The effect of buried AlxGa1-xN isolating layers on the transport properties of GaN deposited on sapphire substrate by molecular beam epitaxy using NH3

It is believed that the highly dislocated region near the GaN/sapphire interface is a degenerate layer. In this paper a direct evidence for such a proposal is presented. By inserting a buried AlxGa1-xN (x > 0.5) isolating layer to separate the interface region from the bulk region, the background electron concentration can be significantly reduced, while care must be taken to guarantee that there is no degrading of Hall mobility when choosing the thickness of the isolating layer. (C) 1998 Elsevier Science B.V. All rights reserved.

Size-Dependent Elastic Properties Of Ni Nanofilms By Molecular Dynamics Simulation

Size-dependent elastic properties of Ni nanofilms are investigated by molecular dynamics ( MD) simulations with embedded atom method (EAM). The surface effects are considered by calculating the surface relaxation, surface energy, and surface stress. The Young's modulus and yield stress are obtained as functions of thickness and crystallographic orientation. It is shown that the surface relaxation has important effects on the the elastic properties at nanoscale. When the surface relaxation is outward, the Young's modulus decreases with the film thickness decreasing, and vice versa. The results also show that the yield stresses of the films increase with the films becoming thinner. With the thickness of the nanofilms decreasing, the surface effects on the elastic properties become dominant.

Molecular Dynamics Simulation of the Bio-Adhesion in Molecular Motors

Molecular dynamics (MD) simulation is employed to study the bio-adhesion in F1 ATP molecular motor. Histidine-peptide is widely used as linkage in micro systems because of its strong binding strength to metals. This paper focuses on the adhesion between a synthetic peptide containing 6xHis-tag (Gly-Gly-Lys-Gly-Gly-Lys-Gly-Gly-His-His-His-His-His-His) and metal substrate, which is used to define the position of the F1 ATP molecular motor on the metal substrate. It is shown that the binding strength between histidine and nickel substrate is the strongest, while that of copper is smaller and that of gold substrate is the smallest. From the result of simulation, we find that the stability of adhesion between histidine and the metal substate result of the ringed structure in histidine.

Size-dependent elastic properties of Ni nanofilms by molecular dynamics simulation

Size-dependent elastic properties of Ni nanofilms are investigated by molecular dynamics ( MD) simulations with embedded atom method (EAM). The surface effects are considered by calculating the surface relaxation, surface energy, and surface stress. The Young's modulus and yield stress are obtained as functions of thickness and crystallographic orientation. It is shown that the surface relaxation has important effects on the the elastic properties at nanoscale. When the surface relaxation is outward, the Young's modulus decreases with the film thickness decreasing, and vice versa. The results also show that the yield stresses of the films increase with the films becoming thinner. With the thickness of the nanofilms decreasing, the surface effects on the elastic properties become dominant.

Effect Of Water On Brittle Fracture Of Sio2 By Molecular Dynamics Study

The influence of water on the brittle behavior of beta-cristobalite is studied by means of molecular dynamics (MD) simulation With the TTAM potential. Crack extension of mode 1 type is observed as the crack opening is filled LIP With water. The critical stress intensity factor K-lc(MD) is used to characterize the crack extension of MD simulation. The surface energy of SiO2 covered with layers of water is calculated at temperature of 300 K. Based oil the Griffith fracture criterion, the critical stress intensity factor K-lc(Griffith) is calculated, and it is in good agreement with that of MD simulation. (C) 2008 Elsevier B.V. All rights reserved.

Structural analysis of human CCR2b and primate CCR2b by molecular modeling and molecular dynamics simulation

CCR2b, a chemokine receptor for MCP-1, -2, -3, -4, plays an important role in a variety of diseases involving infection, inflammation, and/or injury, as well as being a coreceptor for HIV-1 infection. Two models of human CCR2b (hCCR2b) were generated by h

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Multiple in-to-Africa dispersals of labeonin fishes (Teleostei: Cyprinidae) revealed by molecular phylogenetic analysis

An out-of-Africa dispersal route has been proposed for many organisms, including modern man. However, counter examples of in-to-Africa dispersal routes are less common. In the present article, the phylogenetic relationships within the Labeoninae, a subfamily of cyprinid fishes distributed in Asia and Africa, were analyzed to investigate the biogeographic processes governing the modern distribution of these Asian and African cyprinids. The mitochondrial DNA cytochrome b gene was used as a molecular marker. The phylogenetic analysis indicated that the subfamily Labeoninae is a monophyletic group, with some Asian labeonins located at the basal position. Two subclades were found that contained both African and Asian species, which highlighted a need for further biogeographic analysis. Based on this analysis, it is proposed that the centre of origin of the Labeoninae was in East Asia. Molecular clock estimation suggests that the Labeoninae arose by the Early Miocene (similar to 23 MYA) during the period of the second Tibetan uplift. Subsequently, two dispersal events of labeonins from Asia into Africa occured in the Early Miocene (similar to 20 MYA) and Late Miocene (similar to 9 MYA) and serve as examples counter to out-of-Africa dispersal.

Influence of V/III ratio on the structural and photoluminescence properties of In0.52AlAs/In0.53GaAs metamorphic high electron mobility transistor grown by molecular beam epitaxy

A series of metamorphic high electron mobility transistors (MMHEMTs) with different V/III flux ratios are grown on GaAs (001) substrates by molecular beam epitaxy (XIBE). The samples are analysed by using atomic force microscopy (AFM), Hall measurement, and low temperature photoluminescence (PL). The optimum V/III ratio in a range from 15 to 60 for the growth of MMHEMTs is found to be around 40. At this ratio, the root mean square (RMS) roughness of the material is only 2.02 nm; a room-temperature mobility and a sheet electron density are obtained to be 10610.0cm(2)/(V.s) and 3.26 x 10(12)cm(-2) respectively. These results are equivalent to those obtained for the same structure grown on InP substrate. There are two peaks in the PL spectrum of the structure, corresponding to two sub-energy levels of the In0.53Ga0.47 As quantum well. It is found that the photoluminescence intensities of the two peaks vary with the V/III ratio, for which the reasons are discussed.

Optimization of metamorphic InGaAs quantum wells on GaAs grown by molecular beam epitaxy

We investigate the molecular beam epitaxy growth of metamorphic InxGa(1-x)As materials (x up to 0.5) on GaAs substrates systematically. Optimization of structure design and growth parameters is aimed at obtaining smooth surface and high optical quality. The optimized structures have an average surface roughness of 0.9-1.8 nm. It is also proven by PL measurements that the optical properties of high indium content (55%) InGaAs quantum wells are improved apparently by defect reduction technique and by introducing Sb as a surfactant. These provide us new ways for growing device quality metamorphic structures on GaAs substrates with long-wavelength emissions.

Evolution of surface morphology and photoluminescence characteristics of 1.3-mu m In0.5Ga0.5As/GaAs quantum dots grown by molecular beam epitaxy

Evolution of surface morphology and optical characteristics of 1.3-mu m In0.5Ga0.5As/GaAs quantum dots (QDs) grown by molecular beam epitaxy (MBE) are investigated by atomic force microscopy (AFM) and photoluminescence (PL). After deposition of 16 monolayers (ML) of In0.5Ga0.5As, QDs are formed and elongated along the [110] direction when using sub-ML depositions, while large size InGaAs QDs with better uniformity are formed when using ML or super-ML depositions. It is also found that the larger size QDs show enhanced PL efficiency without optical nonlinearity, which is in contrast to the elongated QDs.

GaAs-Based Metamorphic Long-Wavelength InAs Quantum Dots Grown by Molecular Beam Epitaxy

A bilayer stacked InAs/GaAs quantum dot structure grown by molecular beam epitaxy on an In0.05Ga0.95As metamorphic buffer is investigated. By introducing a InGaAs Sb cover layer on the upper InAs quantum dots (QDs) layers, the emission wavelength of the QDs is extended successfully to 1.533 mu m at room temperature, and the density of the QDs is in the range of 4 x 10(9) -8 x 10(9) cm(-2). Strong photoluminescence (PL) intensity with a full width at half maximum of 28.6 meV of the PL spectrum shows good optical quality of the bilayer QDs. The growth of bilayer QDs on metamorphic buffers offers a useful way to extend the wavelengths of GaAs-based materials for potential applications in optoelectronic and quantum functional devices.

Growth and characterization of GaInNAs by molecular beam epitaxy using a nitrogen irradiation method

We propose an innovative technique, making use of the In segregation effect, referred as the N irradiation method, to enhance In-N bonding and extend the emission wavelength of GaInNAs quantum wells (QWs). After the formation of a complete In floating layer, the growth is interrupted and N irradiation is initiated. The majority of N atoms are forced to bond with In atoms and their incorporation is regulated independently by the N exposure time and the As pressure. The effect of the N exposure time and As pressure on the N incorporation and the optical quality of GaInNAs QWs were investigated. Anomalous photoluminescence (PL) wavelength red shifts after rapid thermal annealing (RTA) were observed in the N-irradiated samples, whereas a normal GaInNAs sample revealed a blue shift. This method provides an alternative way to extend the emission wavelength of GaInNAs QWs with decent optical quality. We demonstrate light emission at 1546 nm from an 11-nm-thick QW, using this method and the PL intensity is similar to that of a 7-nm-thick GaInNAs QW grown at a reduced rate. (C) 2008 Elsevier B.V. All rights reserved.