Scientific Publications 2006
2006. "Mechanical Properties of Ultrananocrystalline Diamond Prepared in a Nitrogen-Rich Plasma: A Theoretical Study." Physical Review. B, Condensed Matter 74:184112/1-9. doi:10.1103/PhysRevB.74.184112 Abstract An abstract for this journal article is not available at this time.
2006. "Theoretical and experimental evaluation of the low m/z transmission of an electrodynamic ion funnel." Journal of the American Society for Mass Spectrometry 17(4):586-592. Abstract The transmission of ions at low m/z can be either necessary for an application or problematic (e.g. when large numbers of low m/z ions consume a large fraction of an ion trap’s capacity). The low m/z ion transmission limit of an electrodynamic ion funnel has been characterized using both experimental and theoretical approaches. A theoretical model is developed based on a series of infinite wire conductors that represent the ring electrodes of the ion funnel. Mathematical relationships for both low and high m/z cutoffs of the idealized two-dimensional system are derived. The low m/z cutoff is also evaluated through a series of experiments that show it is influenced by both the RF frequency and the DC electric field gradient. However, unlike multipole ion guides, there is no marked dependence of the low m/z cutoff on the RF amplitude, in agreement with theoretical results. With this new understanding, ion funnels can be designed and configured to better match the m/z range requirements for various applications.
2006. "Tip-Enhanced Near-Field Raman Spectroscopy Probing Single Dye-Sensitized TiO2 Nanoparticles." Applied Physics Letters 88(9):Art. No. 093121. Abstract The correlated metallic tip-enhanced Raman spectroscopy and atomic force microscopy (AFM) technique was used to characterize an interfacial electron transfer system of dye-sensitized titanium oxide (TiO2) nanoparticles. We have obtained the near-field Raman spectra that are associated with the photo-induced charge transfer reaction in Ru(4, 4’-dicarboxy-2,2’-bipyridine)2(NCS)2- sensitized TiO2 single nanoparticles. This method demonstrates that tip-enhanced near-field Raman spectroscopy is an effective approach for probing in homogeneous interfacial electron transfers with nanoscale spatial resolution.
2006. "Quantitative Proteome Analysis of Breast Cancer Cell Lines using 18O-Labeling and an Accurate Mass and Time Tag Strategy." Proteomics 6(9):2903-2915. doi:10.1002/pmic200500582 Abstract Proteome comparison of cell lines derived from breast cancer and normal breast epithelium provide opportunities to identify differentially expressed proteins and pathways associated with specific phenotypes. We employed trypsin-catalyzed 16O/18O peptide labeling, FTI-CR mass spectrometry, and the accurate mass and time (AMT) tag strategy to calculate compare the relative protein abundances of hundreds of proteins simultaneously in non-cancer and cancer cell lines derived from breast tissue. A reference panel of cell lines was created to facilitate comparisons of relative protein abundance amongst multiple cell lines and across multiple experiments. A peptide database generated from multidimensional LC separations and MS/MS analysis was used to facilitate subsequent AMT tag-based peptide identifications. This peptide database represented a total of 2,299 proteins, including 514 that were quantified using the AMT tag and 16O/18O strategies. Eighty-six proteins showed at least a 3-fold protein abundance change between cancer and non-cancer cell lines. A comparison of protein expression profiles with previously published gene expression data revealed that 21 of these proteins also had >3-fold differences between the non-cancer and cancer cell lines at the transcriptional level. Clustering of protein abundance ratios revealed that several groups of proteins were differentially expressed between the cancer cell lines
2006. "Electron-Stimulated Production of Molecular Oxygen in Amorphous Solid Water." Journal of Physical Chemistry B 110(6):2723-2731. Abstract The low-energy, electron-stimulated production of molecular oxygen from pure amorphous solid water (ASW) films and ASW films co-dosed with H2O2 is investigated. Layered films of H216O and H218O are used to determine the spatial profile of the reactions in the films leading to O2. The O2 yield is dose-dependent, indicating that precursors are involved in the O2 production. For temperatures below ~80 K, the O2 yield at steady state is relatively low and nearly independent of temperature. At higher temperatures, the yield increases rapidly. The O2 yield is enhanced from H2O2-dosed water films, but the experiments show that H2O2 is not the final precursor in the reactions leading to O2. Instead, a stable precursor for O2 is produced through a multi-step reaction sequence probably involving the reactions of OH radicals to produce H2O2 and then HO2. The O2 is produced in a non-thermal reaction from the HO2. For relatively thick films, the reactions leading to O2 occur at or near the ASW/vacuum interface. However, the electronic excitations which initiate the reactions occur over a larger range in the film. A kinetic model which qualitatively accounts for all of the observations is presented.
2006. "Electron-Stimulated Production of Molecular Oxygen in Amorphous Solid Water on Pt(111): Precursor Transport Through the Hydrogen Bonding Network." Journal of Chemical Physics 125(12):124702 (11 p.). Abstract The low-energy, electron-stimulated production of molecular oxygen from thin amorphous solid water (ASW) films adsorbed on Pt(111) is investigated. For ASW coverages less than ~60 monolayers (ML), the O2 ESD yield depends on coverage in a manner that is very similar to the H2 ESD yield. In particular, both the O2 and H2 ESD yields have a pronounced maximum at ~20 ML due to reactions at the Pt/water interface. The O2 yield is dose-dependent and several precursors (OH, H2O2 and HO2) are involved in the O2 production. Layered films of H216O and H218O are used to profile the spatial distribution of the electron-stimulated reactions leading to oxygen within the water films. Independent of the ASW film thickness, the final reactions leading to O2 occur at or near the ASW/vacuum interface. However for ASW coverages less than ~40 ML, the results indicate that dissociation of water molecules at the ASW/Pt interface contributes to the O2 production at the ASW/vacuum interface presumably via the generation of OH radicals near the Pt substrate. The OH (or possibly OH-) segregates to the vacuum interface where it contributes to the reactions at that interface. The electron-stimulated migration of precursors to the vacuum interface occurs via transport through the hydrogen bond network of the ASW without motion of the oxygen atoms. A simple kinetic model of the non-thermal reactions leading to O2, which was previously used to account for reactions in thick ASW films, is modified to account for the electron-stimulated migration of precursors.
2006. "Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information." Analytical Chemistry 78(14):5026-5039. doi:10.1021/ac060143p Abstract We describe an improved artificial neural network (ANN)-based method for predicting peptide retention times in reversed phase liquid chromatography. In addition to the peptide amino acid composition, this study investigated several other peptide descriptors to improve the predictive capability, such as peptide length, sequence, hydrophobicity and hydrophobic moment, and nearest neighbor amino acid, as well as peptide predicted structural configurations (i.e., helix, sheet, coil). An ANN architecture that consisted of 1052 input nodes, 24 hidden nodes, and 1 output node was used to fully consider the amino acid residue sequence in each peptide. The network was trained using ~345,000 non-redundant peptides identified from a total of 12,059 LC-MS/MS analyses of more than 20 different organisms, and the predictive capability of the model was tested using 1303 confidently identified peptides that were not included in the training set. The model demonstrated an average elution time precision of ~1.5% and was able to distinguish among isomeric peptides based upon the inclusion of peptide sequence information. The prediction power represents a significant improvement over our earlier report (Petritis et al., Anal. Chem. 2003, 75, 1039-1048) and other previously reported models.
2006. "Atomistic Simulations on the Thermal Stability of the Antisite Pair in 3C- and 4H-SiC." Physical Review. B, Condensed Matter 73(12):125206: 1-8. doi:10.1103/PhysRevB.73.125206 Abstract The thermal stability of the first-neighbor antisite pair configurations in 3C- and 4H-SiC is investigated by a comprehensive atomistic study. At first the structure and energetics of these defects is determined in order to check the accuracy of the Gao-Weber interatomic potential used. The results are comparable with literature data obtained by the density-functional theory. Then, the lifetime of the antisite pair configurations is calculated for temperatures between 800 and 2500 K. Both in 3C- and 4H-SiC the thermal stability of the antisite pairs is rather low. In contrast to previous theoretical interpretations, the antisite pair can be therefore not correlated with the DI photoluminescence center that is stable to above 2000 K. The atomic mechanisms during the recombination of the antisite pair in 3C-SiC and of three antisite pair configurations in 4H-SiC is a modified concerted exchange. Due to the different sizes of the silicon and the carbon atoms, this process is not identical with the concerted exchange in Si. Two intermediate metastable configurations found during the recombination are similar to the bond defect in Si. Since the SiC lattice contains two types of atoms, there are also two different types of bond defects. The two bond defects can be considered as the result of the incomplete recombination of a carbon vacancy and a neighboring mixed dumbbell interstitial. For selected temperatures the thermal stability of the antisite pair in 3C-SiC is investigated by molecular dynamics simulations that are based on the density-functional theory. Their results are very similar to those of the atomistic study, i.e. the Gao-Weber potential describes the antisite pair and its recombination reasonably well. The antisite pair in 4H-SiC with the two atoms on hexagonal sites has a slightly different formation energy than the other three antisite pair configurations in 4H-SiC. Its lifetime shows another dependence on the temperature, and its recombination is characterized by a separate motion of atoms.
2006. "Dopant Distribution, Oxygen Stoichiometry and Magnetism of Nanoscale Sn0.99Co0.01O₂." Solid State Communications 139:434-438. doi:10.1016/j.ssc.2005.09.040 Abstract In a recent work, we have shown that chemically synthesized Sn₁-xCoxO₂ nanoscale powders with x ≤ 0.01 are ferromagnetic at room-temperature when prepared by annealing the reaction precipitate in the narrow temperature window of 350 to 600 °C. Combined high resolution x-ray photoelectron spectroscopy and magnetometry measurements on as-prepared and Ar⁺ ion sputtered samples showed that a uniform distribution of Co observed in the 350-600 °C annealed Sn0.99Co0.01O₂ samples is essential to produce stable ferromagnetism, while surface segregation of the dopant atoms in samples annealed at >600 °C destroys it.
2006. "Magnetic Gas Sensing Using a Dilute Magnetic Semiconductor." Applied Physics Letters 89(Art. No. 112509):, doi:10.1063/1.2349284 Abstract The authors report on a magnetic gas sensing methodology to detect hydrogen using the ferromagnetic properties of a nanoscale dilute magnetic semiconductor Sn0.95Fe0.05O2. This work demonstrates the systematic variation of saturation magnetization, coercivity, and remanence of Sn0.95Fe0.05O2 with the hydrogen gas flow rate, thus providing clear experimental evidence of the concept of magnetic gas sensing (using the magnetic property of a material as a gas sensing parameter). Based on the results of using hydrogen as an example for reducing gases, it is believed that any reducing gas capable of changing the oxygen stoichiometry of Sn0.95Fe0.05O2 can be detected using this method. Furthermore, this method presents an alternative gas sensing technology without the use of the electrical contacts.