Lateral periodicity in highly-strained (GaIn)As/Ga(PAs) superlattices investigated by X-ray scattering techniques

In this work we investigate the lateral periodicity of symmetrically strained (GaIn)As/GaAs/Ga(PAs)/GaAs superlattices by means of X-ray scattering techniques. The multilayers were grown by metalorganic Vapour phase epitaxy on (001)GaAs substrates, which were intentionally off-oriented towards the [011]-direction. The substrate off-orientation and the strain distribution was found to affect the structural properties of the superlattices inducing the generation of laterally ordered macrosteps. Several high-resolution triple-crystal reciprocal space maps, which were recorded for different azimuth angles in the vicinity of the (004) Bragg diffraction and contour maps of the specular reflected beam collected in the vicinity of the (000) reciprocal lattice point, are reported and discussed. The reciprocal space maps clearly show a two-dimensional periodicity of the X-ray peak intensity distribution which can be ascribed to the superlattice periodicity in the direction of the surface normal and to a lateral periodicity in a crystallographic direction coinciding with the miscut orientation. The distribution and correlation of the vertical as well as of the lateral interface roughness was investigated by specular reflectivity and diffuse scattering measurements. Our results show that the morphology of the roughness is influenced by the off-orientation angle and can be described by a 2-dimensional waviness.

Characterization of deep centers in AlGaAs/InGaAs/GaAs pseudomorphic HEMT structures grown by molecular beam epitaxy and hydrogen treatment

In AlGaAs/InGaAs/GaAs PM-HEMT structures, the characterization of deep centers, the degradation in electrical and optical properties and their effects on electrical performance of the PM-HEMTs have been investigated by DLTS, SIMS, PL and conventional van der Pauw techniques. The experimental results confirm that the deep level centers correlate strongly with the oxygen content in the AlGaAs layer, the PL response of PM-HEMTs, and the electrical performance of the PM-HEMTs. Hydrogen plasma treatment was used to passivate/annihilate these centers, and the effects of hydrogenation were examined.

Gas source molecular beam epitaxy and thermal stability of Si1-xGex/Si superlattice materials

Gas source molecular beam epitaxy has been used to grow Si1-xGex alloys and Si1-xGex/Si multi-quantum wells (MQWs) on (100) Si substrates with Si2H6 and GeH4 as sources. Heterostructures and MQWs with mirror-like surface morphology, good crystalline qualify, and abrupt interfaces have been studied by a variety of in situ and ex situ techniques. The structural stability and strain relaxation in Si1-xGex/Si heterostructures have been investigated, and compared to that in the As ion-implanted Si1-xGex epilayers. The results show that the strain relaxation mechanism of the non-implanted Si1-xGex epilayers is different from that of the As ion-implanted Si1-xGex epilayers.

Genomic organization, nucleotide sequence analysis of the core histone genes cluster in Chlamys farreri and molecular evolution assessment of the H2A and H2B

This work represents the nucleotide sequence of the core histone gene cluster from scallop Chlamys farreri. The tandemly repeated unit of 5671 bp containing a copy of the four core histone genes H4, H2B, H2A and H3 was amplified and identified by the techniques of homology cloning and genomic DNA walking. All the histone genes in the cluster had the structures in their 3' flanking region which related to the evolution of histone gene expression patterns throughout the cell cycle, including two different termination signals, the hairpin structure and at least one AATAAA polyadenylation signal. In their 5' region, the transcription initiation sites with a conserved sequence of 5'-PyATTCPu-3' known as the CAP site were present in all genes except to H2B, generally 37-45 bp upstream of the start code. Canonical TATA and CAAT boxes were identified only in certain histone genes. In the case of the promoters of H2B and H2A genes, there was a 5'-GATCC-3' element, which had been found to be essential to start transcription at the appropriate site. After this element, in the promoter of H2B, there was another sequence, 5'-GGATCGAAACGTTC-3', which was similar to the consensus sequence of 5'-GGAATAAACGTATTC-3' corresponding to the H2B-specific promoter element. The presence of enhancer sequences (5'-TGATATATG-3') was identified from the H4 and H3 genes, matching perfectly with the consensus sequence defined for histone genes. There were several slightly more complex repetitive DNA in the intergene regions. The presence of the series of conserved sequences and reiterated sequences was consistent with the view that mollusc histone gene cluster arose by duplicating of an ancestral precursor histone gene, the birth-and-death evolution model with strong purifying selection enabled the histone cluster less variation and more conserved function. Meanwhile, the H2A and the H2B were demonstrated to be potential good marks for phylogenetic analysis. All the results will be contributed to the characterization of repeating histone gene families in molluscs.

Introduction to Molecular Analysis of Ectomycorrhizal Communities

A number of methods are available for those researchers considering the addition of molecular analyses of ectomycorrhizal (EcM) fungi to their research projects and weighing the various approaches they might take. Analyzing natural EcM fungal communities has traditionally been a highly skilled, time-consuming process relying heavily on exacting morphological characterization of EcM root tips. Increasingly powerful molecular methods for analyzing EcM communities make this area of research available to a much wider range of researchers. Ecologists can gain from the body of work characterizing EcM while avoiding the requirement for exceptional expertise by carefully combining elements of traditional methods with the more recent molecular approaches. A cursory morphological analysis can yield a traditional quantification of EcM fungi based on tip numbers, a unit with functional and historical significance. Ectomycorrhizal root DNA extracts may then be analyzed with molecular methods widely used for characterizing microbiota. These range from methods applicable only to the simple mixes resulting from careful morphotyping, to community-oriented methods that identify many types in mixed samples as well as provide an estimate of their relative abundances. Extramatrical hyphae in bulk soil can also be more effectively studied, extending characterization of EcM fungal communities beyond the rhizoplane. The trend toward techniques permitting larger sample sets without prohibitive labor and time requirements will also permit us to more frequently address the issues of spatial and temporal variability and better characterize the roles of EcM fungi at multiple scales.

Stable Isotope Probing:Linking Functional Activity to Specific Members of Microbial Communities

Linking organisms or groups of organisms to specific functions within natural environments is a fundamental challenge in microbial ecology. Advances in technology for manipulating and analyzing nucleic acids have made it possible to characterize the members of microbial communities without the intervention of laboratory culturing. Results from such studies have shown that the vast majority of soil organisms have never been cultured, highlighting the risks of culture-based approaches in community analysis. The development of culture-independent techniques for following the flow of substrates through microbial communities therefore represents an important advance. These techniques, collectively known as stable isotope probing (SIP), involve introducing a stable isotope-labeled substrate into a microbial community and following the fate of the substrate by extracting diagnostic molecular species such as fatty acids and nucleic acids from the community and determining which specific molecules have incorporated the isotope. The molecules in which the isotope label appears provide identifying information about the organism that incorporated the substrate. Stable isotope probing allows direct observations of substrate assimilation in minimally disturbed communities, and thus represents an exciting new tool for linking microbial identity and function. The use of lipids or nucleic acids as the diagnostic molecule brings different strengths and weaknesses to the experimental approach, and necessitates the use of significantly different instrumentation and analytical techniques. This short review provides an overview of the lipid and nucleic acid approaches, discusses their strengths and weaknesses, gives examples of applications in various settings, and looks at prospects for the future of SIP technology.

A novel nanometer-scale "gold electrode-molecular wires-silver" junction: An efficient test bed for electrochemical investigation of electron transportation through molecular wires in self-assembled monolayers

A novel "gold electrode-molecular wires-silver" junction was facilely fabricated for electrochemical study on the electron transportation through molecular wires. Rapid electron transportation through this sandwich-like structure was indeed observed by cyclic voltammograms and ac impedance measurements. Since rather reproducible and reliable results are easily available by electrochemical techniques, it would be an efficient and reliable test bed for electrochemical investigation of charge transportation through molecular wires in self-assembled monolayers on electrodes.

Metal-containing molecular wires and their electron transportation properties

Metal-containing conjugated bisthioester 1 was synthesized. It was fabricated into "gold electrode - molecular wires monolayers - gold nanoparticles" junction using self-assembly and nanoparticles deposition techniques. The junction is suitable for investigating the electron transportation property of molecular wires.

Temperature dependence of the distribution of the first passage time: Results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Go-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T-opt*. The optimal folding temperature T-opt* is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T-opt* and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T-opt* and start to diverge when the temperature is lower than T-opt*. The distribution of FPT is close to a log-normal-like distribution at T* greater than or equal to T-opt*. At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.

High-sensitivity molecular mass determination of lysozyme prior to MALDI-MS

Sodium dodecyl sulfate(SDS) is a powerful solubilizing detergent which is often used during the separation of highly complex protein mixtures by one- or two-dimensional (2D) gel electrophoresis. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a widely used technique for mass spectrometric analysis of some protein molecules compared to other techniques. But the presence of SDS or some salts usually leads to signal deterioration when using MALDI-MS. A method for using nitrocellulose membrane as the solid-phase carrier combined with n-octyl-beta-D-glucopyranoside in the matrix highly enhances the sensitivity of the molecular mass determination of lysozyme. This technique has the advantage that the signal-to-noise of the molecular weight profile is improved compared with the mass spectrum and the profile is relatively easy to interpret.

Investigating mechanical response of single chain polystyrene particles by scanning probe techniques

Single chain polystyrene particles were obtained by dilute solution casting method. The sample with both single chain polystyrene particles and multi-chain (more than 1000 molecular chains) polystyrene particles was obtained by a little more concentrate solution. Force modulation technique showed that single chain polystyrene particles were softer than multichain polystyrene particles. On the other hand, nanoindentation experiments on multi-chain particles and bulk polystyrene manifested that the elastic modulus of multi-chain polystyrene particles was very close to that of bulk polystyrene. Therefore, it was concluded that single chain polystyrene particles were softer than bulk polystyrene,which indicated that the density of intrachain entanglement points in the single chain polystyrene particles was not as large as that of the interchain entanglement points in the bulk state.

Encapsulation of Eu(TTA)(3) into MCM-41 mesoporous molecular sieve by sol-gel method

The rare earth complex Eu(TTA)(3) was successfully encapsulated into MCM-41 mesoporous molecular sieve by the addition of the complex into the sol-gel mixture for the synthesis of MCM-41 mesoporous material under microwave radiation. The as-synthesized MCM-41-hosted Eu(TTA)(3) mesophase was confirmed to possess hexagonally ordered mesostructure and a uniform crystal. size of about 30 nm with XRD and HRTEM techniques. Moreover, the IR spectrum, photoluminescence effect and fluorescence lifetime of the Eu(TTA)(3)/MCM-41 hybrid were also studied. An increase in Stokes' shift and no change in luminescence lifetime were observed to the resultant mesophase in comparison with Eu(TTA)(3) in ethanol solution.

Rapid electron propagation through molecular wire monolayers sandwiched between two gold electrodes

Conjugated bisthioester 1 was synthesized applying Sonogashira coupling reactions. Using self-assembly in combination with nanoparticles deposition techniques, we developed a novel method to fabricate a "gold electrode-molecular wire monolayers-gold nanoparticles" sandwich-like structure. Rapid electron propagation through this sandwich-like structure was observed by cyclic voltammetry and ac impedance measurements.

Atom space distance and computing of molecular similarity

A mathematical model on computation of molecular similarity was suggested, The algorithmic techniques for measuring the degree of similarity between pairs of three-dimensional chemical molecules was represented by modified interatomic distance matrices. Current work was carried out on Indigo 2 work station with Sybyl software. Four groups of molecules were used to compute the molecules similarity to testing the mathematical model with satisfactory results.

Characterization of the structural and functional changes of hemoglobin in dimethyl sulfoxide by spectroscopic techniques

Circular dichroism (CD), fourier transform infrared (FTIR), and fluorescence spectroscopy were used to explore the effect of dimethyl sulfoxide (DMSO) on the structure and function of hemoglobin (Hb). The native tertiary structure was disrupted completely when the concentration of DMSO reached 50% (v/v), which was determined by loss of the characteristic Soret CD spectrum. Loss of the native tertiary structure could be mainly caused by breaking the hydrogen bonds, between the heme propionate groups and nearby surface amino acid residues, and by disorganizing the hydrophobic interior of this protein. Upon exposure of Hb to 52% DMSO for ca. 12 h in a D2O medium no significant change in 1652 cm(-1) band of the FTIR spectrum was produced, which demonstrated that alpha-helical structure predominated. When the concentration of DMSO increased to 57%: (1) the band at 1652 cm(-1) disappeared with the appearance of two new bands located at 1661 and 1648 cm(-1); (2) another new band at 1623 cm(-1) was attributed to the formation of intermolecular beta-sheet or aggregation, which was the direct consequence of breaking of the polypeptide chain by the competition of S=O groups in DMSO with C=O groups in amide bonds. Further increasing the DMSO concentration to 80%, the intensity at 1623 cm(-1) increased, and the bands at 1684, 1661 and 1648 cm(-1) shifted to 1688, 1664 and 1644 cm(-1), respectively. These changes showed that the native secondary structure of Hb was last and led to further aggregation and increase of the content of 'free' amide C=O groups. In pure DMSO solvent, the major band at 1664 cm(-1) indicated that almost all of both the intermolecular beta-sheet and any residual secondary structure were completely disrupted. The red shift of the fluorescence emission maxima showed that the tryptophan residues were exposed to a greater hydrophilic environment as the DMSO content increased. GO-binding experiment suggested that the biological function of Hb was disrupted seriously even if the content of DMSO was 20%. (C) 1998 Elsevier Science B.V. All rights reserved.