Chemical studies of the passivation of GaAs surface recombination using sulfides and thiols

Steady-state photoluminescence, time-resolved photoluminescence, and x-ray photoelectron spectroscopy have been used to study the electrical and chemical properties of GaAs surfaces exposed to inorganic and organic sulfur donors. Despite a wide variation in S2–(aq) concentration, variation of the pH of aqueous HS–solutions had a small effect on the steady-state n-type GaAs photoluminescence intensity, with surfaces exposed to pH=8, 0.1-M HS–(aq) solutions displaying comparable luminescence intensity relative to those treated with pH=14, 1.0-M Na2S·9H2O(aq). Organic thiols (R-SH, where R=–CH2CH2SH or –C6H4Cl) dissolved in nonaqueous solvents were found to effect increases in steady-state luminescence yields and in time-resolved luminescence decay lifetimes of (100)-oriented GaAs. X-ray photoelectron spectroscopy showed that exposure of GaAs surfaces to these organic systems yielded thiols bound to the GaAs surface, but such exposure did not remove excess elemental As and did not form a detectable As2S3 overlayer on the GaAs. These results imply that complete removal of As0 or formation of monolayers of As2S3 is not necessary to effect a reduction in the recombination rate at etched GaAs surfaces. Other compounds that do not contain sulfur but that are strong Lewis bases, such as methoxide ion, also improved the GaAs steady-state photoluminescence intensity. These results demonstrate that a general class of electron-donating reagents can be used to reduce nonradiative recombination at GaAs surfaces, and also imply that prior models focusing on the formation of monolayer coverages of As2S3 and Ga2S3 are not adequate to describe the passivating behavior of this class of reagents. The time-resolved, high level injection experiments clearly demonstrate that a shift in the equilibrium surface Fermi-level energy is not sufficient to explain the luminescence intensity changes, and confirm that HS– and thiol-based reagents induce substantial reductions in the surface recombination velocity through a change in the GaAs surface state recombination rate

Fuel cell applications for novel metalloporphyrin catalysts

This project utilized Computer-Aided Molecular Design (CAMD) to develop a new class of metalloporphyrin materials for use as catalysts for two fuel cell reactions. The first reaction is the reduction of oxygen at the fuel cell cathode, and this reaction was the main focus of the research. The second reaction we attempted to catalyze was the oxidation of methanol at the anode. Two classes of novel metalloporphyrins were developed. The first class comprised the dodecaphenylporphyrins whose steric bulk forces them into a non-planar geometry having a pocket where oxygen or methanol is more tightly bound to the porphyrin than it is in the case of planar porphyrins. Significant improvements in the catalytic reduction of oxygen by the dodecaphenyl porphyrins were measured in electrochemical cells. The dodecaphenylporphyrins were further modified by fluorinating the peripheral phenyl groups to varying degrees. The fluorination strongly affected their redox potential, but no effect on their catalytic activity towards oxygen was observed. The second class of porphyrin catalysts was a series of hydrogen-bonding porphyrins whose interaction with oxygen is enhanced. Enhancements in the interaction of oxygen with the porphyrins having hydrogen bonding groups were observed spectroscopically. Computer modeling was performed using Molecular Simulations new CERIUS2 Version 1.6 and a research version of POLYGRAF from Bill Goddard`s research group at the California Institute of Technology. We reoptimized the force field because of an error that was in POLYGRAF and corrected a problem in treatment of the metal in early versions of the program. This improved force field was reported in a J. Am. Chem. Soc. manuscript. Experimental measurements made on the newly developed catalysts included the electrochemical testing in a fuel cell configuration and spectroscopic measurements (UV-Vis, Raman and XPS) to characterize the catalysts

TEMPO2, a new pulsar timing package. I: Overview

Contemporary pulsar timing experiments have reached a sensitivity level where systematic errors introduced by existing analysis procedures are limiting the achievable science. We have developed tempo2, a new pulsar timing package that contains propagation and other relevant effects implemented at the 1ns level of precision (a factor of ~100 more precise than previously obtainable). In contrast with earlier timing packages, tempo2 is compliant with the general relativistic framework of the IAU 1991 and 2000 resolutions and hence uses the International Celestial Reference System, Barycentric Coordinate Time and up-to-date precession, nutation and polar motion models. Tempo2 provides a generic and extensible set of tools to aid in the analysis and visualisation of pulsar timing data. We provide an overview of the timing model, its accuracy and differences relative to earlier work. We also present a new scheme for predictive use of the timing model that removes existing processing artifacts by properly modelling the frequency dependence of pulse phase.Comment: Accepted by MNRA

Gravitational wave astronomy of single sources with a pulsar timing array

Abbreviated: We investigate the potential of detecting the gravitational wave from individual binary black hole systems using pulsar timing arrays (PTAs) and calculate the accuracy for determining the GW properties. This is done in a consistent analysis, which at the same time accounts for the measurement of the pulsar distances via the timing parallax. We find that, at low redshift, a PTA is able to detect the nano-Hertz GW from super massive black hole binary systems with masses of \sim10^8 - 10^{10}\,M_{\sun} less than $\sim10^5$\,years before the final merger, and those with less than $\sim10^3 - 10^4$ years before merger may allow us to detect the evolution of binaries. We derive an analytical expression to describe the accuracy of a pulsar distance measurement via timing parallax. We consider five years of bi-weekly observations at a precision of 15\,ns for close-by ($\sim 0.5 - 1$\,kpc) pulsars. Timing twenty pulsars would allow us to detect a GW source with an amplitude larger than $5\times 10^{-17}$. We calculate the corresponding GW and binary orbital parameters and their measurement precision. The accuracy of measuring the binary orbital inclination angle, the sky position, and the GW frequency are calculated as functions of the GW amplitude. We note that the "pulsar term", which is commonly regarded as noise, is essential for obtaining an accurate measurement for the GW source location. We also show that utilizing the information encoded in the GW signal passing the Earth also increases the accuracy of pulsar distance measurements. If the gravitational wave is strong enough, one can achieve sub-parsec distance measurements for nearby pulsars with distance less than $\sim 0.5 - 1$\,kpc.Comment: 16 pages, 5 figure,, accepted by MNRA

Electron spin resonance in membrane research: protein–lipid interactions from challenging beginnings to state of the art

Conventional electron paramagnetic resonance (EPR) spectra of lipids that are spin-labelled close to the terminal methyl end of the acyl chains are able to resolve the lipids directly contacting the protein from those in the fluid bilayer regions of the membrane. This allows determination of both the stoichiometry of lipid–protein interaction (i.e., number of lipid sites at the protein perimeter) and the selectivity of the protein for different lipid species (i.e., association constants relative to the background lipid). Spin-label EPR data are summarised for 20 or more different transmembrane peptides and proteins, and 7 distinct species of lipids. Lineshape simulations of the two-component conventional spin-label EPR spectra allow estimation of the rate at which protein-associated lipids exchange with those in the bulk fluid regions of the membrane. For lipids that do not display a selectivity for the protein, the intrinsic off-rates for exchange are in the region of 10 MHz: less than 10× slower than the rates of diffusive exchange in fluid lipid membranes. Lipids with an affinity for the protein, relative to the background lipid, have off-rates for leaving the protein that are correspondingly slower. Non-linear EPR, which depends on saturation of the spectrum at high radiation intensities, is optimally sensitive to dynamics on the timescale of spin-lattice relaxation, i.e., the microsecond regime. Both progressive saturation and saturation transfer EPR experiments provide definitive evidence that lipids at the protein interface are exchanging on this timescale. The sensitivity of non-linear EPR to low frequencies of spin exchange also allows the location of spin-labelled membrane protein residues relative to those of spin-labelled lipids, in double-labelling experiments

A Recent Class of Chemosensory Neurons Developed in Mouse and Rat

In most animal species, the vomeronasal organ ensures the individual recognition of conspecifics, a prerequisite for a successful reproduction. The vomeronasal organ expresses several receptors for pheromone detection. Mouse vomeronasal type-2 receptors (V2Rs) are restricted to the basal neurons of this organ and organized in four families. Family-A, B and D (family ABD) V2Rs are expressed monogenically (one receptor per neuron) and coexpress with either Vmn2r1 or Vmn2r2, two members of family-C V2Rs. Thus, basal neurons are characterized by specific combinations of two V2Rs. To investigate this issue, we raised antibodies against all family-C V2Rs and analyzed their expression pattern. We found that six out of seven family-C V2Rs (Vmn2r2-7) largely coexpressed and that none of the anti-Vmn2r2-7 antibodies significantly stained Vmn2r1 positive neurons. Thus, basal neurons are divided into two complementary subsets. The first subset (Vmn2r1-positive) preferentially coexpresses a distinct group of family-ABD V2Rs, whereas the second subset (Vmn2r2-7-positive) coexpresses the remaining group of V2Rs. Phylogenetic reconstruction and the analysis of genetic loci in various species reveal that receptors expressed by this second neuronal subset are recent branches of the V2R tree exclusively present in mouse and rat. Conversely, V2Rs expressed in Vmn2r1 positive neurons, are phylogenetically ancient and found in most vertebrates including rodents. Noticeably, the more recent neuronal subset expresses a type of Major Histocompatibility Complex genes only found in murine species. These results indicate that the expansion of the V2R repertoire in a murine ancestor occurred with the establishment of a new population of vomeronasal neurons in which coexists the polygenic expression of a recent group of family-C V2Rs (Vmn2r2-7) and the monogenic expression of a recent group of family-ABD V2Rs. This evolutionary innovation could provide a molecular rationale for the exquisite ability in individual recognition and mate choice of murine species

Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

Several recent studies have examined different aspects of mammalian higher order chromatin structure - replication timing, lamina association and Hi-C inter-locus interactions - and have suggested that most of these features of genome organisation are conserved over evolution. However, the extent of evolutionary divergence in higher order structure has not been rigorously measured across the mammalian genome, and until now little has been known about the characteristics of any divergent loci present. Here, we generate a dataset combining multiple measurements of chromatin structure and organisation over many embryonic cell types for both human and mouse that, for the first time, allows a comprehensive assessment of the extent of structural divergence between mammalian genomes. Comparison of orthologous regions confirms that all measurable facets of higher order structure are conserved between human and mouse, across the vast majority of the detectably orthologous genome. This broad similarity is observed in spite of many loci possessing cell type specific structures. However, we also identify hundreds of regions (from 100 Kb to 2.7 Mb in size) showing consistent evidence of divergence between these species, constituting at least 10% of the orthologous mammalian genome and encompassing many hundreds of human and mouse genes. These regions show unusual shifts in human GC content, are unevenly distributed across both genomes, and are enriched in human subtelomeric regions. Divergent regions are also relatively enriched for genes showing divergent expression patterns between human and mouse ES cells, implying these regions cause divergent regulation. Particular divergent loci are strikingly enriched in genes implicated in vertebrate development, suggesting important roles for structural divergence in the evolution of mammalian developmental programmes. These data suggest that, though relatively rare in the mammalian genome, divergence in higher order chromatin structure has played important roles during evolution

Replication Fork Polarity Gradients Revealed by Megabase-Sized U-Shaped Replication Timing Domains in Human Cell Lines

In higher eukaryotes, replication program specification in different cell types remains to be fully understood. We show for seven human cell lines that about half of the genome is divided in domains that display a characteristic U-shaped replication timing profile with early initiation zones at borders and late replication at centers. Significant overlap is observed between U-domains of different cell lines and also with germline replication domains exhibiting a N-shaped nucleotide compositional skew. From the demonstration that the average fork polarity is directly reflected by both the compositional skew and the derivative of the replication timing profile, we argue that the fact that this derivative displays a N-shape in U-domains sustains the existence of large-scale gradients of replication fork polarity in somatic and germline cells. Analysis of chromatin interaction (Hi-C) and chromatin marker data reveals that U-domains correspond to high-order chromatin structural units. We discuss possible models for replication origin activation within U/N-domains. The compartmentalization of the genome into replication U/N-domains provides new insights on the organization of the replication program in the human genome