Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

First-principles prediction of the magnetism of 3d transition-metal-doped Rocksalt MgO

Using first-principles band structure methods, we have systematically studied the electronic structures, magnetic stabilities, and half-metal properties of 3d transition-metal (TM) doped Rocksalt MgO compounds TMMg3O4 (TM = V, Cr, Mn, Fe, Co, and Ni). The calculations reveal that only CrMg3O4 has a ferromagnetic stability among the six compounds, which is explained by double-exchange mechanism. The magnetic stability is affected by the doping concentration of TM if the top valance band is composed of partially occupied t(2g) states. In addition, CrMg3O4 is a half-metallic ferromagnet. The origins of half-metallic and ferromagnetic properties are explored. The Curie temperature (T-c) of CrMg3O4 is 182 K. And it is hard for CrMg3O4 to deform due to the large bulk modulus and shear modulus, so it is a promising spintronic material. Our calculations provide the first available information on the magnetic properties of 3d TM-doped MgO.

The formation and electronic structures of 3d transition-metal atoms doped in silicon nanowires

Using first-principles methods, we systematically study the mechanism of defect formation and electronic structures for 3d transition-metal impurities (V, Cr, Mn, Fe, and Co) doped in silicon nanowires. We find that the formation energies of 3d transition-metal impurities with electrons or holes at the defect levels always increase as the diameters of silicon nanowires decrease, which suggests that self-purification, i.e., the difficulty of doping in silicon nanowires, should be an intrinsic effect. The calculated results show that the defect formation energies of Mn and Fe impurities are lower than those of V, Cr, and Co impurities in silicon nanowires. It indicates that Mn and Fe can easily occupy substitutional site in the interior of silicon nanowires. Moreover, they have larger localized moments, which means that they are good candidates for Si-based dilute magnetic semiconductor nanowires. The doping of Mn and Fe atom in silicon nanowires introduces a pair of energy levels with t(2) symmetry. One of which is dominated by 3d electrons of Mn or Fe, and the other by neighboring dangling bonds of Si vacancies. In addition, a set of nonbonding states localized on the transition-metal atom with e symmetry is also introduced. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.3000445]

First-principles study of the electronic structures and magnetic properties of 3d transition metal-doped anatase TiO2

We study the electronic structures and magnetic properties of the anatase TiO2 doped with 3d transition metals (V, Cr, Mn, Fe, Co, Ni), using first-principles total energy calculations based on density functional theory (DFT). Using a molecular-orbital bonding model, the electronic structures of the doped anatase TiO2 are well understood. A band coupling model based on d-d level repulsions between the dopant ions is proposed to understand the chemical trend of the magnetic ordering. Ferromagnetism is found to be stabilized in the V-, Cr-, and Co-doped samples if there are no other carrier native defects or dopants. The ferromagnetism in the Cr- and Co-doped samples may be weakened by the donor defects. In the Mn-, and Fe-doped samples, the ferromagnetism can be enhanced by the acceptor and donor defects, respectively.

First-Principles Study of Magnetic Properties of 3d Transition Metals Doped in ZnO Nanowires

The defect formation energies of transition metals (Cr, Fe, and Ni) doped in the pseudo-H passivated ZnO nanowires and bulk are systematically investigated using first-principles methods. The general chemical trends of the nanowires are similar to those of the bulk. We also show that the formation energy increases as the diameter of the nanowire decreases, indicating that the doping of magnetic ions in the ZnO nanowire becomes more difficult with decreasing diameter. We also systematically calculate the ferromagnetic properties of transition metals doped in the ZnO nanowire and bulk, and find that Cr ions of the nanowire favor ferromagnetic state, which is consistent with the experimental results. We also find that the ferromagnetic coupling state of Cr is more stable in the nanowire than in the bulk, which may lead to a higher T (c) useful for the nano-materials design of spintronics.

Structural and optical properties of 3D growth multilayer InGaN/GaN quantum dots by metalorganic chemical vapor deposition

Multilayer InGaN/GaN quantum dots (QDs) were grown on sapphire substrates through a three-dimensional growth mode, which was initiated by a special passivation processing introduced into the normal growth procedure. Surface morphology and photoluminescence properties of QDs with different stacking periods (from one to four) were investigated. The temperature dependences of the PL peak energies were found to show a great difference between two-layer and three-layer QDs. The fast redshift and the reversed sigmoidal temperature dependences of the PL energies for the former were attributed to the thermally activated carrier transfer from small to large dots. However, the increase of both the dot size and the spatial space among dots with the growing stacking periods reduced the carrier escape and retrapping. (C) 2004 Elsevier B.V. All rights reserved.

Size quantization effects in InAs self-assembled islands on InP(001) at the onset of 2D-to-3D transition

Photoluminescence spectroscopy has been used to investigate self-assembled InAs islands in InAlAs grown on InP(0 0 1) by molecular beam epitaxy, in correlation with transmission electron microscopy. The nominal deposition of 3.6 monolayers of InAs at 470 degrees C achieves the onset stage of coherent island formation. In addition to one strong emission around 0.74 eV, the sample displaces several emission peaks at 0.87, 0.92. 0.98, and 1.04 eV. Fully developed islands that coexist with semi-finished disk islands account for the multipeak emission. These results provide strong evidence of size quantization effects in InAs islands. (C) 1999 Elsevier Science B.V. All rights reserved.

High-quality-factor EH modes in microcylinder resonators predicted by 3D FDTD simulation

The mode characteristis of a microcylinders with center layer thickness 0.2 mu m and radius 1 mu m are investigated by the three-dimensional (31)) finite-difference time-domain (FDTD) technique and the Pade approximation. The mode quality factor (Q-factor) of the EH71 mode obtained by 3D FDTD increase with the increase of the refractive index of the cladding layer n(2) as n(2) smaller than 3.17, and can be as large as 2.4 x 10(4) as the vertical refractive index distribution is 3.17/3.4/3.17, which is much larger than that of the HE71 mode with the same vertical refractive index distribution.

tilt menu: using the 3d orientation information of pen devices to extend the selection capability of pen-based user interfaces

We present a new technique called‘Tilt Menu’ for better extending selection capabilities of pen-based interfaces.The Tilt Menu is implemented by using 3D orientation information of pen devices while performing selection tasks.The Tilt Menu has the potential to aid traditional onehanded techniques as it simultaneously generates the secondary input (e.g., a command or parameter selection) while drawing/interacting with a pen tip without having to use the second hand or another device. We conduct two experiments to explore the performance of the Tilt Menu. In the first experiment, we analyze the effect of parameters of the Tilt Menu, such as the menu size and orientation of the item, on its usability. Results of the first experiment suggest some design guidelines for the Tilt Menu. In the second experiment, the Tilt Menu is compared to two types of techniques while performing connect-the-dot tasks using freeform drawing mechanism. Results of the second experiment show that the Tilt Menu perform better in comparison to the Tool Palette, and is as good as the Toolglass.

the tilt cursor: enhancing stimulus-response compatibility by providing 3d orientation cue of pen

In order to improve stimulus-response compatibility of touchpad in pen-based user interface, we present the tilt cursor, i.e. a cursor dynamically reshapes itself to providing the 3D orientation cue of pen. We also present two experiments that evaluate the tilt cursor’s performance in circular menu selection and specific marking menu selection tasks. Results show that in a specific marking menu selection task, the tilt cursor significantly outperforms the shape-fixed arrow cursor and the live cursor [4]. In addition, results show that by using the tilt cursor, the response latencies for adjusting drawing directions are smaller than that by using the other two kinds of cursors.

co-creativepen toolkit: a pen-based 3d toolkit for children cooperatly designing virtual environment

Co-CreativePen Toolkit is a pen-based 3D toolkit for children cooperatly designing virtual environment. This toolkit is used to construct different applications involved with distributedpen-based 3D interaction. In this toolkit,sketch method is encapsulated as kinds of interaction techniques. Children can use pen to construct 3D and IBR objects, to navigate in the virtual world, to select and manipulate virtual objects, and to communicate with other children. Children can use pen to select other children in the virtual world, and use pen to write message to children selected The distributed architecture of Co-CreativePen Toolkit is based on the CORBA. A common scene graph is managed in the server with several copies of this graph are managed in every client.Every changes of the scene graph in client will cause the change in the server and other client.

基于场景语义的3D交互体系结构

借鉴真实世界的认知心理学原理,将虚拟场景的可视表达和语义信息结合起来共同服务于用户的交互过程,多种3D交互技术被融合在一个统一的交互框架内,使复杂虚拟环境中的3D用户界面更容易被用户理解和使用.通过增强场景图的语义处理能力,建立支持高层语义的3D用户界面体系结构,3D交互系统不仅在几何层上而且还能在语义层上支持交互任务的执行.最后介绍了一个应用实例.