Scientific Publications 2010
2010. "Robust Trypsin Coating on Electrospun Polymer Nanofibers in Rigorous Conditions and Its Uses for Protein Digestion." Biotechnology and Bioengineering 107(6):917-923. Abstract An efficient protein digestion in proteomic analysis requires the stabilization of proteases such as trypsin. In the present work, trypsin was stabilized in the form of enzyme coating on electrospun polymer nanofibers (EC-TR), which crosslinks additional trypsin molecules onto covalently-attached trypsin (CA-TR). EC-TR showed better stability than CA-TR in rigorous conditions, such as at high temperatures of 40 °C and 50 °C, in the presence of organic co-solvents, and at various pH's. For example, the half-lives of CA-TR and EC-TR were 0.24 and 163.20 hours at 40 ºC, respectively. The improved stability of EC-TR can be explained by covalent-linkages on the surface of trypsin molecules, which effectively inhibits the denaturation, autolysis, and leaching of trypsin. The protein digestion was performed at 40 °C by using both CA-TR and EC-TR in digesting a model protein, enolase. EC-TR showed better performance and stability than CA-TR by maintaining good performance of enolase digestion under recycled uses for a period of one week. In the same condition, CA-TR showed poor performance from the beginning, and could not be used for digestion at all after a few usages. The enzyme coating approach is anticipated to be successfully employed not only for protein digestion in proteomic analysis, but also for various other fields where the poor enzyme stability presently hampers the practical applications of enzymes.
2010. "Mexico City Aerosol Analysis during MILAGRO using High Resolution Aerosol Mass Spectrometry at the Urban Supersite (T0). Part 2: Analysis of the Biomass Burning Contribution and the Modern Carbon Fraction." Atmospheric Chemistry and Physics 10(12):5315-5341. doi:10.5194/acp-10-5315-2010 Abstract Submicron aerosol was analyzed during the MILAGRO field campaign in March 2006 at the T0 urban supersite in Mexico City with a High-Resolution Aerosol Mass Spectrometer (AMS) and complementary instrumentation. Positive Matrix Factorization (PMF) of high resolution AMS spectra identified a biomass burning OA (BBOA) component, which includes several large plumes that appear to be from forest fires within the region. Here, we show that the AMS BBOA concentration at T0 correlates with fire counts in the vicinity of Mexico City and that most of the BBOA variability is captured when the FLEXPART model is used for the dispersion of fire emissions as estimated from satellite fire counts. The resulting FLEXPART fire impact index correlates well with the observed BBOA, CH3CN, levoglucosan, and potassium, indicating that wildfires in the region surrounding Mexico City are the dominant source of BBOA at T0 during MILAGRO. The impact of distant BB sources such as the Yucatan is very small during this period. All fire tracers are correlated, with BBOA and levoglucosan showing little background, acetonitrile having a well-known tropospheric background of ~100-150 ppt, and PM2.5 potassium having a background of ~160 ng m-3 (two-thirds of its average concentration), which does not appear to be related to BB sources.
2010. "High Pressure Hydrogen Materials Compatibility of Piezoelectric Films." Applied Physics Letters 97(22):Paper No. 221911. doi:10.1063/1.3517445 Abstract Abstract: Hydrogen is being considered as a next-generation clean burning fuel. However, hydrogen has well known materials issues, including blistering and embrittlement in metals. Piezoelectric materials are used as actuators in hydrogen fuel technology. We present studies of materials compatibility of piezoelectric films in a high pressure hydrogen environment. Absorption of high pressure hydrogen was studied with Elastic Recoil Detection Analysis (ERDA) and Rutherford Back Scattering (RBS) in lead zirconate titanate (PZT) and barium titanate (BTO) thin films. Hydrogen surface degradation in the form of blistering and Pb mixing was also observed.
2010. "A Model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface:A Coarse Grained Approach." Computer Physics Communications 181(12):2001-2007. doi:10.1016/j.cpc.2010.08.029 Abstract New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6–8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like chain model. Each link is considered a sphere of 6 base pairs in length for dsDNA, and 1.5 bases for ssDNA (requiring an always even number of spheres). For this demonstration of the model, the chain is tethered to a surface by a fixed length, non-interacting 0.536 nm linker. Configurational sampling was achieved via Monte Carlo simulation. Our model successfully reproduces end to end distance averages from experimental results, in agreement with polymer theory and all-atom simulations. Our average tilt results are also in agreement with allatom simulations for the case of dense systems.
2010. "Modeling the Noble Metal/TiO2 (110) Interface with Hybrid DFT Functionals:A Periodic Electrostatic Embedded Cluster Model Study." Journal of Chemical Physics 133(16):164703 to 164703-15. doi:10.1063/1.3497037 Abstract The interaction of Aun and Ptn (n=2,3) clusters with the stoichiometric and partially reduced rutile TiO2 (110) surfaces has been investigated using periodic slab and periodic electrostatic embedded cluster models. Compared to Au clusters, Pt clusters interact strongly with both stoichiometric and reduced TiO2 (110) surfaces and are able to enhance the reducibility of the TiO2 (110) surface, i.e., reduce the oxygen vacancy formation energy. The focus of this study is the effect of Hartree–Fock exchange on the description of the strength of chemical bonds at the interface of Au/Pt clusters and the TiO2 (110) surface. Hartree–Fock exchange helps describing the changes in the electronic structures due to metal cluster adsorption as well as their effect on the reducibility of the TiO2 surface. Finally, the performance of periodic embedded cluster models has been assessed by calculating the Pt adsorption and oxygen vacancy formation energies. Cluster models, together with hybrid PBE0 functional, are able to efficiently compute reasonable electronic structures of the reduced TiO2 surface and predict charge localization at surface oxygen vacancies, in agreement with the experimental data, that significantly affect computed adsorption and reaction energies.
2010. "Spatio-temporal changes in CO2 emissions during the second ZERT injection, August-September 2008." Environmental Earth Sciences 60(2):263-272. doi:10.1007/s12665-009-0402-0 Abstract This study reports the first field test of a multi-channel, auto-dilution, steady-state, soil-CO2 flux monitoring system being developed to help understand the pathways by which fugitive CO2 from a geologic sequestration site migrates to the surface. The test was conducted from late August through mid-October 2008 at the Zero Emissions Research and Technology (ZERT) project site located in Bozeman, MT. Twenty steady-state and five non-steady-state flux chambers were installed in a 10x15 m area, one boundary of which was directly above a shallow (2-m depth) horizontal injection well located 0.5 m below the water table. A total flux of 52 kg CO2 d-1.was injected into the well for 13 days and the efflux from the soil was monitored by the chambers before, during, and for 33 days after the injection. The results showed a rapid increase in soil efflux once injection started, with maximal values reached within 3-7 d in most chambers. Efflux returned to background levels within a similar time period after injection ceased. A radial efflux pattern was observed to at least 2 m from the injection well, and evidence for movement of the CO2 plume during the injection, presumably due to groundwater flow, was seen. The steady-state chambers yielded very stable data, but 3- to 5-fold higher fluxes than the non-steady-state chambers. The higher fluxes were attributed to vacuum induced in the steady-state chambers by narrow vent tubes. High winds resulted in significant decreases in measured soil CO2 efflux, presumably by enhancing efflux from soil outside the chambers.
2010. "Linking Carbon and Boron-Nitride Nanotubes: Heterojunction Energetics and Band Gap Tuning." The Journal of Physical Chemistry Letters 1(15):2269-2273. doi:10.1021/jz100753x Abstract We investigate the energetics of forming heteronanotubes, which are combinations of pure carbon nanotube (CNT) segments and boron-nitride nanotube (BNNT)segments. Our density functional theory calculations predict that the adverse impacts of heterojunctions on the nanotube stability can be minimized if the CNTand/or the BNNT building block segments are sufficiently large along the axial direction (corresponding to circular junctions). As such, carbon-boron-nitride heteronanotubes can be thermodynamically competitive in stability, as compared to pure CNTs and BNNTs of similar geometry, and this is in good agreement with previous experimental observations. In addition, we find that the highest occupied crystal orbital/lowest unoccupied crystal orbital (HOCO-LUCO) gap of carbon-boron-nitride heteronanotubes can be significantly tuned by modifying the CNT and BNNT combinations, the tube chirality, or the junction geometry (i.e., circular or linear).
2010. "Structural, Electronic, and Magnetic Features of Platinum Alloy Strings Templatedon A Boron-Doped Carbon Nanotube." Physical Review. B, Condensed Matter and Materials Physics 81(20):205433-1 through 205433-8. doi:10.1103/PhysRevB.81.205433 Abstract We present density-functional-theory calculations of structural, electronic, and magnetic properties of platinum-alloy strings templated on a boron-doped single-wall carbon nanotube (6,6) model, B-SWCNT(6,6). Our calculations show that the alloy strings demonstrate strong molecular recognition, forming well-defined covalent bonds with the substrate and lead to the self-assembly of stable monatomic chains. The electronic and magnetic features of the Pt-alloy string/B-SWCNT(6,6)composite systems are mainly controlled by the presence of a magnetic alloying element (i.e., Fe, Co, and Ru). By changing the composition of the Pt alloy, the easy magnetization axis of the system can oscillate between the directions parallel and perpendicular to the tube axis. Our studies suggest that pure transition-metal (TM) or TM-alloy strings anchored on a substrate via strong molecular interactions can still possess sizable magnetic anisotropy due to spin-orbital coupling effects.
2010. "Proteome Analysis of Borrelia burgdorferi Response to Environmental Change." PLoS One 5(11):Article No.: e13800. doi:10.1371/journal.pone.0013800 Abstract We examined global changes in protein expression in the B31 strain of Borrelia burgdorferi, in response to two environmental cues (pH and temperature) chosen for their reported similarity to those encountered at different stages of the organism’s life cycle. Multidimensional nano-liquid chromatographic separations coupled with tandem mass spectrometry were used to examine the array of proteins (i.e., the proteome) of B. burgdorferi for different pH and temperature culture conditions. Changes in pH and temperature elicited in vitro adaptations of this spirochete known to cause Lyme disease and led to alterations in protein expression that are associated with increased microbial pathogenesis. We identified 1031 proteins that represent 59% of the annotated genome of B. burgdorferi and elucidated a core proteome of 414 proteins that were present in all environmental conditions investigated. Observed changes in protein abundances indicated varied replicon usage, as well as proteome functional distributions between the in vitro cell culture conditions. Surprisingly, the pH and temperature conditions that mimicked B. burgdorferi residing in the gut of a fed tick showed a marked reduction in protein diversity. Additionally, the results provide us with leading candidates for exploring how B. burgdorferi adapts to and is able to survive in a wide variety of environmental conditions and lay a foundation for planned in situ studies of B. burgdorferi isolated from the tick midgut and infected animals.
2010. "Solution NMR structure of the plasmid-encoded fimbriae regulatory protein PefI from Salmonella enterica serovar Typhimurium." Proteins. Structure, Function, and Bioinformatics 79(1):335-339. doi:10.1002/prot.22869 Abstract The surfaces of many bacteria feature pili or fimbriae, proteinaceous filaments that play an integral role in the adhesion of bacteria to host cells and, hence, in their pathogenicity.1,2 These extracellular structures are key virulence factors and potential targets for antibacterial drug and vaccine development. In certain Salmonella enterobacteria strains, one such class of fimbriae, the virulence plasmid-encoded fimbriae encoded by the pef operon,3,4 has been shown to be important for adhesion to murine small intestine and fluid accumulation.5 Although regulation of fimbrial expression is complex, transcription of the pef operon, induced under acidic conditions, is modulated by the PefI regulatory protein.6 PefI represses plasmid-encoded fimbrial protein production by activating the leucine-responsive regulatory protein (Lrp) mediated inhibition of DNA methylation within the pef promoter region.6 PefI expression also inhibits transcription of flagellar proteins and consequently cell motility.7 Here we present the solution NMR structure of the 70-residue PefI transcription regulator from Salmonella enterica serovar Typhimurium LT2 [UniProtKB/TrEMBL ID, Q04822_SALTY; NESG ID, StR82; hereafter referred to as stPefI], a member of the FaeA-like protein domain family (Pfam identifier, PF04703). The sequence alignment of stPefI with its functional homolog in Escherichia coli, PapI, is shown in Fig. 1(A). We demonstrate that the structure of stPefI adopts a winged helix-turn-helix motif,8,9 consistent with its role as a DNA-binding transcriptional regulator. Moreover, in spite of their relatively low sequence identity (29%), the structure of stPefI is highly similar to that of E. coli PapI,10 which activates the expression of pyelonephritis-associated pili.11,12
2010. "Adsorption of Water Monomer and Clusters on Platinum(111) Terrace and Related Steps and Kinks I. Configurations, Energies, and Hydrogen Bonding." Surface Science 604(21-22):1978-1986. doi:10.1016/j.susc.2010.08.007 Abstract Adsorption and rotation of water monomer, dimer, and trimer on the (111) terrace, (221) and (322) stepped, and (763) and (854) kinked surfaces of platinum were studied by density functional theory calculations using the PW91 approximation to the energy functional. On the (111) terrace, water monomer and the donor molecule of the dimer and trimer adsorb at atop sites. The permolecule adsorption energies of the monomer, dimer, and trimer are 0.30, 0.45, and 0.48 eV, respectively. Rotation of monomers, dimers, and trimers on the terrace is facile with energy barriers of 0.02 eV or less. Adsorption on steps and kinks is stronger than on the terrace, as evidenced by monomer adsorption energies of 0.46 to 0.55 eV. On the (221) stepped surface the zigzag extended configuration is most stable with a per-molecule adsorption energy of 0.57 eV. On the (322) stepped surface the dimer, two configurations of the trimer, and the zigzag configuration have similar adsorption energies of 0.55 ± 0.02 eV. Hydrogen bonding is strongest in the dimer and trimer adsorbed on the terrace, with respective energies of 0.30 and 0.27 eV, and accounts for their increased adsorption energies relative to the monomer. Hydrogen bonding is weak to moderate for adsorption at steps, with energies of 0.04 to 0.15 eV, as the much stronger water-metal interactions inhibit adsorption geometries favorable to hydrogen bonding. Correlations of hydrogen bond angles and energies with hydrogen bond lengths are presented. On the basis of these DFT/PW91 results, a model for water cluster formation on the Pt(111) surface can be formulated where kink sites nucleate chains along the top of step edges, consistent with the experimental findings of Morgenstern et al., Phys. Rev. Lett., 77 (1996) 703.
2010. "Computational Studies of the Thermochemistry for Conversion of Glucose to Levulinic Acid." Journal of Physical Chemistry B 114(27):9002-9009. doi:10.1021/jp101418f Abstract The thermochemistry of the conversion of glucose to levulinic acid through fructofuranosyl intermediates is investigated using the high-level ab initio methods G4 and G4MP2. The calculated gas phase reaction enthalpies indicate that the first two steps involving water molecule elimination are highly endothermic, while the other steps, including additional water elimination and rehydration to form levulinic acid, are exothermic. The calculated gas phase free energies indicate that inclusion of entropic effects makes the dehydration steps more favorable, although the elimination of the first water is still endothermic. Elevated temperatures and aqueous reaction environments are also predicted to make the dehydration reaction steps thermodynamically more favorable. On the basis of these enthalpy and free energy calculations, the first dehydration step in conversion of glucose to levulinic acid is likely a key step in controlling the overall progress of the reaction. An assessment of density functional theories and other theoretical methods for the calculation of the dehydration and hydration reactions in the decomposition of glucose is also presented.
2010. "Omics.pnl.gov: A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information." Journal of Proteomics and Bioinformatics 3(1):1-4. Abstract The data production of scientific studies is growing at a nearly exponential rate, leading to challenges in disseminating primary experimental results for peer review and public access, while simultaneously providing information that enables reproducing the studies and/or analyzing the results in a proper context. Recent mandates from various public funding agencies are requiring data release plans be included as a project goal. This requirement is coupled with an increased need for transparency in complex research, as evidenced by the data release policies of respected peer-reviewed journals. This combination of good scientific citizenship and funding requirements has brought the data distribution issue to the domain of scientific information management researchers. Herein, we present a web site designed to address these goals, the Biological MS Data and Software Distribution Center. This site leverages vast amounts of pre-existing experimental metadata stored in our purpose-built data management system to streamline the process of making these data available.
2010. "Binding Energy of d¹º Transition Metals to Alkenes By Wave Function Theory and Density Functional Theory." Journal of Molecular Catalysis. A, Chemical. 324(1-2):80-88. doi:10.1016/j.molcata.2010.03.016 Abstract The structures of Pd(PH₃)₂ and Pt(PH₃) ₂ complexes with ethene and conjugated CnHn˖₂ systems (n=4, 6, 8, and 10) were studied. Their binding energies were calculated using both wave function theory (WFT) and density functional theory (DFT). Previously it was reported that the binding energy of the alkene to the transition metal does not depend strongly on the size of the conjugated CnHn+2 ligand, but that DFT methods systematically underestimate the binding energy more and more significantly as the size of the conjugated system is increased. Our results show that recently developed density functionals predict the binding energy for these systems much more accurately. New benchmark calculations carried out by the coupled cluster method based on Brueckner orbitals with double excitations and a quasiperturbative treatment of connected triple excitations (BCCD(T)) with a very large basis set agree even better with the DFT predictions than do the previous best estimates. The mean unsigned error in absolute and relative binding energies of the alkene ligands to Pd(PH₃)₂ is 2.5 kcal/mol for the ωB97 and M06 density functionals and 2.9 kcal/mol for the M06-L functional. Adding molecular mechanical damped dispersion yields even smaller mean unsigned errors: 1.3 kcal/mol for the M06-D functional, 1.5 kcal/mol for M06- L-D, and 1.8 kcal/mol for B97-D and ωB97X-D. The new functionals also lead to improved accuracy for the analogous Pt complexes. These results show that recently developed density functionals may be very useful for studying catalytic systems involving Pd d¹º centers and alkenes.