Scientific Publications 2010
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2010. "Energy Dissipation and Defect Generation for Nanocrystalline Silicon Carbide." Physical Review. B, Condensed Matter and Materials Physics 81(18):Article No.184101. doi:10.1103/PhysRevB.81.184101 Abstract Large-scale molecular dynamics simulations have been employed to study defect generation and primary damage state in nano crystalline (NC) SiC of average grain diameters from 5 to 21 nm. Primary knock-on atom (PKA) kinetic energies of 10 keV are simulated, and cascade structures in NC SiC with a grain size smaller than 12 nm are generally different from those generated in single crystalline SiC. It is found that the local stresses near the grain boundaries (GBs) strongly affect the behavior of the PKA and secondary recoil atoms (SRAs), and the GBs act as sinks for deposition of kinetic energy. A striking feature is that the PKA and SRAs preferentially deposit energy along the GBs for grains with average size less 12 nm, which results in atomic displacements primarily within the GBs; whereas for larger grain sizes, most defects are produced within the grains. There exists a crossover in defect production, which is manifested in switching from grain boundary damage to grain damage. The most common defects created in NC SiC are antisite defects, following by vacancies and interstitials, in contrast to those produced in a single crystalline SiC, where the dominate defects are Frenkel pairs. Defect production efficiency increases with increasing the grain size, with a typical value of 0.18 for small grains and rising to 0.5 for larger grains.
2010. "Mössbauer Spectroscopy Investigation and Hydrodesulfurization Properties of Iron–nickel Phosphide Catalysts." Journal of Catalysis 272(1):18-27. doi:10.1016/j.jcat.2010.03.016 Abstract Unsupported and silica-supported FexNi2-xPy catalysts having a range of metal compositions (0 < x 6 2.0) were investigated using Mössbauer spectroscopy, and the results correlated with the surface and hydrodesulfurization (HDS) properties of the supported catalysts. Mössbauer spectroscopy permits determination of the relative site occupancy of Fe atoms in tetrahedral (M(1)) and pyramidal (M(2)) sites in the FexNi2-xPy materials. Fe atoms preferentially occupy M(2) sites for materials with significant Fe contents (x > ~0.60), but the Fe site preference reverses as the Fe content decreases (x < ~0.60). Similar occupation trends are observed for the unsupported and silica-supported FexNi2-xPy materials. Thiophene HDS measurements of the FexNi2-xPy/SiO2 catalysts revealed catalysts with high Fe contents (0.80 6 x 6 2.00) to have low activities, while the activities of Ni-rich catalysts increased dramatically with increased Ni content (0.03 6 x 6 0.60). The highest HDS activity was measured for a catalyst having a nominal precursor composition of Fe0.03Ni1.97P2.00/SiO2; this catalyst was 40% more active than a optimized nickel phosphide catalyst prepared from a precursor having a nominal composition of Ni2.00P1.60/SiO2. The 25 wt.% Fe0.03Ni1.97P2.00/SiO2 catalyst also had a dibenzothiophene HDS activity just over 10% higher than that of the 25 wt.% Ni2.00P1.60/SiO2 catalyst at 548 K. The trend of increasing HDS activity for the FexNi2-xPy/ SiO2 catalysts correlates with preferential Fe occupation of M(1) sites (and, therefore, Ni occupation of M(2) sites). Supported by X-ray photoelectron spectroscopy and oxygen chemisorption measurements, we conclude that the high activity of Ni-rich FexNi2-xPy/SiO2 catalysts can be traced to a high surface density of Ni in M(2) sites that are resistant to site blockage due to S incorporation.
2010. "Bonded Paths and van der Waals Interactions in Orpiment, As2S3." Journal of Physical Chemistry A 114(23):6550-6557. Abstract Bond critical properties and bond paths have been calculated for the thioarsenide molecular crystal orpiment, As2S3. In addition to the intramolecular As-S bond paths and van der Waals As-S and S-S bond paths within the layers, intermolecular S-S, As-S and As-As van der Waals paths exist between the layers. The S-S bond paths between the layers are identified with the main interlayer restoring forces responsible for the vibrational internal-mode splitting and the low frequency rigid layer modes previously documented in infrared and Raman studies of orpiment. These S-S bond paths are comparable with those calculated for orthorhombic native sulfur and the As4Sn (n = 3,4,5) molecules for several arsenide molecular crystals. The As-S bond paths show that the two nonequivalent arsenic atoms are each coordinated by a highly distorted octahedral array of sulfur atoms. The octahedra consist of three As-S intramolecular bonded interactions and three longer van der Waals interactions (two intramolecular and one intermolecular). One of the arsenic atoms is also coordinated by an arsenic atom in an interlayer As-As bonded interaction. Laplacian isosurface envelopes calculated for the arsenic and sulfur atoms are comparable with those calculated for native arsenic and orthorhombic sulfur. The intermolecular As-S bond paths connect Lewis acid domains on arsenic and an Lewis base domains on sulfur. Van der Waals interactions are traditionally defined as attractive interactions other than those ascribed to bond formation. However, theoretical evidence and arguments, as well as the connection between the bond paths and the vibrational spectra, indicate that the van der Waals interactions in orpiment are directed bonded interactions in the Slater sense. The experimental bond lengths for the As-S and S-S bonded interactions decrease nonlinearly with the increasing value of the electron density at the bond critical point, concomitant with a decrease in the bonded radii of arsenic and sulfur. On the basis of the local energy density, the intramolecular As-S bonded interactions classify as shared interactions and the intramolecular and intermolecular As-S and S-S bonded interactions and the intermolecular As-As van der Waals interactions classify as closed-shell interactions. The so called planar lone electron pair micelle picture for orpiment is spanned by bond paths, substantiating the claim that the layers in the orpiment structure are linked by weak van der Waals bonded interactions.
2010. "EOMCC, MRPT, and TDDFT Studies of Charge Transfer Processes in Mixed-Valence Compounds: Application to the Spiro Molecule ." Journal of Physical Chemistry A 114(33):8764-8771. doi:10.1021/jp101761d Abstract The proper description of electron transfer (ET) processes in mixed-valence compounds poses a significant challenge for commonly used theoretical approaches. In this paper we analyze the 12A2 and 22A2 potential energy surfaces of the Spiro cation which is a frequently used model to study ET processes. We compare and contrast the results obtained with three different methods: Multireference Perturbation Theory, Equation-of-Motion Coupled Cluster Theory, Time-Dependent Density Functional Theory. We demonstrate that the proper inclusion of dynamical correlation effects plays a crucial role in the description of an avoided crossing between potential energy surfaces. We also find that proper balancing of the ground- and excited-state correlation effects is especially challenging in the vicinity of the 12A2 and 22A2 avoided crossing region.
2010. "On the Ordering of Orbital Energies in High-Spin ROHF." Journal of Physical Chemistry A 114(33):8772-8777. doi:10.1021/jp101758y Abstract The Restricted Open-Shell Hartree-Fock (ROHF) method is a standard tool used by quantum chemists for studying molecules with unpaired electrons. In this work a problem with some implementations of the ROHF method is presented along with an elegant solution, which has since been added to the GAMESS code. The ground state 2A2 potential energy surface of the 5,5’(4H,4H’)-spirobi[cyclopenta[c]pyrrole] 2,2’6,6’ tetrahydro cation is the molecular test case, which elucidates the underlying problem. The method proposed will also fix Aufbau principle violations reported by Plakhutin in 2009.
2010. "The Role of Non-Bonded Interactions in the Conformational Dynamics of Organophosphorous Hydrolase Adsorbed onto Functionalized Mesoporous Silica Surfaces." Journal of Physical Chemistry B 114(1):531-540. Abstract The enzyme organophosphorous hydrolase (OPH) catalyzes the hydrolysis of a wide variety of organophosphorous compounds with high catalytic efficiency and broad substrate specificity. The immobilization of OPH in functionalized mesoporous silica surfaces increases significantly its catalytic specific activity compared to the enzyme in solution with important applications for the detection and decontamination of insecticides and chemical warfare agents. Experimental measurements of immobilization efficiency as function of the charge and coverage percentage of different functional groups have been interpreted as electrostatic forces being the predominant interactions underlying the adsorption of OPH onto functionalized mesoporous silica surfaces. Explicit solvent molecular dynamics simulations have been performed for OPH in bulk solution and adsorbed onto two distinct interaction potential models of the mesoporous silica functional groups in order to investigate the relative contributions of non-bonded interactions to the conformational dynamics and adsorption of the protein. Our results support the conclusion that while electrostatic interactions are responsible for the specific binding of OPH to the FMS surface, van der Waals forces are detrimental for enhanced interfacial adhesion. Key-words: molecular dynamics simulations; bacterial phosphotriesterase; conformational changes; confined environments; coarse-grain and atomistic models; silanol molecular model.
2010. "Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set." Journal of Chemical Theory and Computation 6(8):2365-2376. doi:10.1021/ct1002253 Abstract In this paper, an extension of the S22 data set of Jurecka et al. (Jurečka, P.; Šponer, J.; Černý, J.; Hobza, P. Phys. Chem. Chem. Phys. 2006, 8, 1985.), the data set of benchmark CCSD(T)/CBS interaction energies of twenty-two noncovalent complexes in equilibrium geometries, is presented. The S22 data set has been extended by including the stretched (one shortened and three elongated) complex geometries of the S22 data set along the main noncovalent interaction coordinate. The goal of this work is to assess the accuracy of the popular wave function methods (MP2-, MP3- and, CCSD-based) and density functional methods (with and without empirical correction for the dispersion energy) for noncovalent complexes based on a statistical evaluation not only in equilibrium, but also in nonequilibrium geometries. The results obtained in this work provide information on whether an accurate and balanced description of the different interaction types and complex geometry distortions can be expected from the tested methods. This information has an important implication in the calculation of large molecular complexes, where the number of distant interacting molecular fragments, often in far from equilibrium geometries, increases rapidly with the system size. The best performing WFT methods were found to be the SCS-CCSD (spin-component scaled CCSD, according to Takatani, T.; Hohenstein, E. G.; Sherrill, C. D. J. Chem. Phys. 2008, 128, 124111), MP2C (dispersion-corrected MP2, according to Hesselmann, A. J. Chem. Phys. 2008, 128, 144112), and MP2.5 (scaled MP3, according to Pitoňák, M.; Neogrády, P.; Černý, J.; Grimme, S.; Hobza, P. ChemPhysChem 2009, 10, 282.). Since none of the DFT methods fulfilled the required statistical criteria proposed in this work, they cannot be generally recommended for large-scale calculations. The DFT methods still have the potential to deliver accurate results for large molecules, but most likely on the basis of an error cancellation.
2010. "Heats of Formation of XeF₃⁺, XeF₃⁻, XeF₅⁺, XeF₇⁺, XeF₇⁻,and XeF₈ from High Level Electronic Structure Calculations." Inorganic Chemistry 49(1):261-270. doi:10.1021/ic901956g Abstract Atomization energies at 0 K and heats of formation at 0 and 298 K are predicted for XeF₃⁺, XeF₃⁻, XeF₅⁺, XeF₇⁻, and XeF₈ from coupled cluster theory (CCSD(T)) calculations with effective core potential correlation-consistent basis sets for Xe and including correlation of the nearest core electrons. Additional corrections are included to achieve near chemical accuracy of ±1 kcal/mol. Vibrational zero point energies were computed at the MP2 level of theory. Unlike the other neutral xenon fluorides, XeF₈ is predicted to be thermodynamically unstable with respect to loss of F₂ with the reaction calculated to be exothermic by 22.3 kcal/mol at 0 K. XeF₇⁺ is also predicted to be thermodynamically unstable with respect to the loss of F₂ by 24.1 kcal/mol at 0 K. For XeF₃⁺, XeF₅⁺, XeF₃⁻, XeF₅⁻ and XeF₇⁻, the reactions for loss of F₂ are endothermic by 14.8, 37.8, 38.2, 59.6, and 31.9 kcal/mol at 0 K, respectively. The F⁻ affinities of Xe, XeF₂, XeF₄, and XeF₆ are predicted to be 165.1, 155.3, 172.7, and 132.5 kcal/mol, and the corresponding F⁻ affinities are 6.3, 19.9, 59.1, and 75.0 kcal/mol at 0 K, respectively.
2010. "A note on the visualization of wetting film structures and a nonwetting immiscible fluid in a pore network micromodel using a solvatochromic dye ." Water Resources Research 46:W11602. doi:10.1029/2010WR009419 Abstract Nile Red is demonstrated as a single dye whose solvatochromism enables selective visualization of two immiscible liquid fluids in a micromodel containing a homogeneous array of pillars creating a porous network. Nile Red dissolves in and partitions between hexadecane as a nonwetting fluid and PEG200 as a hydrophilic fluid that wets the silicon oxide surfaces in the micromodel. Both the absorption spectra and fluorescence emission spectra are sensitive to the solvent environment, such that the two phases can be distinguished by the observed color or the fluorescence emission band. Bright field, hyperspectral, epifluorescence, and confocal fluorescence methods were used to image the micromodel after displacing PEG200 in the model with hexadecane. The use of Nile Red with these imaging methods facilitates visualization of phase identity at specific locations; the interfaces between the two immiscible liquid phases; wetting behavior of the wetting phase within the porous structure; and retention of the wetting phase as thin films around pillars and as bridges across the pore throats. The pillars and wetting phase bridges create a network of obstacles defining a tortuous preferential flow path for the nonwetting phase.
2010. "Advances in Assays and Analytical Approaches for Botulinum Toxin Detection." Trends in Analytical Chemistry. TrAC 29(10):1137-1156. doi:10.1016/j.trac.2010.07.005 Abstract Methods to detect botulinum toxin, the most poisonous substance known, are reviewed. Current assays are being developed with two main objectives in mind: 1) to obtain sufficiently low detection limits to replace the mouse bioassay with an in vitro assay, and 2) to develop rapid assays for screening purposes that are as sensitive as possible while requiring an hour or less to process the sample an obtain the result. This review emphasizes the diverse analytical approaches and devices that have been developed over the last decade, while also briefly reviewing representative older immunoassays to provide background and context.
2010. "Structural Effects on Trends in the Deposition and Dissolution of Metal-Supported Metal Adstructures." Electrochimica Acta 55(20):5545-5550. doi:10.1016/j.electacta.2010.04.055 Abstract A simple thermodynamic formalism is combined with Density Functional Theory calculations to determine periodic trends in the reversible deposition/dissolution potentials of admetals on a variety of transition metal substrates. For each admetal/substrate combination (81 in total), the deposition/ dissolution potential shift (referenced to the corresponding potential of the admetal in its bulk, elemental form) is calculated for isolated adatoms, for dimers, and for more extended kink structures. Clear periodic trends are found for the potential shifts across the space of different admetals and substrates. In addition, for the significant majority of these admetal/substrate systems, the structural effects are found to be a strong function of the local coordination number of the metal atoms, thereby verifying an important assumption that has been widely used in semiempirical models of deposition and dissolution.
2010. "Comparison of parameter sensitivities between a laboratory and field scale model of uranium transport in a dual domain, distributed-rate reactive system." Water Resources Research 46:Article No. W09509. doi:10.1029/2009WR008781 Abstract A laboratory-derived conceptual and numerical model for U(VI) transport at the Hanford 300A site, Washington, USA, was applied to a range of field-scale scenarios of different complexity to systematically evaluate model parameter sensitivities. The model, originally developed from column experiment data, included distributed-rate surface complexation kinetics of U(VI), aqueous speciation, and physical non-equilibrium transport processes. A rigorous parameter sensitivity analysis was carried out with respect to different state variables: concentrations, mass fluxes, total mass and spatial moments of dissolved U(VI) for laboratory systems, and various simulation scenarios that represented the field-scale characteristics at the Hanford 300A site. The field-scenarios accounted for transient groundwater flow and variable geochemical conditions driven by frequent water level changes of the nearby Columbia River. Simulations indicated that the transient conditions significantly affected U(VI) plume migration at the site. The parameter sensitivities were largely similar between the laboratory and field scale systems. Where differences existed, they were shown to result from differing degrees of U(VI) adsorption disequilibrium caused by hydraulic or hydrogeochemical conditions. Adorption disequilibrium was found to differ (i) between short duration peak flow events at the field scale and much longer flow events in the laboratory, (ii) for changing groundwater chemical compositions due to river water intrusion, and (iii) for different sampling locations at the field scale. Parameter sensitivities were also found to vary with respect to the different investigated state variables. An approach is demonstrated that elucidates the most important parameters of a laboratory-scale model that must constrained in both the laboratory and field for meaningful field application.
2010. "DsrR, a Novel IscA-like Protein Lacking Iron- and Fe-S-Binding Functions, Involved in the Regulation of Sulfur Oxidation in Allochromatium Vinosum." Journal of Bacteriology 192(6):1652-1661. doi:10.1128/JB.01269-09 Abstract In the purple sulfur bacterium Allochromatium vinosum, the reverse-acting dissimilatory sulfite reductase (DsrAB) is the key enzyme responsible for the oxidation of intracellular sulfur globules. The genes dsrAB are the first and the gene dsrR is the penultimate of the 15 genes of the dsr operon in A. vinosum. Genes homologous to dsrR occur in a number of other environmentally important sulfur-oxidizing bacteria utilizing Dsr proteins. DsrR exhibits sequence similarities to A-type scaffolds, like IscA, that partake in the maturation of proteinbound iron-sulfur clusters. We used nuclear magnetic resonance (NMR) spectroscopy to solve the solution structure of DsrR and to show that the protein is indeed structurally highly similar to A-type scaffolds. However, DsrR does not retain the Fe-S- or the iron-binding ability of these proteins, which is due to the lack of all three highly conserved cysteine residues of IscA-like scaffolds. Taken together, these findings suggest a common function for DsrR and IscA-like proteins different from direct participation in iron-sulfur cluster maturation. An A. vinosum _dsrR deletion strain showed a significantly reduced sulfur oxidation rate that was fully restored upon complementation with dsrR in trans. Immunoblot analyses revealed a reduced level of DsrE and DsrL in the _dsrR strain. These proteins are absolutely essential for sulfur oxidation. Transcriptional and translational gene fusion experiments suggested the participation of DsrR in the posttranscriptional control of the dsr operon, similar to the alternative function of cyanobacterial IscA as part of the sense and/or response cascade set into action upon iron limitation.
2010. "Variable Denticity in Carboxylate Binding to the Uranyl Coordination Complexes." Journal of the American Society for Mass Spectrometry 21(5):719-727. Abstract Tris-carboxylate complexes of the uranyl [UO2]2+ cation with acetate and benzoate were generated using electrospray ionization mass spectrometry, and then isolated in a Fourier transformion cyclotron resonance mass spectrometer. Wavelength-selective infrared multiple photon dissociation (IRMPD) of the tris-acetatouranyl anion resulted in a redox elimination of an acetate radical, which was used to generate an IR spectrum that consisted of six prominent absorption bands. These were interpreted with the aid of density functional theory calculations in terms of symmetric and antisymmetric -CO2 stretches of both the monodentate and bidentate acetate, CH3 bending and umbrella vibrations, and a uranyl O-U-O asymmetric stretch. The comparison of the calculated and measured IR spectra indicated that the tris-acetate complex contained two acetate ligands bound in a bidentate fashion, while the third acetate was monodentate. In similar fashion, the tris-benzoate uranyl anion was formed and photodissociated by loss of a benzoate radical, enabling measurement of the infrared spectrum that was in close agreement with that calculated for a structure containing one monodentate, and two bidentate benzoate ligands.
2010. "Vibrational Spectra of Discrete UO₂²⁺ Halide Complexes in the Gas Phase." International Journal of Mass Spectrometry 297(1-3):67-75. doi:10.1016/j.ijms.2010.06.013 Abstract The intrinsic binding of halide ions to the metal center in the uranyl molecule is a topic of ongoing research interest in both the actinide separations and theoretical communities. Investigations of structure in the condensed phases is frequently obfuscated by solvent interactions that can alter ligand binding and spectroscopic properties. The approach taken in this study is to move the uranyl halide complexes into the gas phase where they are free from solvent interactions, and then interrogate their vibrational spectroscopy using infrared multiple photon dissociation (IRMPD). The spectra of cationic coordination complexes having the composition [UO₂(X)(ACO)₃]+ (where X = F, Cl, Br and I; ACO = acetone) were acquired using electrospray for ion formation, and monitoring the ion signal from the photoelimination of ACO ligands. The studies showed that the asymmetric Ʋ₃ UO₂ frequency was insensitive to halide identity as X was varied from Cl to I, suggesting that in these pseudo-octahedral complexes, changing the nucleophilicity of the halide did not appreciably alter its binding in the complex. The Ʋ₃ peak in the spectrum of the F-containing complex was 9 cm-1 lower indicating stronger coordination in this complex. Similarly the ACO carbonyl stretches showed that the C=O frequency was relatively insensitive to the identity of the halide, although a modest shift to higher wavenumber was seen for the complexes with the more nucleophilic anions, consistent with the idea that they loosen solvent binding. Surprisingly, the Ʋ1 stretch was activated when the softer anions Cl, Br and I were present in the complexes. IR studies of the anionic complexes [UO₂X₃]- (where X = Cl-, Br- and I-) compared the Ʋ₃ UO₂ modes versus halide, and showed that the Ʋ₃ values decreased with increasing anion nucleophilicity. This observation was consistent with DFT calculations that indicated that [UO₂X₂]--X. and [UO₂X₂].-X- dissociation energies decreased on the order F > Cl > Br > I. The trifluoro complex could not be photodissociated in these experiments.
2010. "Density Functional Theory Calculations on Magnetic Properties of Actinide Compounds." Physical Chemistry Chemical Physics. PCCP 12(38):12273-12278. doi:10.1039/C0CP00372G Abstract We have performed a detailed analysis of the magnetic (collinear and non-collinear) order and the atomic and electron structures of UO2, PuO2 and UN on the basis of density functional theory with the Hubbard electron correlation correction (DFT + U). We have shown that the 3-k magnetic structure of UO2 is the lowest in energy for the Hubbard parameter value of U = 4.6 eV (and J = 0.5 eV) consistent with experiments when Dudarev’s formalism is used. In contrast to UO2, UN and PuO2 show no trend for a distortion towards rhombohedral structure and, thus, no complex 3-k magnetic structure is to be anticipated in these materials.
2010. "Helium Behavior in Oxide Nuclear Fuels: First Principles Modeling." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 268(19):3090-3094. doi:10.1016/j.nimb.2010.05.054 Abstract UO2 and (U, Pu)O2 solid solutions (the so-called MOX) nowadays are used as commercial nuclear fuels in many countries. One of the safety issues during the storage of these fuels is related to their self-irradiation that produces and accumulates point defects and helium therein. We present density functional theory (DFT) calculations for UO2, PuO2 and MOX containing He atoms in octahedral interstitial positions. In particular, we calculated basic MOX properties and He incorporation energies as functions of Pu concentration within the spin-polarized, generalized gradient approximation (GGA) DFT calculations. We also included the on-site electron correlation corrections using the Hubbard model (in the framework of the so-called DFT + U approach). We found that PuO2 remains semiconducting with He in the octahedral position while UO2 requires a specific lattice distortion. Both materials reveal a positive energy for He incorporation, which, therefore, is an exothermic process. The He incorporation energy increases with the Pu concentration in the MOX fuel.
2010. "Simulating the Heterogeneity in Braided Channel Belt Deposits: 2. Examples of Results and Comparison to Natural Deposits." Water Resources Research 46:Article Number: W04516. Abstract In Part 1 of this series we presented a methodology and a code for modeling the hierarchical sedimentary architecture in braided channel belt deposits. Here, in Part 2, the code was used to create a digital model of this architecture, and the corresponding spatial distribution of permeability. The simulated architecture was compared to the real stratal architecture observed in an abandoned channel belt of the Sagavanirktok River, Alaska by Lunt et al. (2004). The comparisons included assessments of similarity which were both qualitative and quantitative. From the qualitative comparisons we conclude that a synthetic deposit created by the code has unit types, at each level, with a geometry which is generally consistent with the geometry of unit types observed in the field. The digital unit types would generally be recognized as representing their counterparts in nature, including cross stratasets, lobate and scroll bar deposits, channel fills, etc. Furthermore, the synthetic deposit has a hierarchical spatial relationship among these units which represents how the unit types are observed in field exposures and in geophysical images. In quantitative comparisons the proportions and the length, width, and height of unit types at different scales, across all levels of the stratal hierarchy compare well between the digital and the natural deposits. A number of important attributes of the channel belt model were shown to be influenced by more than one level within the hierarchy of stratal architecture. First, the high-permeability open-framework gravels percolated at all levels and thus formed preferential flow pathways. Open framework gravels are indeed known to form preferential flow pathways in natural channel belt deposits. The nature of a percolating cluster changed across different levels of the hierarchy of stratal architecture. As a result of this geologic structure, the percolation occurs at proportions of open-framework gravels below the theoretical percolation threshold for random infinite media. Second, when the channel belt model was populated with permeability distributions by lowest-level unit type, the composite permeability semivariogram contained structures that were identifiable at more than one scale, and each of these structures could be directly linked to unit types of different scales existing at different levels within the hierarchy of strata. These collective results are encouraging with respect to our goal that this model be relevant as a base case in future studies for testing ideas in research addressing the upscaling problem in aquifers and reservoirs with multi-scale heterogeneity.
2010. "Analyzing Protease Specificity and Detecting in Vivo Proteolytic Events Using Tandem Mass Spectrometry." Proteomics 10(15):2833-2844. Abstract While trypsin remains the most commonly used protease in mass spectrometry, other proteases may be employed for increasing peptide-coverage or generating overlapping peptides. Knowledge of the accurate specifcity rules of these proteases is helpful for database search tools to detect peptides, and becomes crucial when mass spectrometry is used to discover in vivo proteolytic cleavages. In this study, we use tandem mass spectrometry to analyze the specifcity rules of selected proteases and describe MS- Proteolysis, a software tool for identifying putative sites of in vivo proteolytic cleavage. Our analysis suggests that the specifcity rules for some commonly used proteases can be improved, e.g., we find that V8 protease cuts not only after Asp and Glu, as currently expected, but also shows a smaller propensity to cleave after Gly for the conditions tested in this study. Finally, we show that comparative analysis of multiple proteases can be used to detect putative in vivo proteolytic sites on a proteome-wide scale.
2010. "A Component-Based Framework for Smoothed Particle Hydrodynamics Simulations of Reactive Fluid Flow in Porous Media. ." International Journal of High Performance Computing Applications 24(2):228-239. doi:10.1177/1094342009358415 Abstract The development of a framework to support smoothed particle hydrodynamics (SPH) simulations of fluid flow and transport in porous media is described. The framework is built using the Common Component Architecture (CCA) toolkit and supports SPH simulations using a variety of different SPH models and setup formats. The SPH simulation code is decomposed into independent components that represent self-contained units of functionality. Different physics models can be developed within the framework by re-implementing key components but no modification of other components is required. The model for defining components and developing abstract interfaces for them that support a high degree of modularity and minimal dependencies between components is discussed in detail.
