Computing: SGI 16-processor Graphics Server (nwvisus) Publications

2013

Yang Y, CA Mims, D Mei, CHF Peden, and CT Campbell. 2013. "Mechanistic Studies of Methanol Synthesis over Cu from CO/CO2/H2/H2O Mixtures: the Source of C in Methanol and the Role of Water." Journal of Catalysis 298:10-17. doi:10.1016/j.jcat.2012.10.028 Abstract The low temperature (403 – 453K) conversions of CO:hydrogen and CO2:hydrogen mixtures (6 bar total pressure) to methanol over copper catalysts are both assisted by the presence of small amounts of water (mole fraction ~0.04%-0.5%). For CO2:hydrogen reaction mixtures, the water product from both methanol synthesis and reverse water gas shift serves to initiate both reactions in an autocatalytic manner. In the case of CO:D2 mixtures, very little methanol is produced until small amounts of water are added. The effect of water on methanol production is more immediate than in CO2:D2, yet the steady state rates are similar. Tracer experiments in 13CO:12CO2:hydrogen (with or without added water), show that the dominant source of C in the methanol product gradually shifts from CO2 to CO as the temperature is lowered. Cu-bound formate, the major IR visible surface species under CO2:hydrogen, is not visible in CO:moist hydrogen. Though formate is visible in the tracer experiments, the symmetric stretch is absent. These results, in conjunction with recent DFT calculations on Cu(111), point to carboxyl as a common intermediate for both methanol synthesis and reverse water gas shift, with formate playing a spectator co-adsorbate role.
Yang X, TD Scheibe, MC Richmond, WA Perkins, SJ Vogt, SL Codd, JD Seymour, and MI Mckinley. 2013. "Direct Numerical Simulation of Pore-Scale Flow in a Bead Pack: Comparison with Magnetic Resonance Imaging Observations." Advances in Water Resources 54:288-241. doi:10.1016/j.advwatres.2013.01.009 Abstract A significant body of current research is aimed at developing methods for numerical simulation of flow and transport in porous media that explicitly resolve complex pore and solid geometries, and at utilizing such models to study the relationships between fundamental pore-scale processes and macroscopic manifestations at larger (i.e., Darcy) scales. A number of different numerical methods for pore-scale simulation have been developed, and have been extensively tested and validated for simplified geometries. However, validation of pore-scale simulations of fluid velocity for complex, three-dimensional (3D) pore geometries that are representative of natural porous media is challenging due to our limited ability to measure pore-scale velocity in such systems. Recent advances in magnetic resonance imaging (MRI) offer the opportunity to measure not only the pore geometry, but also local fluid velocities under steady-state flow conditions in 3D and with high spatial resolution. In this paper, we present a 3D velocity field measured at sub-pore resolution (tens of micrometers) over a centimeter-scale 3D domain using MRI methods. We have utilized the measured pore geometry to perform 3D simulations of Navier-Stokes flow over the same domain using direct numerical simulation techniques. We present a comparison of the numerical simulation results with the measured velocity field. It is shown that the numerical results match the observed velocity patterns well overall except for a variance and small systematic scaling which can be attributed to the known experimental error in the MRI measurements. The comparisons presented here provide strong validation of the pore-scale simulation methods and new insights for interpretation of uncertainty in MRI measurements of pore-scale velocity. This study also provides a potential benchmark for future comparison of other pore-scale simulation methods.
Devanathan R, F Gao, and CJ Sundgren. 2013. "Role of cation choice in the radiation tolerance of pyrochlores." RSC Advances 3(9):2901-2909. doi:10.1039/C2RA22745B Abstract We have used atomistic computer simulations to study anion diffusion coefficients and the response to swift heavy ion irradiation of Gd2TixZr2-xO7 pyrochlore for x values of 0, 0.5, 1, 1.5 and 2. In Gd2Ti2O7, thermal energy deposition per unit length of 12 keV/nm results in a cylindrical amorphous track of radius 2 nm in good agreement with experiment. The volume swelling of the track is 4%, which suggests that it is partially amorphous. Gd vacancies and Ti interstitials along with cation exchange play a role in damage accumulation in the titanate. In sharp contrast, Gd2Zr2O7 does not swell and merely transforms from fluorite to pyrochlore under the same conditions. The activation energy barrier for oxygen hopping by the vacancy mechanism in these pyrochlores is 0.26-0.44 eV. The radiation tolerance of gadolinium zirconate pyrochlore is related to the efficient annihilation of cation Frenkel pairs, the low energy cost and negligible volume expansion associated with the resulting cation exchange, and efficient annealing of anion sublattice damage.
Alexandrov VY, A Neumann, M Scherer, and KM Rosso. 2013. "Electron Exchange and Conduction in Nontronite from First-Principles." Journal of Physical Chemistry C 117(5):2032-2040. doi:10.1021/jp3110776 Abstract Fe-bearing clay minerals serve as an important source and sink for electrons in redox reactions in various subsurface geochemical environments, and electron transfer (ET) properties of the Fe2+/Fe3+ redox couple play a decisive role in a variety of physicochemical processes involving clays. Here, we apply first-principles calculations using both periodic GGA+U planewave and Hartree-Fock molecular-cluster frameworks in conjuction with small polaron hopping approach and Marcus electron transfer theory to examine electron exchange mobilities in an Fe-rich smectite, taking nontronite as a case study. GGA+U calculations of the activation barrier for small-polaron migration provide rates of electron hopping that agree very well with values deduced from variable temperature Mössbauer data (M. V. Schaefer, et. al., Environ. Sci. Technol. 45, 540, (2011)), indicating a surprisingly fast electron mobility at room temperature. Based on molecular cluster calculations, we show that the state with tetrahedral Fe2+ ion in the nontronite lattice is about 0.9 eV higher than the one with octahedral Fe2+. Also, evaluation of the ET rates for the Fe2+/Fe3+ electron hopping in tetrahedral (TS) and octahedral sheets (OS), as well as across the sheets (TS–OS) shows that the dominant contribution to the bulk electronic conductivity should come from the ET within the OS. Deprotonation of structural OH groups mediating ET between the Fe ions in the OS is found to decrease the internal reorganization energy and to increase the magnitude of the electronic coupling matrix element, whereas protonation (to OH2 groups) has the opposite effect. Overall, our calculations suggest that the major factors affecting ET rates are the nature and structure of the nearest-neighbor local environment and the degree of covalency of the bonds between Fe and ligands mediating electron hops. The generally higher reorganization energy and weaker electronic coupling found in Fe-bearing clay minerals leads to electron mobilities much lower than in iron oxides.
Guedes S, P Moreira, R Devanathan, WJ Weber, and JC Hadler. 2013. "Improved zircon fission-track annealing model based on reevaluation of annealing data." Physics and Chemistry of Minerals 40(2):93-106. doi:10.1007/s00269-012-0550-8 Abstract The thermal recovery (annealing) of mineral structure modified by the passage of fission fragments has long been studied by the etching technique. In minerals like apatite and zircon, the annealing kinetics are fairly well constrained from the hour to the million-year timescale and have been described by empirical and semi-empirical equations. On the other hand, laboratory experiments, in which ion beams interact with minerals and synthetic ceramics, have shown that there is a threshold temperature beyond which thermal recovery impedes ion-induced amorphization. In this work, it is assumed that this behavior can be extended to the annealing of fission tracks in minerals. It is proposed that there is a threshold temperature, T 0, beyond which fission tracks are erased within a time t 0, which is independent of the current state of lattice deformation. This implies that iso-annealing curves should converge to a fanning point in the Arrhenius pseudo-space (ln t vs. 1/T). Based on the proposed hypothesis, and laboratory and geological data, annealing equations are reevaluated. The geological timescale estimations of a model arising from this study are discussed through the calculation of partial annealing zone and closure temperature, and comparison with geological sample constraints found in literature. It is shown that the predictions given by this model are closer to field data on closure temperature and partial annealing zone than predictions given by previous models.

2012

Wu C, A Kalyanaraman, and WR Cannon. 2012. "pGraph: Efficient Parallel Construction of Large-Scale Protein Sequence Homology Graphs." IEEE Transactions on Parallel and Distributed Systems 23(10):1923-1933. doi:10.1109/TPDS.2012.19 Abstract Detecting sequence homology between protein sequences is a fundamental problem in computational molecular biology, with a pervasive application in nearly all analyses that aim to structurally and functionally characterize protein molecules. While detecting the homology between two protein sequences is relatively inexpensive, detecting pairwise homology for a large number of protein sequences can become computationally prohibitive for modern inputs, often requiring millions of CPU hours. Yet, there is currently no robust support to parallelize this kernel. In this paper, we identify the key characteristics that make this problemparticularly hard to parallelize, and then propose a new parallel algorithm that is suited for detecting homology on large data sets using distributed memory parallel computers. Our method, called pGraph, is a novel hybrid between the hierarchical multiple-master/worker model and producer-consumer model, and is designed to break the irregularities imposed by alignment computation and work generation. Experimental results show that pGraph achieves linear scaling on a 2,048 processor distributed memory cluster for a wide range of inputs ranging from as small as 20,000 sequences to 2,560,000 sequences. In addition to demonstrating strong scaling, we present an extensive report on the performance of the various system components and related parametric studies.
Du J, R Devanathan, LR Corrales, and WJ Weber. 2012. "First-principles calculations of the electronic structure, phase transition and properties of ZrSiO4 polymorphs." Computational and Theoretical Chemistry 987(1):62–70. doi:10.1016/j.comptc.2011.03.033 Abstract First-principles periodic density functional theory (DFT) calculations have been performed to understand the electronic structure, chemical bonding, phase transition, and physical properties of the mineral zircon (in the chemical composition of ZrSiO4) and its high pressure phase reidite. Temperature effect on phase transition and thermal–mechanical properties such as heat capacity and bulk modulus have been studied by combining the equation of states obtained from DFT calculations with the quasi-harmonic Debye model to take into account the entropy contribution to free energy. Local density approximation (LDA) and generalized gradient approximation (GGA) DFT functionals have been systematically compared in predicting the structure and property of this material. It is found that the LDA functional provides a better description of the equilibrium structure and bulk modulus, while GGA predicts a transition pressure closer to experimental values. Both functionals correctly predict the relative stability of the two phases, with GGA giving slightly larger energy differences. The calculated band structures show that both zircon and reidite have indirect bandgaps and the reidite phase has a narrower bandgap than the zircon phase. The electronic density of states and atomic charges analyses show that bonding in the high-pressure reidite phase has a stronger covalent character.
Balter AI, G Lin, and AM Tartakovsky. 2012. "Effect of Nonlinearity in Hybrid Kinetic Monte Carlo-Continuum Models." Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 85(1):Article No. 016707. doi:10.1103/PhysRevE.85.016707 Abstract Recently there has been interest in developing efficient ways to model heterogeneous surface reactions with hybrid computational models that couple a KMC model for a surface to a finite difference model for bulk diffusion in a continuous domain. We consider two representative problems that validate a hybrid method and also show that this method captures the combined effects of nonlinearity and stochasticity. We first validate a simple deposition/dissolution model with a linear rate showing that the KMC-continuum hybrid agrees with both a fully deterministic model and its analytical solution. We then study a deposition/dissolution model including competitive adsorption, which leads to a nonlinear rate, and show that, in this case, the KMC-continuum hybrid and fully deterministic simulations do not agree. However, we are able to identify the difference as a natural result of the stochasticity coming from the KMC surface process. Because KMC captures inherent fluctuations, we consider it to be more realistic than a purely deterministic model. Therefore, we consider the KMC-continuum hybrid to be more representative of a real system.
Choi YJ, Y Xu, WJ Shaw, and E Ronnebro. 2012. "Hydrogen Storage Properties of New Hydrogen-Rich BH3NH3-Metal Hydride (TiH2, ZrH2, MgH2, and/or CaH2) Composite Systems." Journal of Physical Chemistry C C116(15):8349-8358. doi:10.1021/jp210460w Abstract Ammonia borane (AB = NH3BH3) is one of the most attractive materials for chemical hydrogen storage due to its high hydrogen contents of 19.6 wt.%, however, impurity levels of borazine, ammonia and diborane in conjunction with foaming and exothermic hydrogen release calls for finding ways to mitigate the decomposition reactions. In this paper we present a solution by mixing AB with metal hydrides (TiH2, ZrH2, MgH2 and CaH2) which have endothermic hydrogen release in order to control the heat release and impurity levels from AB upon decomposition. The composite materials were prepared by mechanical ball milling, and their H2 release properties were characterized by thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). The formation of volatile products from decomposition side reactions, such as borazine (N3B3H6) was determined by mass spectrometry (MS). Sieverts type pressure-composition-temperature (PCT) gas-solid reaction instrument was adopted to observe the kinetics of the H2 release reactions of the combined systems and neat AB. In situ 11B MAS-NMR revealed a destabilized decomposition pathway. We found that by adding specific metal hydrides to AB we can eliminate the impurities and mitigate the heat release.
van der Eide EF, TL Liu, DM Camaioni, ED Walter, and RM Bullock. 2012. "Facile Thermal W-W Bond Homolysis in the N-Heterocyclic Carbene-Containing Tungsten Dimer [CpW(CO)2(IMe)]2." Organometallics 31(5):1775-1789. doi:10.1021/om201162g Abstract The thermal W-W bond homolysis in [CpW(CO)2(IMe)]2 (IMe = 1,3-dimethylimidazol-2-ylidene) was investigated and was found to occur to a large extent compared to other tungsten dimers such as [CpW(CO)3]2. CpW(CO)2(IMe)H was prepared by heating a solution of [IMeH]+[CpW(CO)2(PMe3)]−, and exists in solution as a mixture of interconverting cis and trans isomers. The carbene rotation in CpW(CO)2(IMe)H was explored by DFT calculations, and low enthalpic barriers (< 3.5 kcal mol−1) are predicted. CpW(CO)2(IMe)H has pKaMeCN = 31.5(3) and deprotonation with KH gives K+[CpW(CO)2(IMe)]− (• MeCN). Hydride abstraction from CpW(CO)2(IMe)H with Ph3C+PF6− in the presence of a coordinating ligand L (MeCN or THF) gives [CpW(CO)2(IMe)(L)]+PF6−. Electrochemical measurements on the anion [CpW(CO)2(IMe)]− in MeCN, together with digital simulations, give an E1/2 of −1.54(2) V vs Cp2Fe+/0 for the [CpW(CO)2(IMe)]•/− couple. A thermochemical cycle provides the solution bond dissociation free energy of the W-H bond of CpW(CO)2(IMe)H as 61.3(6) kcal mol−1. In the electrochemical oxidation of [CpW(CO)2(IMe)]−, reversible dimerization of the electrogenerated radical CpW(CO)2(IMe)• occurs, and digital simulation provides kinetic and thermodynamic parameters for the monomer-dimer equilibrium: kdimerization ~ 2.5  104 M−1 s−1, khomolysis ~ 0.5 s−1 (i.e., Kdim ~ 5  104 M−1). Reduction of [CpW(CO)2(IMe)(MeCN)]+PF6− with cobaltocene gives the dimer [CpW(CO)2(IMe)]2, which in solution exists as a mixture of anti and gauche rotomers. As expected from the electrochemical experiments, the dimer is in equilibrium with detectable amounts of CpW(CO)2(IMe)•. This species was observed by IR spectroscopy, and its presence in solution is also in accordance with the observed reactivity toward 2,6-di-tert-butyl-1,4-benzoquinone, chloroform and dihydrogen. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Biosciences and Geosciences. Pacific Northwest National Laboratory is a multiprogram national laboratory operated for DOE by Battelle. The EPR studies were performed at EMSL, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at Pacific Northwest National Laboratory.

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