Spatial distribution of ions in a linear octopole radio-frequency ion trap in the space-charge limit

We have explored the spatial distribution of an ion cloud trapped in a linear octopole radio-frequency (rf) ion trap. The two-dimensional distribution of the column density of stored silver dimer cations was measured via photofragment-ion yields as a function of the position of the incident laser beam over the transverse cross section of the trap. The profile of the ion distribution was found to be dependent on the number of loaded ions. Under high ion-loading conditions with a significant space-charge effect, ions form a ring profile with a maximum at the outer region of the trap, whereas they are localized near the center axis region at low loading of the ions. These results are explained quantitatively by a model calculation based on equilibrium between the space-charge-induced potential and the effective potential of the multipole rf field. The maximum adiabaticity parameter \eta_max is estimated to be about 0.13 for the high ion-density condition in the present octopole ion trap, which is lower than typical values reported for low ion densities; this is probably due to additional instability caused by the space charge.Comment: 8 pages, 5 figure

GaInNAs-based Hellish-vertical cavity semiconductor optical amplifier for 1.3 μm operation

Hot electron light emission and lasing in semiconductor heterostructure (Hellish) devices are surface emitters the operation of which is based on the longitudinal injection of electrons and holes in the active region. These devices can be designed to be used as vertical cavity surface emitting laser or, as in this study, as a vertical cavity semiconductor optical amplifier (VCSOA). This study investigates the prospects for a Hellish VCSOA based on GaInNAs/GaAs material for operation in the 1.3-μm wavelength range. Hellish VCSOAs have increased functionality, and use undoped distributed Bragg reflectors; and this coupled with direct injection into the active region is expected to yield improvements in the gain and bandwidth. The design of the Hellish VCSOA is based on the transfer matrix method and the optical field distribution within the structure, where the determination of the position of quantum wells is crucial. A full assessment of Hellish VCSOAs has been performed in a device with eleven layers of Ga0.35In0.65N0.02As0.08/GaAs quantum wells (QWs) in the active region. It was characterised through I-V, L-V and by spectral photoluminescence, electroluminescence and electro-photoluminescence as a function of temperature and applied bias. Cavity resonance and gain peak curves have been calculated at different temperatures. Good agreement between experimental and theoretical results has been obtained

Gain studies of 1.3-μm dilute nitride HELLISH-VCSOA for optical communications

The hot electron light emitting and lasing in semiconductor heterostructure-vertical-cavity semiconductor optical amplifier (HELLISH-VCSOA) device is based on Ga0.35In0.65 N0.02As0.08/GaAs material for operation in the 1.3-μm window of the optical communications. The device has undoped distributed Bragg reflectors (DBRs). Therefore, problems such as those associated with refractive index contrast and current injection, which are common with doped DBRs in conventional VCSOAs, are avoided. The gain versus applied electric field curves are measured at different wavelengths using a tunable laser as the source signal. The highest gain is obtained for the 1.3-μm wavelength when an electric field in excess of 2 kV/cm is applied along the layers of the device

Resonant Raman study of local vibrational modes in AlGaAsN layers

We report on resonant inelastic light scattering in dilute AlGaAsN films. Intense narrow peaks associated to N-related local vibration modes (LVM) have been observed around 325, 385, 400, 450, 500 and 540 cm−1. Their frequencies are compared to density functional theory supercell calculations of AlnGa4−nN complexes (n=1−4). We find clear indications of the formation of Al4N complexes. The values of the extended phonon frequencies reveal changes in the N distribution depending on the growth conditions. The LVM spectra are resonant in the energy range from 1.75 to 1.79 eV, which corresponds to an N-related electronic transition. Our results confirm the preferential bonding of N to Al in AlGaAsN

Effect of Co-60 gamma-ray irradiation on electrical properties of Ti/Au/GaAs1-xNx Schottky diodes

Current-voltage (I-V), capacitance-voltage-frequency (C-V-f) and conductance-voltage-frequency (G/ω-V-f) measurements at room temperature are used to study 50 kGy 60Co γ-ray electrical properties irradiation dependence of Ti/Au/GaAs1−xNx Schottky diodes with 0.2%; 0.4%; 0.8% and 1.2% nitrogen dilution. This γ-ray irradiation induces a permanent damage that has increased ideality factor and series resistance for all samples. It was accompanied by a decrease in Schottky barrier height with nitrogen content up to 0.4%N and remained constant thereafter. Radiation was also found to degrade the reverse leakage current. At high frequency (1 MHz), capacitance and conductance decreased after radiation due to a decrease in net doping concentration. Interface state density and series resistance were determined from C-V-f and G/ω-V-f characteristics using Hill-Coleman methods. Interface states density exponentially decreased with increasing frequency confirming the behavior of interface traps response to ac signal. Series resistance increases after irradiation is attributed to carrier's removal effect and mobility degradation. It has two peaks in the accumulation and inversion region for some diodes (0.4%N, 0.8%N). γ-ray irradiation produced traps levels and recombination centers that reduce relaxation time. An increase in %N content can impede irradiation damage with even some compensation when the percent of diluted nitrogen is high (1.2%N)

Optical gain in 1.3-μm electrically driven dilute nitride VCSOAs

We report the observation of room-temperature optical gain at 1.3 μm in electrically driven dilute nitride vertical cavity semiconductor optical amplifiers. The gain is calculated with respect to injected power for samples with and without a confinement aperture. At lower injected powers, a gain of almost 10 dB is observed in both samples. At injection powers over 5 nW, the gain is observed to decrease. For nearly all investigated power levels, the sample with confinement aperture gives slightly higher gain

Conflict between Translation Initiation and Elongation in Vertebrate Mitochondrial Genomes

The strand-biased mutation spectrum in vertebrate mitochondrial genomes results in an AC-rich L-strand and a GT-rich H-strand. Because the L-strand is the sense strand of 12 protein-coding genes out of the 13, the third codon position is overall strongly AC-biased. The wobble site of the anticodon of the 22 mitochondrial tRNAs is either U or G to pair with the most abundant synonymous codon, with only one exception. The wobble site of Met-tRNA is C instead of U, forming the Watson-Crick match with AUG instead of AUA, the latter being much more frequent than the former. This has been attributed to a compromise between translation initiation and elongation; i.e., AUG is not only a methionine codon, but also an initiation codon, and an anticodon matching AUG will increase the initiation rate. However, such an anticodon would impose selection against the use of AUA codons because AUA needs to be wobble-translated. According to this translation conflict hypothesis, AUA should be used relatively less frequently compared to UUA in the UUR codon family. A comprehensive analysis of mitochondrial genomes from a variety of vertebrate species revealed a general deficiency of AUA codons relative to UUA codons. In contrast, urochordate mitochondrial genomes with two tRNA(Met) genes with CAU and UAU anticodons exhibit increased AUA codon usage. Furthermore, six bivalve mitochondrial genomes with both of their tRNA-Met genes with a CAU anticodon have reduced AUA usage relative to three other bivalve mitochondrial genomes with one of their two tRNA-Met genes having a CAU anticodon and the other having a UAU anticodon. We conclude that the translation conflict hypothesis is empirically supported, and our results highlight the fine details of selection in shaping molecular evolution

The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria

<p>Abstract</p> <p>Background</p> <p>The Hemichordata comprises solitary-living Enteropneusta and colonial-living Pterobranchia, sharing morphological features with both Chordata and Echinodermata. Despite their key role for understanding deuterostome evolution, hemichordate phylogeny is controversial and only few molecular data are available for phylogenetic analysis. Furthermore, mitochondrial sequences are completely lacking for pterobranchs. Therefore, we determined and analyzed the complete mitochondrial genome of the pterobranch <it>Rhabdopleura compacta </it>to elucidate deuterostome evolution. Thereby, we also gained important insights in mitochondrial tRNA evolution.</p> <p>Results</p> <p>The mitochondrial DNA of <it>Rhabdopleura compacta </it>corresponds in size and gene content to typical mitochondrial genomes of metazoans, but shows the strongest known strand-specific mutational bias in the nucleotide composition among deuterostomes with a very GT-rich main-coding strand. The order of the protein-coding genes in <it>R. compacta </it>is similar to that of the deuterostome ground pattern. However, the protein-coding genes have been highly affected by a strand-specific mutational pressure showing unusual codon frequency and amino acid composition. This composition caused extremely long branches in phylogenetic analyses. The unusual codon frequency points to a selection pressure on the tRNA translation system to codon-anticodon sequences of highest versatility instead of showing adaptations in anticodon sequences to the most frequent codons. Furthermore, an assignment of the codon AGG to Lysine has been detected in the mitochondrial genome of <it>R. compacta</it>, which is otherwise observed only in the mitogenomes of some arthropods. The genomes of these arthropods do not have such a strong strand-specific bias as found in <it>R. compacta </it>but possess an identical mutation in the anticodon sequence of the tRNA_Lys.</p> <p>Conclusion</p> <p>A strong reversed asymmetrical mutational constraint in the mitochondrial genome of <it>Rhabdopleura compacta </it>may have arisen by an inversion of the replication direction and adaptation to this bias in the protein sequences leading to an enigmatic mitochondrial genome. Although, phylogenetic analyses of protein coding sequences are hampered, features of the tRNA system of <it>R. compacta </it>support the monophyly of Ambulacraria. The identical reassignment of AGG to Lysine in two distinct groups may have occurred by convergent evolution in the anticodon sequence of the tRNA_Lys.</p