Scientific Publications 2007
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2007. "Growth and surface characterization of sputter-deposited molybdenum oxide thin films." Applied Surface Science 253(12):5368-5374. doi:10.1016/j.apsusc.2006.12.012 Abstract Molybdenum oxide thin films were produced by magnetron sputtering using a molybdenum (Mo) target. The sputtering was performed in a reactive atmosphere of argon-oxygen gas mixture under varying conditions of substrate temperature (Ts) and oxygen partial pressure (pO2). The effect of Ts and pO2 on the growth and microstructure of molybdenum oxide films was examined in detail using reflection high-energy electron diffraction (RHEED), Rutherford backscattering spectrometry (RBS), energy dispersive X-ray spectrometry (EDS), X-ray photoelectron spectroscopy (XPS), and scanning electron microscopy (SEM) measurements. The analyses indicate that the effect of Ts and pO2 on the microstructure and phase of the grown molybdenum oxide thin films is remarkable. RHEED and RBS results indicate that the films grown at 445 *C under 62.3% O2 pressure were stoichiometric and polycrystalline MoO3. Films grown at lower pO2 were nonstoichiometric MoOx films with the presence of secondary phase. The microstructure of the grown Mo oxide films is discussed and conditions were optimized to produce phase pure, stoichiometric, and highly textured polycrystalline MoO3 films.
2007. "NMR structure and binding studies confirm that PA4608 from Pseudomonas aeruginosa is a PilZ domain and a c-di-GMP binding protein ." Proteins. Structure, Function, and Bioinformatics 66(2):266-271. doi:10.1002/prot.21199 Abstract PA4608 is a 125 residue protein with a proposed identification as a PilZ domain and c-di-GMP adaptor protein that plays a role in bacterial second-messenger regulated processes. The NMR structure of PA4608 has been determined and c-di-GMP binding has been confirmed by NMR titration studies. The monomeric structure of PA4608 contains a six-stranded anti-parallel barrel flanked by three helices. Conserved surface residues among PA4608 homologs suggest the the c-di-GMP binding site is at one end of the barrel and includes residues in the helices as well as in the unstructured N-terminus. Chemical shift changes upon binding to c-di-GMP confirm that PA4608 binds to c-di-GMP. This evidence supports the hypothesis that proteins containing PilZ domains are the long-sought c-di-GMP adaptor proteins.
2007. "Effect of Mn doping on the structural, morphological, optical and magnetic properties of indium tin oxide films." Journal of Materials Science. Materials in Electronics 18(12):1197-1201. doi:10.1007/s10854-007-9277-6 Abstract We report high temperature ferromagnetism in Mn (3 - 4 at.%) doped optically transparent indium tin oxide (ITO) films prepared by a sol-gel based technique. The films showed 16 - 18 nm sized uniformly distributed particles with high phase purity. Magnetic measurements yield a coercivity Hc ~ 80 Oe and a saturation magnetization Ms ~ 0.39 B/Mn2+ ion at 300 K with a Tc > 600 K for the 3.2% Mn doped ITO film. Magnetic force microscopy showed convincing evidence of a uniformly distributed ferromagnetic phase with well defined magnetic domains spread over hundreds of independent nanoparticles.
2007. "On the room-temperature ferromagnetism of Zn1-xCrxO thin films deposited by reactive co-sputtering." Solar Energy Materials and Solar Cells 91(15-16):1496-1502. doi:10.1016/j.solmat.2007.03.012 Abstract We report on the preparation and detailed characterization of ferromagnetic Zn1-xCrxO thin films deposited on Si substrates using reactive co-sputtering of Cr and Zn in controlled oxygen atmospheres. X-ray diffraction data showed wurtzite ZnO peaks in the ferromagnetic films prepared with lower Cr powers, whose position and intensities are influenced by Cr doping. However, samples prepared with higher Cr powers did not show ferromagnetism but displayed evidence of Cr2O3 and ZnCr2O4 phases with no ZnO phase. The magnetization is higher (saturation magnetization Ms = 18 emu/cm3) for lower Cr concentrations and decreases for higher Cr doping. The samples were investigated extensively to understand the film composition, dopant distribution, homogeneity and potential origin of the observed ferromagnetism. Particle induced x-ray emission studies were employed to determine the chemical composition as well as the Cr/Zn ratio in the films. Film uniformity and homogeneity, investigated using Rutherford backscattering spectrometry, showed a relatively uniform ZnO layer in the as-prepared samples but, in a sample annealed at 800 oC, showed some diffusion of Si from the substrate. X-ray photoelectron spectroscopy studies indicated that Cr ions are in the oxidized state, but showed changes in the binding energy and Cr concentration when measured after removing 10 nm from the surface using Ar ion sputtering. Possible origins of the observed ferromagnetic behavior are discussed based on the comprehensive characterization results.
2007. "A complete backbone spectral assignment of human apolipoprotein AI on a 38 kDa preβHDL (Lp1-AI) particle ." Biomolecular NMR Assignments 1(1):69-71. doi:DOI 10.1007/S12104-007-9020-5 Abstract Apolipoprotein A-I (apoAI, 243-residues) is the major protein component of the high-density lipoprotein (HDL) that has been a hot subject of interests because of its anti-atherogenic properties. This important property of apoAI is related to its roles in reverse cholesterol transport pathway. Upon lipid-binding, apoAI undergoes conformational changes from lipid-free to several different HDL-associated states (1). These different conformational states regulate HDL formation, maturation and transportation. Two initial conformational states of apoAI are lipid-free apoAI and apoAI/preβHDL that recruit phospholipids and cholesterol to form HDL particles. In particular, lipid-free apoAI specifically binds to phospholipids to form lipid-poor apoAI, including apoAI/preβ-HDL (~37 kDa). As a unique class of lipid poor HDL, both in vitro and in vivo evidence demonstrates that apoAI/preβ-HDLs are the most effective acceptors specifically for free cholesterol in human plasma and serves as the precursor of HDL particles (2). Here we report a complete backbone spectral assignment of human apoAI/preβHDL. Secondary structure prediction using backbone NMR parameters indicates that apoAI/preβHDL displays a two-domain structure: the N-terminal four helix-bundle domain (residues 1-186) and the C-terminal flexible domain (residues 187-243). A structure of apoAI/preβ-HDL is the first lipid-associated structure of apoAI and is critical for us to understand how apoAI recruits cholesterol to initialize HDL formation. BMRB deposit with accession number: 15093.
2007. "Protein Composition of the Vaccinia Virus Mature Virion." Virology 358(1):233-247. Abstract The protein content of vaccinia virus mature virions, purified by rate zonal and isopycnic centrifugation and solubilized by SDS or a solution of urea and thiourea, was determined by the accurate mass and time tag technology which uses both tandem mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry to detect tryptic peptides separated by high-resolution liquid chromatography. Eighty vaccinia virus-encoded proteins representing 37% of the 218 genes annotated in the complete genome sequence were detected in at least three analyses. Ten proteins accounted for approximately 80% of the mass, while the least abundant proteins made up 1% or less of the mass. Thirteen identified proteins were not previously reported as components of virions. On the other hand, 8 previously described virion proteins were not detected here, presumably due to technical reasons including small size and hydrophobicity. In addition to vaccinia virus-encoded proteins, 24 host proteins omitting isoforms were detected. The most abundant of these were cytoskeletal proteins, heat shock proteins, and proteins involved in translation.
2007. "Dissociative Scattering of Hyperthermal Energy CF3+ Ions from Modified Surfaces." Journal of Chemical Physics 126(8):Art. No. 084701. doi:10.1063/1.2484290 Abstract We have studied surface-induced dissociation (SID) of a small polyatomic ion, CF3+, at several collision energies between 29 eV and 159 eV in collision with fluorinated alkyl thiol on gold 111 crystal.
2007. "Evidence for the Bulk Nature of Self-Assembled Monolayer Surface of Fluorinated Alkyl Thiol from Hyperthermal Energy Ion-Surface Collisions." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 264(2):400-403. doi:10.1016/j.nimb.2007.08.083 Abstract Kinetic energy distributions of fragment ions from hyperthermal energy collisions of CF3+ ions with a self-assembled monolayer surface of fluorinated alkyl thiol on gold substrate have been measured as a function of scattering angle and fragment ion mass. These distributions show two energetically and angularly distrinct pathways for the dissociation of the primary ions. A plot of the velocities of the fragment ions as a Newton disagram for these two processes clearly demonstrates that one process is due to the collision of ions with a fraction of the molecular chain of the monolayer surface molecule with scattering over a broader angular range while the other process is due to collision of the projectile ions with the monolayer surface acting as a bulk surface with fragment ions scattering close to the surface parallel.
2007. "Structural Flexibility of the Nucleosome Core Particle at Atomic Resolution studied by Molecular Dynamics Simulation." Biopolymers 85(5):407-421. doi:10.1002/bip.20690 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Comparative explicit solvent molecular dynamics (MD) simulations have been performed on a complete nucleosome core particle with and without N-terminal histone tails for more than 20 ns. Main purpose of the simulations was to study the dynamics of mobile elements such as histone N-terminal tails and how packing and DNA-bending influences the fine structure and dynamics of DNA. Except for the tails, histone and DNA molecules stayed on average close to the crystallographic start structure supporting the quality of the current force field approach. Despite the packing strain, no increase of transitions to noncanonical nucleic acid backbone conformations compared to regular B-DNA was observed. The pattern of kinks and bends along the DNA remained close to the experiment overall. In addition to the local dynamics, the simulations allowed the analysis of the superhelical mobility indicating a limited relative mobility of DNA segments separated by one superhelical turn (mean relative displacement of approximately 60.2 nm, mainly along the superhelical axis). An even higher rigidity was found for relative motions (distance fluctuations) of segments separated by half a superhelical turn (approximately 60.1 nm). The N-terminal tails underwent dramatic conformational rearrangements on the nanosecond time scale toward partially and transiently wrapped states around the DNA. Many of the histone tail changes corresponded to coupled association and folding events from fully solvent-exposed states toward complexes with the major and minor grooves of DNA. The simulations indicate that the rapid conformational changes of the tails can modulate the DNA accessibility within a few nanoseconds. # 2007 Wiley Periodicals, Inc. Biopolymers 85: 407–421, 2007. Keywords: nucleic acid flexibility; nucleosome dynamics; DNA packing; DNA structure and dynamics; histone– DNA interaction; histone tail motion flexibility
2007. "Monte Carlo Simulations of Defect Recovery within a 10 keV Collision Cascade in 3C-SiC." Journal of Applied Physics 102(10):103508, 1-7. doi:10.1063/1.2812701 Abstract A kinetic lattice Monte Carlo (KLMC) model is developed to investigate the recovery and clustering of defects during annealing of a single 10 keV cascade in cubic silicon carbide. The 10 keV Si cascade is produced by molecular dynamics (MD), and a method of transferring the defects created by MD simulations to the KLMC model is developed. The KLMC model parameters are obtained from molecular dynamics simulations and ab initio calculations of defect migration, recombination and annihilation. The defects are annealed isothermally from 100 K to 1000 K in the KLMC model. Two distinct recovery stages for close Frenkel pairs are observed at about 200 and 550 K, and the growth of complex clusters is observed above 400 K. These simulation results are in good agreement with available experimental results.
2007. "Highly Selective Olefin Epoxidation with Aqueous H₂O₂ Over Surfacemodified TaSBA15 Prepared via the TMP Method." Chemical Communications (32):3350-3352. doi:10.1039/b706443h Abstract Trialkylsiloxy-modified Ta(V) centers on mesoporous silica exhibit excellent selectivity for epoxide formation (>98% after 2 h) in the oxidation of cyclohexene using aqueous H₂O₂ as the oxidant; the modified catalysts exhibit an increased lifetime, retaining high selectivity after 6 h of reaction (>95% epoxide).
