Cluster and periodic DFT calculations of adsorption and activation of CO2 on the Cu(hkl) surfaces

The adsorption behavior and thermal activation of carbon dioxide on the Cu(1 1 1), Cu(1 0 0), and Cu(1 1 0) surfaces have been investigated by means of density functional theory calculations and cluster models and periodic slabs. According to the cluster models, the optimized results indicate that the basis set of C and O atoms has a distinct effect on the adsorption energy, but an indistinct one on the equilibrium geometry. For the CO₂/Cu(hkl) adsorption systems studied here, the final structure of adsorbed CO₂ is near linear and the preferred modes for the adsorption of CO₂ onto the Cu(1 1 1), Cu(1 0 0), and Cu(1 1 0) surfaces are the side-on adsorption at the cross bridge site with an adsorption energy of 13.06 kJ/mol, the side-on adsorption at the short bridge site (13.54 kJ/mol), and the end-on adsorption on the on-top site with C–O bonds located along the short bridge site (26.01 kJ/mol), respectively. However, the calculated adsorption energies from periodic slabs are lower as compared to the experimental data as well as the cluster model data, indicating that the periodic slab approach of generalized gradient approximation in the density function theory may be not suitable to obtain quantitative information on the interaction of CO₂ with Cu(hkl) surfaces.     

Substituent effects on the kinetics for the chemiluminescence reaction of 6-arylimidazo[1,2-a]pyrazin-3(7H)-ones (Cypridina luciferin analogues): support for the single electron transfer (SET)-oxygenation mechanism with triplet molecular oxygen

Kinetics of chemiluminescence reactions of 2-methyl-6-phenylimidazo[1,2-a]pyrazin-3(7H)-one (1c, Cypridina luciferin analogue) and substituent effects of the 6-aryl group of derivatives 1 strongly suggest that the rate-determining step is a single electron transfer from an anion derived from 1 to a triplet molecular oxygen (O₂) in the oxygenation process.     

Atomic structure of InAs quantum dots on GaAs

In recent years, the self-assembled growth of semiconductor nanostructures, that show quantum size effects, has been of considerable interest. Laser devices operating with self-assembled InAs quantum dots (QDs) embedded in GaAs have been demonstrated. Here, we report on the InAs/GaAs system and raise the question of how the shape of the QDs changes with the orientation of the GaAs substrate. The growth of the InAs QDs is understood in terms of the Stranski–Krastanow growth mode. For modeling the growth process, the shape and atomic structure of the QDs have to be known. This is a difficult task for such embedded entities.

In our approach, InAs is grown by molecular beam epitaxy on GaAs until self-assembled QDs are formed. At this point the growth is interrupted and atomically resolved scanning tunneling microscopy (STM) images are acquired. We used preparation parameters known from the numerous publications on InAs/GaAs. In order to learn more about the self-assemblage process we studied QD formation on different GaAs(0 0 1), (1 1 3)A, and ( )B substrates. From the atomically resolved STM images we could determine the shape of the QDs. The quantum “dots” are generally rather flat entities better characterized as “lenses”. In order to achieve this flatness, the QDs are terminated by high-index bounding facets on low-index substrates and vice versa. Our results will be summarized in comparison with the existing literature.     

The surface and materials science of tin oxide

The study of tin oxide is motivated by its applications as a solid state gas sensor material, oxidation catalyst, and transparent conductor. This review describes the physical and chemical properties that make tin oxide a suitable material for these purposes. The emphasis is on surface science studies of single crystal surfaces, but selected studies on powder and polycrystalline films are also incorporated in order to provide connecting points between surface science studies with the broader field of materials science of tin oxide. The key for understanding many aspects of SnO₂ surface properties is the dual valency of Sn. The dual valency facilitates a reversible transformation of the surface composition from stoichiometric surfaces with Sn⁴⁺ surface cations into a reduced surface with Sn²⁺ surface cations depending on the oxygen chemical potential of the system. Reduction of the surface modifies the surface electronic structure by formation of Sn 5s derived surface states that lie deep within the band gap and also cause a lowering of the work function. The gas sensing mechanism appears, however, only to be indirectly influenced by the surface composition of SnO₂. Critical for triggering a gas response are not the lattice oxygen concentration but chemisorbed (or ionosorbed) oxygen and other molecules with a net electric charge. Band bending induced by charged molecules cause the increase or decrease in surface conductivity responsible for the gas response signal. In most applications tin oxide is modified by additives to either increase the charge carrier concentration by donor atoms, or to increase the gas sensitivity or the catalytic activity by metal additives. Some of the basic concepts by which additives modify the gas sensing and catalytic properties of SnO₂ are discussed and the few surface science studies of doped SnO₂ are reviewed. Epitaxial SnO₂ films may facilitate the surface science studies of doped films in the future. To this end film growth on titania, alumina, and Pt(1 1 1) is reviewed. Thin films on alumina also make promising test systems for probing gas sensing behavior. Molecular adsorption and reaction studies on SnO₂ surfaces have been hampered by the challenges of preparing well-characterized surfaces. Nevertheless some experimental and theoretical studies have been performed and are reviewed. Of particular interest in these studies was the influence of the surface composition on its chemical properties. Finally, the variety of recently synthesized tin oxide nanoscopic materials is summarized.     

BRCA1 mutation screening using restriction endonuclease fingerprinting-single-strand conformation polymorphism in an automated capillary electrophoresis system

Efficient mutation scanning techniques are needed for the rapid detection of novel disease-associated mutations and rare-sequence variants of putative importance. The large size of the breast cancer 1 gene (BRCA1) and the many mutations found throughout its entire coding sequence make screening for mutations in this gene particularly challenging. We have developed a method for screening exon 11 of the BRCA1 gene based on restriction enzyme digestion of fluorescence-labeled polymerase chain reaction (PCR) products followed by single-strand conformation polymorphism (SSCP) using an automated capillary electrophoresis system, denoted capillary restriction endonuclease fingerprinting (REF)-SSCP electrophoresis. Using this strategy on a control set of samples, we were able to detect 17 of 18 known sequence alterations. The method was then applied to screen 73 Norwegian females with family histories of breast and/or ovarian cancer. A total of 172 sequence alterations were detected, including substitutions, insertions, and deletions. One novel substitution of unknown function was identified. Sequencing of all samples negative in the capillary REF-SSCP system gave no additional mutations confirming the high sensitivity of the described methodology. Capillary REF-SSCP electrophoresis appeared as a technically convenient technique, requiring amplification of fewer PCR fragments than traditional SSCP. The novel strategy allows high-throughput mutation scanning without radioactive labeling and polyacrylamide gel electrophoresis (PAGE).     

Markov processes in single molecule fluorescence

This article examines the current status of Markov processes in single molecule fluorescence. For molecular dynamics to be described by a Markov process, the Markov process must include all states involved in the dynamics and the first-passage time (FPT) distributions out of those states must be describable by a simple exponential law. The observation of non-exponential FPT distributions or other evidence of non-Markovian dynamics is common in single molecule studies and offers an opportunity to expand the Markov model to include new dynamics or states that improve understanding of the system.     

New understanding of the nature of OH adsorption on Pt(1 1 1) electrodes

The adsorption of hydroxyl on Pt(1 1 1) single crystal electrodes from aqueous acidic solutions is carefully reinvestigated. The effect of small additions (10⁻⁸–10⁻⁵ M) of chloride and bisulphate anions on the OH adsorption region in perchloric acid solution has been studied. Two regions can be differentiated in the voltammetric profile, that behave differently after the addition of the foreign anion. The initial broad adsorption process is unaffected until the highest concentration is attained. However, the sharper peak at higher potentials is affected even at the lower anion concentration. Since mass transport limitations allow to discard the anion adsorption as the main process giving this peak, we propose that the two processes are due to the dissociative adsorption of two different kinds of water, that are affected by the anion in a different way. From this idea, a new model, based on the Frumkin adsorption isotherm, is proposed, which gives an excellent fit of the experimental results.     

Insights on the origin of the structural phase transition in BaV10O15 from electronic structure calculations and the effect of Ti-doping on its structure and electrical transport properties

Band structure calculations at the level of LMTO-ASA provide insight into the electronic structure of BaV₁₀O₁₅ and the origin of the structural phase transition. A crystal orbital Hamiltonian population/integrated crystal orbital Hamiltonian population analysis provides evidence that the crystallographic phase transition is driven by V-V bond formation. As well, the energy bands near the Fermi level are very narrow, <1 eV, consistent with the fact that the observed insulating behavior can be due to electron localization via either Mott-Hubbard correlation and/or Anderson disorder. The partial solid solution, BaV_10−xTi_xO₁₅, was examined to study the effect of Ti-doping at the V sites on the structure and electronic transport properties. In spite of the non-existence of “BaTi₁₀O₁₅”, the limiting x=8, as indicated by a monotonic increase in the cell volume and systematic changes in properties. This limit may be due to the difficulty of stabilizing Ti²⁺ in this structure. For x=0.5 both the first order structural phase transition and the magnetic transition at 40 K are quenched. The samples obey the Curie-Weiss law to x=3 with nearly spin only effective moments along with θ values which range from −1090 K (x=0.5) to −1629 K (x=3). For x>3 a very large, ∼2×10⁻³ emu/mol, temperature independent (TIP) contribution dominates. Conductivity measurements on sintered, polycrystalline samples show semiconducting behavior for all compositions. Activation energies for Mott hopping derived from high temperature data range from ∼0.1 eV for x=0-1 and fall to a plateau of 0.06 eV for x=3-7. Low temperature data for x=3, 5 and 7 show evidence for Mott variable range hoping (VRH) with a T^1/4 law and in one case between 5 and 17 K, a Efros-Shklovskii correlated hopping, T^1/2 law, was seen, in sharp contrast to BaV₁₀O₁₅ where only the E-S law was observed up to 75 K. Seebeck coefficients are small (<35 μV/K), positive, roughly TIP and increase with increasing x up to x=5. This may point to a Heikes hopping of holes but a simple single carrier model is impossible. The compositions for x>3 are remarkable in that local moment behavior is lost, yet a metallic state is not reached. The failure of this system to be driven metallic even at such high doping levels is not fully understood but it seems clear that disorder induced carrier localization plays a major role.     

A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data

Single nucleotide polymorphism (SNP) arrays were used to detect chromosomal regions with DNA copy number alterations. Current statistical methods for microarray-based comparative genomic hybridization (array-CGH) analysis generally assume certain relationships among adjacent markers on the same chromosome, and these assumptions may be questionable. For an SNP-array-based CGH study, multiple normal reference SNP arrays were collected. In order to utilize these normal reference SNP arrays, we derived an empirical distribution of signal ratios for each SNP marker. With an assumed threshold value for the overall error rate control and the defined signal ratio ranges for chromosomal amplification and deletion, we proposed a procedure to identify chromosomal alteration regions based on several bootstrapped one-sample t-tests and the false discovery rate control. When we have multiple arrays for different individuals with the same disease, our method can also be used to detect SNP markers for chromosomal alteration regions that are common among these individuals. We applied our method to a published SNP array data set for breast carcinoma cell lines. For an individual with breast cancer, numerous chromosomal alteration regions were identified. Compared to results of previous studies, our method identified more chromosomal alteration regions, with some being implicated in the literature to harbor genes associated with breast cancer. For multiple cancer arrays, our results suggested the existence of common chromosomal alteration regions. However, a high proportion of false positives also indicated that genetic variations among different individuals with breast cancer can be present.     

Large deviation analysis of the single server queue

We establish the large deviation principle (LDP) for the virtual waiting time and queue length processes in the GI/GI/1 queue. The rate functions are found explicitly. As an application, we obtain the logarithmic asymptotics of the probabilities that the virtual waiting time and queue length exceed high levels at large times. Additional new results deal with the LDP for renewal processes and with the derivation of unconditional LDPs for conditional ones. Our approach applies in large deviations ideas and methods of weak convergence theory.This work was supported in part by AT&T Bell Labs.