Scientific Publications 2005
2005. "Improved Mass Accuracy for Tandem Mass Spectrometry ." Journal of the American Society for Mass Spectrometry 16(4):463-470. doi:10.1016/j.jasms.2004.12.005 Abstract With the emergence of top-down proteomics, the ability to achieve high mass measurement accuracy on tandem MS/MS data will be beneficial for protein identification and characterization. (FT-ICR) Fourier transform ion cyclotron resonance mass spectrometers are the ideal instruments to perform these experiments with their ability to provide high resolution and mass accuracy. A major limitation to mass measurement accuracy in FT-ICR instruments arises from the occurrence of space charge effects. These space charge effects shift the cyclotron frequency of the ions, which compromises the mass measurement accuracy. While several methods have been developed that correct these space charge effects, they have limitations when applied to MS/MS experiments. It has already been shown that additional information inherent in electrospray spectra can be used for improved mass measurement accuracy with the use of a computer algorithm called DeCAL (deconvolution of Coulombic affected linearity). This paper highlights a new application of the strategy for improved mass accuracy in tandem mass analysis. The results show a significant improvement in mass measurement accuracy on complex electron capture dissociation spectra of proteins. We also demonstrate how the improvement in mass accuracy can increase the confidence in protein identification from the fragment masses of proteins acquired in MS/MS experiments.
2005. "Co-doped Anatase TiO₂ Heteroepitaxy on Si(001)." Journal of Applied Physics 97(7):073511-073511-10. doi:10.1063/1.1868854 Abstract Pure anatase TiO₂ and CoxTi₁-x O₂ (0.01 < x < 0.04) epitaxial thin films were deposited by oxygen-plasma-assisted molecular beam epitaxy (OPA-MBE) on Si(001) for evaluation as a potential dilute magnetic semiconductor material suitable for Si-based spintronic devices. Epitaxial growth on Si(001) was facilitated by the deposition of ¼or ½ ML Sr metal on the clean Si(001) surface to form an oxidation resistant silicide layer, followed by deposition of a thin SrTiO₃ buffer layer. Using ½ ML Sr metal to form the silicide allowed the deposition of 10 ML SrTiO₃ without oxidation of the Si interface. Epitaxial anatase could be grown on this heterostructure, although use of the oxygen plasma during deposition resulted in significant SiO₂ formation. Pure anatase films consisted of epitaxial anatase surface particles on a continuous anatase film. For Co-doped films, Co segregation to surface particles of epitaxial anatase was observed by Auger electron spectroscopy and transmission electron microscopy (TEM); faceting of the particles was observed for low Co doping concentrations. Although no secondary phases containing Co were observed in Co-doped anatase films by x-ray diffraction or TEM, x-ray absorption near edge spectroscopy indicated Co was present in the films as a mixture of Co(0), Co(II), and Co(III). All samples were ferromagnetic at room temperature; for lower Co concentrations, the ferromagnetic remanence (9%) and coercive field (100 Oe) were similar to phase-pure Co:TiO₂ / LaAlO₃. However, the presence of Co(0) under strongly oxidizing growth conditions known to oxidize the Si interface implies that under no deposition conditions can Co metal be eliminated while simultaneously protecting the Si interface from oxidation.
2005. "Negligible Magnetism in Excellent Structural Quality CrxTi₁-xO₂ Anatase: Contrast with High-Tc Ferromagnetism in Structurally Defective CrxTi₁-xO₂." Physical Review Letters 95:217203. doi:10.1103/PhysRevLett.95.217203 Abstract The mechanism of ferromagnetism in doped oxides is under active debate. We reexamine doped TiO₂ anatase, using epitaxial Cr:TiO₂ with excellent structural quality as a model system. In contrast to highly oriented but defective Cr:TiO₂ (~0.5 µB/Cr), these structurally superior single crystal films exhibit negligible ferromagnetism. We show for the first time that charge compensating oxygen vacancies alone, as predicted by F-center mediated exchange, are not sufficient to activate ferromagnetism. Instead, the onset of ferromagnetism correlates with the presence of structural defects.
2005. "Ion-Induced Nucleation: The Importance of Chemistry." Physical Review Letters 94(11):116104. Abstract Experiments have shown that ions can substantially increase vapor-to-liquid nucleation rates. However, interpretation of these experiments is complicated by ambiguities arising from the manner in which the ions are produced. Several studies have concluded that water has a general preference for anions over cations. We show that specification of ion’s sign alone is insufficient to provide an understanding of the aqueous ionic cluster thermodynamics and that Classical Ion-Induced Nucleation Theory does not treat the cluster physics properly to describe ion-induced nucleation accurately.
2005. "Charge Transfer in FeO: A combined Molecular-Dynamics and Ab Initio Study." Journal of Chemical Physics 123:224712-224722. doi:10.1063/1.2137319 Abstract Molecular dynamics simulations and ab initio electronic structure calculations were carried out to determine the rate of charge transfer in stoichiometric wüstite (FeO). The charge transfer of interest occurs by II/III valence interchange between nearest-neighbor Fe atoms, with the Fe(III) constituting a ‘hole’ electronic defect. There are two possible nearest-neighbor charge transfers in the FeO lattice, which occur between edge-sharing or corner-sharing FeO6 octahedra. Molecular dynamics simulations predict charge transfer rates of 3.7x1011 and 1.9x109 s-1 for the edge and corner transfers, respectively, in good agreement with those calculated using an ab initio cluster approach (1.6x1011 and 8.0x108 s-1, respectively). The calculated rates are also similar to those along basal and c-axis directions in hematite (α-Fe2O3) determined previously. Therefore, as is the case for hematite, wüstite is predicted to show anisotropic electrical conductivity. Our findings indicate that a rigid ion model does not give acceptable results, thus showing the need to account for the change in polarizability of the system upon charge transfer. Our model achieves this by using a simple mechanical shell model. By calculating the electronic coupling matrix elements for many transition state configurations obtained from the molecular dynamics simulations, we found evidence that the position of the bridging oxygen atoms can greatly affect the amount electronic coupling between the donor and acceptor states. Finally, we address the effect of oxygen vacancies on the charge transfer. It was found that an oxygen vacancy not only creates a driving force for holes to transport away from the vacancy (or equivalently for electrons to diffuse toward the vacancy) but also lowers the free energy barriers for charge transfer. In addition, the reorganization energy significantly differed from the non-defective case in a small radius around the defect.
2005. "Preparation of biocatalytic nanofibers with high activity and stability via enzyme aggregate coating on polymer nanofibers." Nanotechnology 16(7):S382-S388. doi:10.1088/0957-4484/16/7/011 Abstract We have developed a unique approach for the fabrication of enzyme coating on the surface of electrospun polymer nanofibers. This approach employs covalent attachment of seed enzymes onto nanofibers, followed by the glutaraldehyde treatment that crosslinks additional enzymes onto the seed enzyme molecules. These crosslinked enzyme aggregates, covalently attached to the nanofibers via seed enzyme linker, would improve not only the enzyme activity due to increased enzyme loading, but also the enzyme stability. To demonstrate the principle of concept, we fabricated the coating of alpha-chymotrypsin (CT) on the nanofibers electrospun from a mixture of polystyrene and poly(styrene-co-maleic anhydride). The addition of poly(styrene-co-maleic anhydride) makes it much easier to attach the seed enzyme molecules onto electrospun nanofibers without any rigorous functionalization of nanofibers for the attachment of enzymes. The initial activity of final CT coating was 17 and 9 times higher than those of simply-adsorbed CT and covalently-attached CT, respectively. While adsorbed and covalently-attached CT resulted in a serious enzyme leaching during initial incubation in a shaking condition, the CT coating did not show any leaching from the beginning of incubation in the same condition. As a result, the enzyme stability of CT coating was impressively improved with a half-life of 686 days under rigorous shaking while the half-life of covalently-attached CT was only 21 hours. This new approach of enzyme coating with high stability and activity will make a great impact in various applications of enzymes such as bioconversion, bioremediation, and biosensors.
2005. "Structure and Dynamics of the Solvation of Bovine Pancreatic Trypsin Inhibitor in ExplicitWater: A Comparative Study of the Effects of Solvent and Protein Polarizability." Journal of Physical Chemistry B 109(34):16529-16538. doi:10.1021/jp051569v 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. To isolate the effects of the inclusion of polarizability in the force field model on the structure and dynamics of the solvating water in differing electrostatic environments of proteins, we present the results of molecular dynamics simulations of the bovine pancreatic trypsin inhibitor (BPTI) in water with force fields that explicitly include polarization for both the protein and the water. We use three model potentials for water and two model potentials for the protein. Two of the water models and one of the protein models are polarizable. A total of six systems were simulated representing all combinations of these polarizable and nonpolarizable protein and water force fields. We find that all six systems behave in a similar manner in regions of the protein that are weakly electrostatic (either hydrophobic or weakly hydrophilic). However, in the vicinity of regions of the protein with relatively strong electrostatic fields (near positively or negatively charged residues), we observe that the water structure and dynamics are dependent on both the model of the protein and the model of the water. We find that a large part of the dynamical dependence can be described by small changes in the local environments of each region that limit the local density of non-hydrogen-bonded waters, precisely the water molecules that facilitate the dynamical relaxation of the water-water hydrogen bonds. We introduce a simple method for rescaling for this effect. When this is done, we are able to effectively isolate the influence of polarizability on the dynamics. We find that the solvating water’s relaxation is most affected when both the protein and the water models are polarizable. However, when only one model (or neither) is polarizable, the relaxation is similar regardless of the models used.
2005. "Changes in Ba phases in BaO/Al₂O₃ upon thermal aging and H₂O treatment." Catalysis Letters 105(3-4):259-268. doi:10.1007/s10562-005-8700-y Abstract The effects of thermal aging and H₂O treatment on the physicochemical properties of a BaO/Al₂O₃ model catalyst were investigated by means of XRD, BET, TEM/EDX and NO₂ TPD. Thermal aging at 1000 °C for 10 hrs resulted in conversion of dispersed BaCO₃ into low surface area crystalline BaAl₂O₄. It was found that H₂O treatment on a BaO/Al₂O₃ sample at room temperature transformed not only the BaAl₂O₄, but also the dispersed BaCO₃ into highly crystalline BaCO₃ segregated from the Al₂O₃ support, as evidenced in TEM/EDX and XRD analysis. The sample containing dispersed BaCO3 in the initial phase segregated more severely than the BaAl₂O₄ containing one, with the Ba in the BaAl₂O₄ matrix exhibiting higher resistance towards segregation. Contacting the BaO/Al₂O₃ sample with liquid water over a prolong period of time leads to an increase in crystallinity of the segregated BaCO₃. These phenomena imply that special care must be taken during catalyst synthesis and during realistic operation of Pt/BaO/Al₂O₃ NOx trap catalysts since both processes involve potential exposure of the material with liquid H₂O. Based on the results, a model to explain the behavior of Ba containing species upon thermal aging and H₂O treatment is proposed.
2005. "A Magnetically Separable, Highly Stable Enzyme System Based on Nanocomposites of Enzymes and Magnetic Nanoparticles Shipped in Hierarchically Ordered, Mesocellular, Mesoporous Silica." Small 1(12):1203-1207. doi:10.1022/smll.200500245 Abstract Enzymes are versatile nanoscale biocatalysts, and find increasing applications in many areas, including organic synthesis[1-3] and bioremediation.[4-5] However, the application of enzymes is often hampered by the short catalytic lifetime of enzymes and by the difficulty in recovery and recycling. To solve these problems, there have been a lot of efforts to develop effective enzyme immobilization techniques. Recent advances in nanotechnology provide more diverse materials and approaches for enzyme immobilization. For example, mesoporous materials offer potential advantages as a host of enzymes due to their well-controlled porosity and large surface area for the immobilization of enzymes.[6,7] On the other hand, it has been demonstrated that enzymes attached on magnetic iron oxide nanoparticles can be easily recovered using a magnet and recycled for iterative uses. In this paper, we report the development of magnetically-separable and highly-stable enzyme system by the combined use of two different kinds of nanostructured materials: magnetic nanoparticles and mesoporous silica.
2005. "Cryogenic CO2 Formation on Oxidized Gold Clusters Synthesized via Reactive Layer Assisted Deposition." Journal of the American Chemical Society 127(42):14592-93. Abstract We report studies where gas-phase Au atoms are deposited onto a multilayer film of molecular oxygen and demonstrate that this technique produces oxidized gold clusters. This method of producing oxidized gold clusters is an extension of our earlier work synthesizing MgO nanostructures using a technique termed Reactive Layer Assisted Deposition (RLAD). Emp[loying a combination of temperature programmed desorpotion (TPD) and molecular beam techniques we show that the oxidized gold clusters readily react with CO to produce CO2. At present, the structure and size distribution of these clusters are unknown. Nevertheless, these oxidized gold clusters readily catalyze the formation of CO2 at temperatures as low as 35K. Furthermore, above 120K the reaction runs to completion during exposure to gas-phase CO with initial reaction yields as high as 50
2005. "Structural Characterization of Nanoporous Pd Films Grown Via Ballistic Deposition." Surface Science 586(1-3):137-145. Abstract Nanoporous Pd films were vapor-deposited onto an oxidized Mo(100) substrate at 22 K and various dosing angles. Temperature programmed desorption (TPD) of N2 was used to determine the surface area of the Pd films immediately after deposition at 22 K, and following annealing. The surface area of Pd films was found to depend dramatically on the Pd dosing angle and annealing temperature. Pd films grown at 22 K with a 85o deposition angle exhibit the highest surface area of 120 m2/g. Ex situ SEM imaging reveals that these films consist of a tilted array of nanocrystalline filaments. The annealing studies show that the films densify upon annealing and lose approximately 50% of their surface area by 300 K and are almost completely dense by 500 K. Pd deposition at elevated temperatures (< 300 K) produces denser Pd films compared to those grown at 22 K. Growth above 300 K leads to dewetting of Pd from the substrate.
2005. "The Extremely Flat Torsional Potential Energy Surface of Oxalyl Chloride." Journal of Chemical Physics 122(23):234313 1-4. doi:10.1063/1.1926271 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. The conformational behavior of oxalyl chloride has been investigated using ab initio Hartree–Fock (HF) and second-order Møller–Plesset (MP2) perturbation theories, and the coupled-cluster singles and doubles method appended with a perturbative inclusion of connected triple excitations [CCSD(T)]. Correlation consistent polarized valence quadruple-z (cc-pVQZ) and quintuple-z (cc-pV5Z) basis sets were used in this research. At the cc-pVQZ and cc-pV5Z HF levels, there is no stationary point corresponding to a stable gauche conformer. On the other hand, at the cc-pVQZ and cc-pV5Z MP2 levels and with the cc-pVQZ CCSD(T) method, the gauche conformer of oxalyl chloride was found at O=C-C=O dihedral angles of 81.9°, 79.4°, and 83.4°, respectively. At the cc-pV5Z MP2 level, the energy barrier from trans to gauche was predicted to be 0.74 kcal mol−1 and that from gauche to trans to be 0.09 kcal mol−1. Thus, the potential-energy surface along the OvC-CvO torsional mode is exceedingly flat. The existence of the gauche conformation is mainly due to the minimization of steric repulsion.
2005. "Crystalline Ice Growth on Pt(111): Observation of a Hydrophobic Water Monolayer." Physical Review Letters 95(16):166102. Abstract The growth of crystalline water films on Pt(111) is investigated using rare gas physisorption. The water monolayer wets Pt(111) at all temperatures investigated (20-155 K). At low temperatures (T ≤ 120 K) where the water mobility is limited, additional water layers kinetically wet the monolayer surface. However, crystalline ice films grown at higher temperatures (T > 135 K) do not wet the water monolayer. These results are consistent with recent theory and experiments suggesting that the molecules in the water monolayer form a surface with no dangling OH bonds or lone pair electrons, giving rise to a hydrophobic water monolayer on Pt(111).
2005. "Global Profiling of Shewanella oneidensis MR-1: Expression of Hypothetical Genes and Improved functional annotations." Proceedings of the National Academy of Sciences of the United States of America 102(6):2099-2104. Abstract The y-proteobacterium Shewanella oneidensis strain MR-1 is a respiratory versatile organism that can reduce a wide range of organics, metals, and radionuclides. Similar to most other sequenced organisms, approximately 40% of the predicted ORFs in the MR-1 genome were annotated as uncharacterized ‘hypothetical’ genes. We implemented an integrative approach using experimental and computational analyses to provide more detailed insight into their function. Global expression studies were conducted using RNA and protein expression profiling of cells cultivated under aerobic, suboxic, and fumaratereducing conditions, phosphate limitation and UV irradiation. transcriptomic and proteomic analyses confidently identified 538 ‘hypothetical’ genes as expressed in S. oneidensis cells both as mRNAs and proteins (33% of all ‘hypothetical’ proteins). Publicly available analysis tools and databases and our own expression data were applied to improve the annotation of these genes. The annotation results were scored using a seven-category schema that ranked both confidence and precision of the functional assignment. We identified homologs for nearly all of these ‘hypothetical’ proteins (96%), thus allowing us to minimally classify them as ‘conserved proteins’. Computational and/or experimental evidence provided more precise functional assignments for 297 genes (categories 1-4; 55%). These improved functional annotations will significantly widen our understanding of vital cellular processes including signal transduction, ion transport, secondary metabolism, and transcription, as well as structural elements, such as cellular membranes. We propose that this integrative approach offers a viable means to undertake the enormous challenge of characterizing the rapidly growing number of ‘hypothetical’ proteins with each newly sequenced genome.
2005. "Active-Space Coupled-Cluster Study of Electronic States of Be₃." Journal of Chemical Physics 123:074319 (6 pages). Abstract An automated implementation of the active-space coupled-cluster (CC) and equation-of-motion (EOM) CC methods with all singles and doubles, and triples defined via active orbitals (CCSDt, EOMCCSDt) employing Tensor Contraction Engine (TCE), is reported. The TCE-generated CCSDt/ codes are parallel and applicable to closed-and open-shell references. The effectiveness of the new code in describing electronic quasi-degeneracies is illustrated by the CCSDt / EOMCCSDt) calculations for the challenging Be₃system, which is characterized by a large number of low-lying excited states dominated by two-electron transitions and significant high order correlation effects in the ground electronic state. Different strategies for defining triple excitation s within the CCSDt / EOMCCSDt) approach are discussed.
2005. "Erratum To "Heterogeneous Chemistry of Individual Mineral Dust Particles From Different Dust Source Regions: The Importance of Particle Mineralogy" [Atmos.Environ.38 (36)(2004)6253 –6261]." Atmospheric Environment 39(2005):395. Abstract The publisher regrets that there was an error in the information in Table 1 incorrectly identifies the mineral dust and their corresponding composition. The corrected table is given below. In addition, the second full sentence below the table should read “Smaller amounts ≤1% of other elements such as V and Ti were also observed but are not listed in Table 1 and is the reason why the percentages do not total to 100 in Table 1.” In the original article it states that K was not included in Table 1 but clearly it is.
2005. "Ferrous Hydroxy Carbonate is a Stable Transformation Product of Biogenic Magnetite." American Mineralogist 90(2-3):510-515. Abstract A ~1:1 mixture of ferrihydrite and nanocrystalline akaganeite (β-FeOOH; 10-15 nm) was incubated with Shewanella putrefaciens (strain CN32) under anoxic conditions with lactate as an electron donor and anthraquinone-2,6-disulfonate (AQDS) as an electron shuttle. The incubation was carried out in a 1,4-piperazinediethanesulfonic acid (PIPES)-buffered medium, without PO₄³⁻ at circumneutral pH. Iron reduction was measured as a function of time (as determined by 0.5 N HCl extraction), and solids were characterized by X-ray diffraction (XRD), electron microscopy, and Mössbauer spectroscopy. The biogenic reduction of Fe(III) was rapid; with 60% of the total Fe (Feтот) reduced in one day. Only an additional 10% of Feтот was reduced over the next three years. A fine-grained (10 nm), cation-excess (CE) magnetite with a Fe(II)/Feтот ratio of 0.5-0.6 was the sole biogenic product after one day of incubation. The CE magnetite was unstable and partially transformed to micron-sized ferrous hydroxy carbonate [FHC; Fe2 (OH)2CO3⒮], a rosasite-type mineral, with time. Ferrous hydroxy carbonate dominated the mineral composition of the three year incubated sample. The Fe(II)/Feтот ratio of the residual CE magnetite after three years of incubation was lower than the day 1 sample and was close to that of stochiometric magnetite (0.33). To best of our knowledge, this is the first report of biogenic FHC, and only the third observation of this material in nature. Ferrous hydroxy carbonate appeared to form by slow reaction of microbially produced carbonate with Fe(II)-excess magnetite. The FHC may be an overlooked mineral phase that explains the infrequent occurrence of fine-grained, biogenic magnetite in anoxic sediments.
2005. "Communications Overlapping in Fast MultipoleParticle Dynamics Methods." Journal of Computational Physics 203(2):731-743. doi:10.1016/j.jcp.2004.09.012 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. In molecular dynamics the fast multipole method (FMM) is an attractive alternative to Ewald summation for calculating electrostatic interactions due to the operation counts. However when applied to small particle systems and taken to many processors it has a high demand for interprocessor communication. In a distributed memory environment this demand severely limits applicability of the FMM to systems with O(10 K atoms). We present an algorithm that allows for fine grained overlap of communication and computation, while not sacrificing synchronization and determinism in the equations of motion. The method avoids contention in the communication subsystem making it feasible to use the FMM for smaller systems on larger numbers of processors. Our algorithm also facilitates application of multiple time stepping techniques within the FMM. We present scaling at a reasonably high level of accuracy compared with optimized Ewald methods.
2005. "Massively Parallel Implementation of a Fast Multipole Method for Distributed Memory Machines." Journal of Parallel and Distributed Computing 65(7):870-881. Abstract The abstract for this product is not available at this time.