energy of the dot ensemble photoluminescence has not been observed. In addition, we have tuned the emission wavelength of InAs QDs to 1.3 mu m at room temperature.

Temperature dependence of the optical properties of InAs/GaAs self-organized quantum dots with bimodal size distribution

In this work we report the optical and microscopic properties of self-organized InAs/GaAs quantum dots grown by molecular beam epitaxy on (1 0 0) oriented GaAs substrates. A distinctive double-peak feature of the PL spectra from quantum dots has been observed, and a bimodal distribution of dot sizes has also been confirmed by scanning tunneling microscopy (STM) image for uncapped sample. The power-dependent photoluminescence (PL) study demonstrates that the distinctive PL emission peaks are associated with the ground-state emission of islands in different size branches. The temperature-dependent PL study shows that the PL quenching temperature for different dot families is different. It is shown that the coupling between quantum dots plays a key role in unusual temperature dependence of QD photoluminescence. In addition, we have tuned the emission wavelength of InAs QDs to 1.3 mu m at room temperature. (C) 2000 Elsevier Science B.V. All rights reserved.

Morphology and photoluminescence of GeSi self-assembled quantum dot on Si(113)

Morphology of self-assembled GeSi quantum dot grown on Si(113) by Si molecular beam epitaxy has been studied by transmission electron microscopy and atomic force microscopy. Photoluminescence from the as-grown sample and annealed sample was studied. The results were analyzed and explained.

Au(111)电极上分子相互作用扫描隧道显微镜研究

本论文利用扫描隧道显微镜(STM)在Au(111)电极上结合电化学方法在分子水平上观察分子的吸附组装和结构调控等。主要内容如下： (1) 用现场电化学扫描隧道显微镜(ECSTM)在Au(111)电极上研究了巯基己醇(MHO)取代六苯并苯的详细过程。取代速度强烈依赖于MHO的浓度。浓度较低时，反应速度较慢，我们可以用现场ECSTM跟踪观察详细的取代过程。取代首先发生在靠近重构线肘部的位置，出现单分子或多个六苯并苯分子的取代而形成的pits。随着取代过程的进行，这些小的pits生长或合并成较大的pits；pits周围的六苯并苯分子逐渐被MHO取代，最终在限定的区域内形成有序的domain。观察局部区域的取代过程，我们发现沿着重构线的方向扩展速度最快。快速取代之后，MHO在Au(111)电极表面形成( )R30°晶格结构，而慢速取代之后，MHO在表面形成c(4×2)超结构。与MHO在干净的Au(111)电极上的吸附相比，在六苯并苯修饰的Au(111)电极上即使在很低的浓度下也没有观察到平躺的物理吸附相，而是直接形成化学吸附相。这可能是由于六苯并苯的存在，MHO的碳氢链不能直接与Au原子接触。通过数据分析，我们发现取代速率曲线呈倒S形状。 (2) 我们用循环伏安法(CV)和ECSTM研究了腺嘌呤(Adenine，A)，胸腺嘧啶(Thymine，T)和鸟嘌呤(Guanine，G)单组分及混合组分(A+T)的电化学二维相变。施加在Au(111)电极上的电位不同，A会呈现不同的吸附状态，包括物理吸附相和化学吸附相。在物理吸附的电势范围，高分辨ECSTM图像显示，同一个电势下共存着多样性的A的吸附结构。当基底电势变得更正时，一种更倾斜的吸附状态也就是A的化学吸附相会形成。在较负电位下，A和T能通过分子之间氢键作用在Au(111)电极上形成一种新的网络结构，而G能形成多层吸附。 (3) 利用STM研究了不同方法移除硫醇自组装膜之后金电极表面的再生情况。分别使用了化学法和电化学还原脱附法。化学法比较简单，使用的试剂有王水，piranha和NaBH4。王水对金电极表面有强腐蚀作用；piranha和NaBH4对金表面的作用较小，但是NaBH4处理之后的金表面上会有较多的亮岛出现。在移除自组装膜之后的电极上直接组装六苯并苯，我们观察到用piranha和NaBH4处理之后的金电极表面上六苯并苯自组装膜缺陷较多，有序domain也比较小。电化学法脱附可以得到比较干净的金表面，直接组装的六苯并苯自组装膜有序性好，缺陷少。而且，电化学脱附法通过控制电位可以实现硫醇自组装膜和六苯并苯自组装膜的相互转换。

Electron diffraction and photoemission studies of clean and water-covered Si(5,5,12) and Si(112) surfaces

The structure of silicon surfaces in the orientation range (113)-(5,5,12)-(337)-(112) has been investigated using high resolution LEED and photoemission both on a spherical and on flat samples. We find that Si(5,5,12) [5.3 degrees from (113) and 0.7 degrees from (937)] is the only stable orientation between (113) and (111) and confirm the result of Baski et al. [Science 269, 1556 (1995)] that it has a 2 x 1 superstructure with a very large unit cell of 7.68 x 53.5 Angstrom(2). Adsorption measurements of water on Si(5,5,12) yield a mobile precursor kinetics with two kinds of regions saturating at 0.25 and 0.15 ML which are related to adsorption on different sites. Using these results, a modified structure model is proposed. Surfaces between (113) and (5,5,12) separate into facets of these two orientations; between (5,5,12) and (112), they separate into (5,5,12) and (111) facets. (337) facets in this range may be considered as defective (5,5,12) facets.