Scientific Publications 2005
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2005. "Probing Inhomogeneous Vibrational Reorganization Energy Barriers of Interfacial Electron Transfer." Journal of Physical Chemistry B 109(34):16390-16395. Abstract We report an atomic force microscopy (AFM) and confocal Raman microscopy study on the interfacial electron transfer of a dye-sensitization system, alizarin adsorbed upon TiO2 nanoparticles. Resonance Raman and absorption spectral analyses revealed the distribution of the mode-specific vibrational reorganization energies encompassing different local sites (~250 nm spatial resolution), suggesting spatially inhomogeneous vibrational reorganization energy and different Franck-Condon coupling factors of the interfacial electron transfer. We found that the total vibrational reorganization energy was inhomogeneous from site to site, and specifically, the mode-specific analyses indicated that the energy distributions were inhomogeneous for bridging normal modes and homogeneous for nonbridging normal modes, especially for modes far away from the alizarin- TiO2 coupling hydroxyl modes. Our results demonstrate a significant step forward in characterizing site-specific inhomogeneous interfacial charge transfer dynamics.
2005. "Comparison of Normal and Breast Cancer Cell lines using Proteome, Genome and Interactome data." Journal of Proteome Research 4(6):1952-1960. Abstract Normal and cancer cell line proteomes were profiled using high throughput mass spectrometry techniques. Application of both protein-level and peptide-level sample fractionation combined with LC-MS/MS analysis enabled the confident identification of 2,235 unmodified proteins representing a broad range of functional and compartmental classes. An iterative multi-step search strategy was used to identify post-translational modifications and detected several proteins that are preferentially modified in cancer cells. Information regarding both unmodified and modified protein forms was combined with publicly available gene expression and protein-protein interaction data. The resulting integrated dataset revealed several functionally related proteins that are differentially regulated between normal and cancer cell lines.
2005. "Improving the Performance of Direct Coupled Cluster Analytical Gradients Algorithms." Molecular Physics 103:2081-2083. Abstract The flexibility offered by the coupled cluster (CC) energy functional is exploited to solve for the CC T amplitudes and the CC response Λ amplitudes simultaneously as opposed to the traditional two-stage (first for T and then for Λ for the converged T) approach. We have shown numerically that the proposed scheme does not suffer from convergence failures or unmanageable increases in cost. The potential advantages of the proposed scheme for integral direct atomic orbital basis set CC formulations are discussed.
2005. "Pixel Perfect: a real-time image processing system for biology." Scientific Computing & Instrumentation 22(10):16-20. Abstract Scientific visioning systems often rely upon pixel-perfect precision to produce meaningful data. Cutting-edge equipment used in the study of cell signaling is no exception; proper image alignment is critical for successful experiments. Biologists at Pacific Northwest National Laboratory put together a special multi-spectral confocal microscope that was capable of producing live images of cells and proteins in two simultaneous spectral channels. But there was a problem: the dual images resembled poorly registered Sunday comics and were unusable. This article describes how the biologists worked with programmers to fix the difficulty and make the microscope a truly useful and unique device.
2005. "Electron-Stimulated Sputtering of Thin Amorphous Solid Water Films on Pt(111)." Journal of Chemical Physics 123(5):054702 (1-7). Abstract The electron-stimulated sputtering of thin amorphous solid water films deposited on Pt(111) is investigated. The sputtering appears to be dominated by two processes: 1) electron-stimulated desorption of intact water molecules and 2) electron-stimulated reactions leading to the production of molecular hydrogen and molecular oxygen. The electron-stimulated desorption of water increases monotonically with increasing film thickness. In contrast, the total sputtering – which includes all electron-stimulated reaction channels – is maximized for films of intermediate thickness. The sputtering yield versus thickness suggests that erosion of the film occurs due to reactions at both the water/vacuum interface and the Pt/water interface. Experiments with layered films of D2O and H2O demonstrate significant loss of hydrogen due to reactions at the Pt/water interface. The electron-stimulated sputtering is independent of temperature below ~80 K and increases rapidly at higher temperatures. A simple one-dimensional random walk model qualitatively accounts for the experimental observations.
2005. "Low-Energy Electron-Stimulated Luminescence of Thin H20 and D20 Layers on Pt(111)." Journal of Physical Chemistry B 109(33):15835-15841. Abstract The electron-stimulated luminescence (ESL) from amorphous solid water and crystalline ice films deposited on Pt(111) at 100 K is investigated as a function of the film thickness, incident electron energy (5 – 1000 eV), isotopic composition, and film structure. The ESL emission spectrum has a characteristic double-peaked shape that has been attributed to a transition between a superexcited state ( ) and the dissociative, first excited state ( ) in water: . Comparing the electron-stimulated luminescence and O2 electron-stimulated desorption (ESD) yields versus incident electron energy, we find the ESL threshold blue-shifted from the O2 ESD threshold by ~3 eV, which is close to the center of the emission spectrum near 400 nm and supports the assignment for the ESL. For thin films, radiative and non-radiative interactions with the substrate tend to quench the luminescence. The luminescence yield increases with coverage since the interactions with the substrate become less important. The ESL yield from D2O is ~ 4 times higher than from H2O. Using layered films of H2O and D2O, this sizable isotopic effect on the ESL is exploited to spatially profile the luminescence emission within the ASW films. These experiments show that most of the luminescence is emitted from within the penetration depth of the incident electron. However, the results depend on the order of the isotopes in the film, and this asymmetry can be modeled by assuming some migration of the excited states within the film. The ESL is very sensitive to defects and structural changes in solid water, and the emission yield is significantly higher from amorphous films than from crystalline ice.
2005. "Atomistic Study of the Migration of Di- and Tri-Interstitials in Silicon." Physical Review. B, Condensed Matter 71:Article 245202. Abstract A comprehensive study on the migration of di- and tri-interstitials in silicon is performed using classical molecular dynamics simulations with a Stillinger-Weber potential. At first the structures and energetics of the di- and the tri-interstitial are investigated, and the accuracy of the interatomic potential is tested by comparing the results with literature data obtained by tight-binding and density-functional-theory calculations. Then the migration is investigated for temperatures between 800 and 1600 K. Very long simulation times, large computational cells and different initial conditions are considered. The defect diffusivity, the self-diffusion coefficient per defect and the corresponding effective migration barriers are calculated. Compared to a mono-interstitial, the di-interstitial migrates faster, whereas the tri-interstitial diffuses slower. The mobility of the di- and the mono-interstitial is higher than the mobility of the lattice atoms during the diffusion of these defects. On the other hand, the tri-interstitial mobility is lower than the corresponding atomic mobility. The migration mechanism of the di-interstitial shows a pronounced dependence on the temperature. At low temperature a high mobility on zigzag-like lines along a <110> axis within a {110} plane is found, whereas the change between equivalent <110> directions or equivalent {110} planes occurs seldomly and requires a long simulation time, but the rate of directional change increases with increasing temperature. During the diffusion within {110} planes the di-interstitial moves like a wave packet so that the atomic mobility is lower than that of the defect. On the other hand, the change between equivalent {110} migration planes is characterized by frequent atomic rearrangements. The visual analysis of the tri-interstitial diffusion reveals complex migration mechanisms and a high atomic mobility. The diffusivities and effective migration barriers obtained are compared with the few data from the literature. The implications of the present results for the explanation of experimental data on defect evolution and migration are discussed.
2005. "Migration of Di- and Tri-Interstitials in Silicon." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 228(1-4):212-217. Abstract A comprehensive study on the migration of di- and tri-interstitials in silicon is performed using classical molecular dynamics simulations with the Stillinger-Weber potential. The initial di- and tri-interstitial configurations with the lowest formation energies are determined, and then, the defect migration is investigated for temperatures between 800 and 1600 K. The defect diffusivity and the self-diffusion coefficient per defect are calculated. Compared to the mono-interstitial, the di-interstitial migrates faster, whereas the tri-interstitial diffuses slower. The migration mechanism of the di-interstitial shows a pronounced dependence on the temperature. Like in the case of the mono-interstitial, the mobility of the di-interstitial is higher than the mobility of the lattice atoms during the defect diffusion. On the other hand, the tri-interstitial mobility is lower than the corresponding atomic mobility. The results are compared with data from the literature and the implications of the present results for the analysis of experimental data on defect evolution and migration are discussed.
2005. "Solution Structure of Archaeoglobus fulgidis Peptidyl-tRNA Hydrolase(Pth2) Provides Evidence for an Extensive Conserved Family of Pth2 Enzymes in Archaea, Bacteria and Eukaryotes." Protein Science 14(11):2849-2861. Abstract Abstract: The solution structure of protein AF2095 from the thermophilic archaea Archaeglobus fulgidis, a 123-residue (13.6 kDa) protein, has been determined by NMR methods. The structure of AF2095 is comprised of four a-helices and a mixed b-sheet consisting of four parallel and anti-parallel b-strands, where the a-helices sandwich the b-sheet. Sequence and structural comparison of AF2095 with proteins from Homo sapiens, Methanocaldococcus jannaschii and Sulfolobus solfataricus, reveals that AF2095 is a peptidyl-tRNA hydrolase (Pth2). This structural comparison also identifies putative catalytic residues and a tRNA interaction region for AF2095. The structure of AF2095 is also similar to the structure of protein TA0108 from archaea Thermoplasma acidophilum, which is deposited in the Protein Database but not functionally annotated. The NMR structure of AF2095 has been further leveraged to obtain good quality structural models for 55 other proteins. Although earlier studies have proposed that the Pth2 protein family is restricted to archeal and eukaryotic organisms, the similarity of the AF2095 structure to human Pth2, the conservation of key active-site residues, and the good quality of the resulting homology models demonstrate a large family of homologous Pth2 proteins that are conserved in eukaryotic, archaeal and bacterial organisms, providing novel insights in the evolution of the Pth and Pth2 enzyme families.
2005. "Development of high-temperature ferromagnetism in SnO2 and paramagnetism in SnO by Fe doping." Virtual Journal of Nanoscale Science & Technology 12(7):, Abstract We report the development of room-temperature ferromagnetism in chemically synthesized powder samples of Sn1−xFexO2 *0.005*x*0.05* and paramagnetic behavior in an identically synthesized set of Sn1−xFexO. The ferromagnetic Sn0.99Fe0.01O2 showed a Curie temperature TC=850 K, which is among the highest reported for transition-metal-doped semiconductor oxides. With increasing Fe doping, the lattice parameters of SnO2 decreased and the saturation magnetization increased, suggesting a strong structure-magnetic property relationship. When the Sn0.95Fe0.05O2 was prepared at different temperatures between 200 and 900 °C, systematic changes in the magnetic properties were observed. Combined Mössbauer spectroscopy and magnetometry measurements showed a ferromagnetic behavior in Sn0.95Fe0.05O2 samples prepared at and above 350 °C, but the ferromagnetic component decreased gradually as preparation temperature approached 600 °C. All Sn0.95Fe0.05O2 samples prepared above 600 °C were paramagnetic. X-ray photoelectron spectroscopy, magnetometry, and particle induced x-ray emission studies showed that the Fe dopants diffuse towards the surface of the particles in samples prepared at higher temperatures, gradually destroying the ferromagnetism. Mössbauer studies showed that the magnetically ordered Fe3+ spins observed in the Sn0.95Fe0.05O2 sample prepared at 350 °C is only *24% of the uniformly incorporated Fe3+. No evidence of any iron oxide impurity phases were detected in Sn1−xFexO2 or Sn1−xFexO, suggesting that the emerging magnetic interactions in these systems are most likely related to the properties of the host systems SnO2 and SnO, and their oxygen stoichiometry.
2005. "Development of High-Temperature Ferromagnetism in SnO₂ and Paramagnetism in SnO by Fe Doping." Physical Review. B, Condensed Matter and Materials Physics 72(5):054402 (14 p.). Abstract We report the development of room-temperature ferromagnetism in chemically synthesized powder samples of Sn₁-xFexO₂ (0.005 ≤ x ≤ 0.10) and paramagnetic behavior in an identical set of Sn₁-xFexO. The ferromagnetic Sn₀․₉₉Fe₀․₀₁O₂ showed a Curie temperature Tc = 850 K, which is among the highest reported for dilute magnetic semiconductors. No evidence of dopant segregation was detected in Sn₁-xFexO₂ or Sn1-xFexO, suggesting that the emerging magnetic interactions in these systems are strongly related to the properties of the host systems SnO and SnO₂.
