Scientific Publications 2005
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z
O
2005. "Titration Behavior of Residues at the Entrance of the D-Pathway ofCytochrome c Oxidase from Paracoccus denitrificans Investigatedby Continuum Electrostatic Calculations." Biophysical Journal 89(4):2324-2331. doi:10.1529/biophysj.105.062091 Abstract Continuum electrostatic calculations were employed to investigate the titration curves of the fully oxidized state of wild type and several variants of cytochrome c oxidase from Paracoccus denitrificans (N131D, N131C, N131V, and D124N) for different values of the dielectric constant of the protein. The effects of the mutations at the entrance of the D-proton transfer pathway were found to be quite localized to their immediate surroundings. The results can be well interpreted in the light of the available biochemical and structural data and help understanding the effects of mutations on proton conductivity. The mutations of aspartic acid Asp-I-124 to a neutral residue resulted in a decreased pKa value of His-I-28 suggesting that the mutation of His- I-28 may have a significant influence on the coupling of electron and proton transfer in cytochrome c oxidase. We also investigated the effect of the mutations N131D, N131C, and N131V on the residue Glu-I-278 in terms of its pKa value and electrostatic interaction energies.
2005. "Removal of carbon tetrachloride from a layered porous medium by means of soil vapor extraction enhanced by desiccation and water table reduction." Vadose Zone Journal 4:1170-1182. doi:10.2136/vzj2004.0173 Abstract A two-dimensional flow cell experiment was conducted to study the removal of the carbon tetrachloride component of a DNAPL mixture from a layered porous medium through soil vapor extraction (SVE) with moist and dry air. A dual-energy gamma radiation system was used at various times to non-intrusively determine fluid saturations. The mixture, which contained the volatile organic carbon tetrachloride, mimics the DNAPL disposed at the Hanford Site in Washington State. The flow cell, which is 100 cm long, 75 cm high and 5.5 cm wide, was packed with two sloped coarse sand and two sloped silt layers in an otherwise uniform matrix of medium-grained sand. A V-shaped fine sand layer was placed at the bottom of the flow cell to prevent DNAPL from exiting the flow cell. The water table was located 2 cm from the bottom, creating variably saturated conditions. A 500-mL spill was introduced at the top of the flow cell from a small source area. It was observed that the DNAPL largely by-passed the silt layers but easily moved into the coarse sand layers. Residual DNAPL was formed in the medium-grained sand matrix. The DNAPL caused a distinct reduction of the capillary fringe. Most of the DNAPL ended up in a pool on top of the V-shaped fine sand. Through four treatments with moist air soil vapor extraction, most residual carbon tetrachloride was removed from the medium-grained matrix and the coarse sand layers. However, soil vapor extraction with moist air was not able to remove the carbon tetrachloride from the silt layers and the pool. Through a water table reduction and subsequent soil vapor extraction with dry air, the carbon tetrachloride in the silt layers and the pool was effectively removed. Based on gamma measurements and carbon tetrachloride vapor concentration data, it was estimated that after the final remediation treatment, almost 90% of the total mass was removed. Key Words: DNAPL; soil vapor extraction; desiccation; remediation
2005. "Removal of Carbon Tetrachloride from a Layered Porous Medium by Means of Soil Vapor Extraction Enhanced by Desiccation and Water Table Reduction." Vadose Zone Journal 4(4):1170-1182. doi:10.2136/vzj2004.0173 Abstract A two-dimensional flow cell experiment was conducted to study the removal of the carbon tetrachloride component of a DNAPL mixture from a layered porous medium through soil vapor extraction (SVE) with moist and dry air. A dual-energy gamma radiation system was used at various times to non-intrusively determine fluid saturations. The mixture, which contained the volatile organic carbon tetrachloride, mimics the DNAPL disposed at the Hanford Site in Washington State. The flow cell, which is 100 cm long, 75 cm high and 5.5 cm wide, was packed with two sloped coarse sand and two sloped silt layers in an otherwise uniform matrix of medium-grained sand. A V-shaped fine sand layer was placed at the bottom of the flow cell to prevent DNAPL from exiting the flow cell. The water table was located 2 cm from the bottom, creating variably saturated conditions. A 500-mL spill was introduced at the top of the flow cell from a small source area. It was observed that the DNAPL largely by-passed the silt layers but easily moved into the coarse sand layers. Residual DNAPL was formed in the medium-grained sand matrix. The DNAPL caused a distinct reduction of the capillary fringe. Most of the DNAPL ended up in a pool on top of the V-shaped fine sand. Through four treatments with moist air soil vapor extraction, most residual carbon tetrachloride was removed from the medium-grained matrix and the coarse sand layers. However, soil vapor extraction with moist air was not able to remove the carbon tetrachloride from the silt layers and the pool. Through a water table reduction and subsequent soil vapor extraction with dry air, the carbon tetrachloride in the silt layers and the pool was effectively removed. Based on gamma measurements and carbon tetrachloride vapor concentration data, it was estimated that after the final remediation treatment, almost 90% of the total mass was removed.
2005. "A comparison of models describing residual NAPL formation in the vadose zone." Vadose Zone Journal 4(1):163-174. Abstract A major shortcoming of multifluid flow simulators is the inability to predict the retention of nonaqueous phase liquid (NAPL) in the vadose zone after long drainage periods. Recently, three theoretical models, Wipfler and Van Der Zee [J. Contam. Hydrol. 50 (2001); WVDZ model], Van Geel and Roy [J. Contam. Hydrol. 58 (2002); VGR model], and Lenhard et al. [J. Contam. Hydrol. (2004) In Press; LOD model] have been proposed for describing residual NAPL formation. The WVDZ model assumes a critical total liquid saturation below which all NAPL becomes residual. The VGR and LOD models are extensions of an existing hysteretic relative permeability – saturation – capillary pressure model and assume formation of residual NAPL during NAPL drainage and imbibition, respectively. In this paper, we compare model predictions against results of a series of static pressure cell experiments. We found no experimental evidence supporting the WVDZ concept of a critical total liquid saturation. The other two models yielded reasonable predictions. The VGR and LOD models were then incorporated into a multifluid flow simulator and simulations of two transient column experiments were conducted. Both models performed considerably better than simulations without considering the formation of residual NAPL, underwriting the importance of incorporating this process in simulators. Although the VGR and LOD models are based on different conceptual models, no clear performance differences could be observed when simulation results were compared against the transient experimental data.
2005. "Cholesterol Dictates the Freedom of EGF Receptors and HER2 in the Plane of the Membrane." Biophysical Journal 89(2):1362-1373. doi:10.1529/biophysj.104.056192 Abstract The flow of information through the EGF receptor (EGFR) is shaped by molecular interactions in the plasma membrane. The EGFR is associated with lipid rafts, but their role in modulating receptor mobility and subsequent interactions is unclear. To investigate the role of nanoscale rafts in EGFR dynamics, we used single-molecule fluorescence imaging to track individual receptors and their dimerization partner, HER2, in the membrane of human mammary epithelial cells. We found that the motion of both receptors was interrupted by dwellings within nanodomains. EGFR was significantly less mobile than HER2. This difference was likely due to F-actin because its deploymerization led to similar diffusion patterns between the EGFR and HER2. Manipulations of membrane cholesterol content dramatically altered the diffusion pattern of both receptors. Cholesterol depletion led to almost complete confinement of the receptors, whereas cholesterol enrichment extended the boundaries of the restricted areas. Interestingly, F-actin deploymerization partially restored receptor mobility in cholesterol depleted membranes. Our observations suggest that membrane cholesterol provides a dynamic environment that facilitates the free motion of EGFR and HER2, possible by modulating the dynamic state of F-actin. The association of the receptors with lipid rafts could therefore promote their rapid interactions only upon ligand stimulation.
2005. "Growth of Cr-doped TiO₂ Films in the Rutile and Anatase Structures by Oxygen Plasma Assisted Molecular Beam Epitaxy ." Thin Solid Films 484(1-2):289-298. Abstract As part of a search for new spintronic materials, highly ordered films of CrxTi₁-xO₂ in both rutile and anatase structure and for several Cr concentrations ranging from x=0.02 to 0.16 were grown by oxygen-plasma assisted molecular beam epitaxy. X-ray photoelectron diffraction data of the Cr 2p level exhibit the same patterns and the same modulation amplitudes as those observed for Ti 2p, providing a strong indication that a large fraction of the Cr atoms occupy substitutional lattice sites in both structures. The Cr 2p core-level spectra as well as a Cr 3d related dopant signal above the valence band of TiO₂ are characteristic of Cr³⁺ ions. At room temperature, Cr-doped anatase films exhibit ferromagnetic order with a saturation magnetization of ~0.6 µB per Cr atom and strong in-lane anisotropy.
2005. "Parallel Simulations of Aerosol Influence on Clouds Using Cloud-Resolving and Single-Column Models." Journal of Geophysical Research. D. (Atmospheres) 110(D15):D15S10. doi:10.1029/2004JD005088 Abstract The influence of the cloud condensation nucleus (CCN) concentration on the properties of low-level clouds under the conditions observed over the North Central Oklahoma on 24-25 September 1997 is examined in a series of 18-hour simulations using a single column model (SCM) and a cloud-resolving model (CM). Both models predict higher droplet concentration, smaller droplet size, and larger liquid water path in a “polluted” case (CCN concentration = 1000 cm-3) than in a clean case (CCN concentration = 250 cm-3), suggesting that the first and the second indirect effects act in unison under the considered conditions. A comparison of the simulations using the SCM and CM with the same two-moment bulk microphysics parameterization highlights the dominant effect of the dynamical framework on both micro- and macrophysical properties of modeled cloud. This effect is much stronger than the variations in each of the models resulting from changing CCN concentrations. However, the relative liquid water path sensitivity to CCN concentration is similar between the SCM and CM simulations. The CM simulations with the size-resolved and the two-moment bulk microphysical parameterization yield nearly identical structure of boundary layer. Even thought these simulations are in much closer agreement with each other than they are with the SCM results, the variance from the microphysics treatment is still comparable to the effect of quadrupling CCN concentration.
2005. "Process Enhanced Polaron Conductivity of Infrared Transparent Nickel-Cobalt Oxide." Thin Solid Films 483(1-2):175-184. Abstract The effects of gas composition during combinatorial sputtering of p-type polaron conducting films and the effects of total chamber gas pressure and different target-to-substrate distance show correlated variations in electrical and optical properties. Optimum conductivity is achieved from combinatorially deposited films containing equal parts of nickel and cobalt when sputtered in a gas mixture of 50% argon and 50% oxygen from oxide targets, with the best film conductivity of 375 S cm-1 achieved using growth conditions that promote complete oxidation. The gas pressure study shows that deposition at relatively low chamber pressures followed by subsequent quenching of heated samples in air leads to enhanced conductivity. Conductivity is enhanced even further at lower chamber pressure deposition due to a higher growth rate and increased adatom mobility during growth due to the larger molecular mean free path. Increased distance of target to substrate decreased the film density, increased film porosity and decreased conductivity, but increased optical transparency between 2 and10 µm. Post deposition heat treatment improves film conductivity when followed by rapid quenching, but degrades film conductivity when followed by slow cooling in air. Optical transparency degrades as electrical conductivity improves and vice versa. The temperature dependence of conductivity showed that the activation energy of electrical conductivity is lower for films rapidly quenched than for films that are slowly cooled following heat treatment. Rapid cooling of films from 375°C to room temperature is postulated to increase the concentration of defects or induce a disordered charge distribution state that increases the concentration of polarons and lowers the activation energy for electrical conductivity. Slow cooling allows defects to anneal out, resulting in improved transparency across the infrared region but a lower electrical conductivity.
2005. "NO₂ Adsorption on Ultrathin Θ-Al₂O₃ Films: Formation of Nitrite and Nitrate Species." Journal of Physical Chemistry 109(33):15977-15984. Abstract Interaction of NO₂ with an ordered θ-Al₂O₃/NiAl(100) model catalyst surface was investigated using temperature programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS). The origin of the NOx uptake of the catalytic support (i.e. Al₂O₃) in a NOx storage catalyst is identified. Adsorbed NO₂ is converted to strongly bound nitrites and nitrates that are stable on the model catalyst surface at temperatures as high as 300 and 650 K, respectively. The results show that alumina is not completely inert and may stabilize some form of NOx under certain catalytic conditions. The stability of the NOx formed by exposing the θ-Al₂O₃ model catalyst to NO₂ adsorption increases in the order: NO₂ (physisorbed or N₂O₄) < NO₂(chemisorbed) < NO₂- < NO₃-.
2005. "Interaction of Water with Ordered Theta-Al₂0₃ Ultrathin Films grown on NiAl(100)." Journal of Physical Chemistry B 109(8):3431-3436. doi:10.1021/jp0449206 Abstract The structure of an ordered, ultra thin ⊖-Al₂0₃ film grown on a NiAl(100) single crystal surface was studied by Auger electron spectroscopy (AES), X-Ray photoelectron spectroscopy (XPS), and low energy electron diffraction (LEED), and its interaction with water was investigated with temperature programmed desorption (TPD), and XPS. Our results indicate that H₂O adsorption on the ⊖-Al₂0₃/NiAl(100) surface is predominantly molecular rather than dissociative. For ⊖H₂O< 1ML (ML=monolayer), H₂O molecules were found to populate Al³⁺ cation sites to form isolated H₂O species aligned in a row along the cation sites on the oxide surface with a repulsive interaction between them. For ⊖H₂O> 1ML, H₂O overlayers were observed to form three dimensional ice multilayers where water molecules start occupying both cationic and anionic adsorption sites on the oxide surface allowing the formation of hydrogen boding. A small extent of H₂O dissociation was observed to occur on the ⊖-Al₂0₃/NiAl(100) surface which was attributed to the presence of a low concentration of surface defects. Titration of these defect sites with absorbed H₂O molecules revealed an estimated defect density of ~0.-5 ML for the ⊖-Al₂0₃/NiAl(100) system consistent with the ordered nature of the synthesized oxide film.
