Difference in Enzyme Activity and Conformation of Glucose Oxidase Before and After Purification

EEnzyme activity of commercial glucose oxidase was enhanced after purification through a strong anionic exchange resin. In order to get a better insight into this phenomenon, surface pressure–area ( –A) isotherms and surface pressure–time ( –t) isotherms was used to study the interaction and the absorption at different pH values of the subphases between octadecylamine and glucose oxidase purified by a styrene system quaternary ammonium type strongly basic anionic exchange resin. Circular dichroism (CD), electrophoresis and enzyme activity measurements were conducted to study these phenomena. A preliminary hypothesis has been suggested to explain why the enzyme activity of purified glucose oxidase was higher than that of the commercial one. © 2002 Elsevier Science B.V. All rights reserved.

An Amino Acid Substitution Matrix for Protein Conformation Identification

Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived from limited data of structure alignment. Using databases PDB_SELECT and DSSP, we create a database of sequence-conformation blocks which explicitly represent sequence-structure relationship. Members in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformation-specific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational segment search and homolog detection.

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.

Comparative phylogeography of the Yellow River schizothoracine fishes (Cyprinidae): Vicariance, expansion, and recent coalescence in response to the Quaternary environmental upheaval in the Tibetan Plateau

National Natural Science Foundation of China (NSFC) [30225008, 30300036, 30530120]; Key Innovation Plan [KSCX2-SW-106]; National Basic Research Project in China [2005cb422005]; National Natural Science Foundation of China [30600062]

Mg acceptor energy levels in AlxInyGa1-x-yN quaternary alloys: An approach to overcome the p-type doping bottleneck in nitrides

The Mg-Ga acceptor energy levels in GaN and random Al8In4Ga20N32 quaternary alloys are calculated using the first-principles band-structure method. We show that due to wave function localization, the MgGa acceptor energy level in the alloy is significantly lower than that of GaN, although the two materials have nearly identical band gaps. Our study demonstrates that forming AlxInyGa1-x-yN quaternary alloys can be a useful approach to lower acceptor ionization energy in the nitrides and thus provides an approach to overcome the p-type doping difficulty in the nitride system.

Epitaxial Growth of AlInGaN Quaternary Alloys by RF-MBE

AlInGaN quaternary alloys were successfully grown on sapphire substrate by radio-frequency plasma-excited molecular beam epitaxy (RF-MBE). AlInGaN quaternary alloys with different compositions were acquired by changing the Al cell's temperature. The streaky RHEED patterns were observed during AlInGaN quaternary alloys growth. Scanning Electron Microscope (SEM), Rutherford back-scattering spectrometry (RBS), X-Ray diffraction (XRD) and Cathodoluminescence (CL) were used to characterize the structural and optical properties of the AlInGaN alloys. The experimental results show that the AlInGaN quaternary alloys grow on the GaN buffer in the layer-by-layer growth mode. When the Al cell's temperature is 920 degrees C, the Al/In ratio in the AlInGaN quaternary alloys is about 4.7, and the AlInGaN can acquire better crystal and optical quality. The X-ray and CL full-width at half-maximum (FWHM) of the AlInGaN are 5arcmin and 25nm, respectively.

p-type doping of GaInNAs quaternary alloys

Using the first-principles band-structure method, we investigate the p-type doping properties and band structural parameters of the random Ga1-xInxN1-yAsy quaternary alloys. We show that the Mg-Ga substitution is a better choice than ZnGa to realize the p-type doping because of the lower transition energy level and lower formation energy. The natural valence band alignment of GaAs and GaInNAs alloys is also calculated, and we find that the valence band maximum becomes higher with the increasing in composition. Therefore, we can tailor the band offset as desired which is helpful to confine the electrons effectively in optoelectronic devices. (C) 2008 Published by Elsevier B.V.

Indium mole fraction effect on the structural and optical properties of quaternary AlInGaN epilayers

AlInGaN quaternary epilayers with varying In mole fraction were investigated using triple-axis x-ray diffraction and photoluminescence measurements. The indium compositional fluctuation is enhanced with increasing In mole fraction, whereas the mosaicity of the AlInGaN epilayers is determined through the GaN template quality. Based on the analysis of the temperature dependence of the PL peak position, it is found that the localization effect strengthens with increasing In mole fraction due to the larger fluctuations of the In distribution. Increasing the influence of the localized state results in increasing the emission intensity and FWHM with the In content.

Investigations on V-defects in quaternary AlInGaN epilayers

The characteristics of V-defects in quaternary AlInGaN epilayers and their correlation with fluctuations of the In distribution are investigated. The geometric size of the V-defects is found to depend on the In composition of the alloy. The V-defects are nucleated within the AlInGaN layer and associated with threading dislocations. Line scan cathodoluminescence (CL) shows a redshift of the emission peak and an increase of the half width of the CL spectra as the electron beam approaches the apex of the V-defect. The total redshift decreases with decreasing In mole fraction in the alloy samples. Although the strain reduction may partially contribute to the CL redshift, indium segregation is suggested to be responsible for the V-defect formation and has a main influence on the respective optical properties. (C) 2004 American Institute Of Physics.

Structural and optical properties of quaternary AlInGaN epilayers grown by MOCVD with various TMGa flows

AlInGaN quaternary epilayers have been grown with various TMGa flows by metalorganic chemical vapor deposition to investigate the influence of growth rate on the structural and optical properties. Triple-axis X-ray diffraction measurements show AlInGaN epilayers have good crystalline quality. Photolummescence (PL) measurements show that the emission intensity of AlInGaN epilayers is twenty times stronger than that of AlGaN epilayer with comparable Al content. V-shaped pits are observed at the surface of AlInGaN epilayers by atomic force microscopy (AFM) and transmission electron microscopy (TEM). High growth rate leads to increased density and size of V-shaped pits, but crystalline quality is not degraded. (C) 2003 Elsevier B.V. All rights reserved.

Crack-free InAlGaN quaternary alloy films grown on Si(111) substrate by metalorganic chemical vapor deposition

Crack-free In0.08Al0.25Ga0.67N quaternary films, with and without thick (> 1.5 mum) high-temperature-GaN (HTGaN) interlayer, have been grown on Si(1 1 1) substrates by a low-pressure metalorganic chemical vapor deposition (MOCVD) system. Mole fractions of In and Al in quaternary alloy layers are determined by Energy dispersive spectroscopy (EDS) and Rutherford backscattering spectrometry (RBS), which are recorded as similar to8% and similar to25-27%, respectively. High-resolution X-ray diffraction (HRXRD) and room temperature photoluminescence (RT-PL) results evidence the film's single crystal structure and the existence of local In- and/or Al-rich regions. Compared with GaN film grwon on Si(1 1 1) substrate, no crack is observed in the quaternary ones. Two explanations are proposed. First, mismatch-induced strain is relaxed significantly due to gradual changes of In concentration. Second, the weak In-N bond is likely to break when the sample is cooled down to the room temperature, which is expected to favor the releasing of thermal stress. (C) 2004 Elsevier B.V. All rights reserved.