Computing Related User Projects

• Role of Microenvironments and Transition Zones in Subsurface Reactive Contaminant Transport
  Project Lead: James McKinley
  Project Lead Institution: Pacific Northwest National Laboratory
  Abstract
  This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL. The research proposed will resolve critical Hanford and basic subsurface science issues through integrated, multi-disciplinary, science-theme focused research on the role of microenvironments and transition zones in the reactive transport of technetium (Tc), uranium (U), and plutonium (Pu). The overall ten-year goals of the SFA are to develop: i.) an integrated conceptual model for microbial ecology in the Hanford subsurface and its influence on contaminant migration, ii.) a fundamental understanding of chemical reaction, biotransformation, and physical transport processes in microenvironments and transition zones, and iii.) quantitative biogeochemical reactive transport models for Tc, U, and Pu that integrate multi-process coupling at different spatial scales for field-scale application. Targeted contaminant chemical reaction and biotransformation processes include heterogeneous/biologic electron transfer, precipitation and dissolution, and surface complexation. The EMSL component of this research will be laboratory experiments and measurements to further the understanding of field-scale phenomena. We will use sediments and microbial isolates from various Hanford settings to explore molecular, microscopic, and macroscopic processes underlying field-scale contaminant migration. The SFA will partner with the PNNL Environmental Molecular Sciences Laboratory (EMSL) to develop molecular understandings of key processes, and the Hanford Integrated Field Challenge (IFC) for access to, and samples from subsurface environments where these zones exist and are important.
• First-principle Studies for Correlated Materials
  Project Lead: Enrique Batista
  Project Lead Institution: Los Alamos National Laboratory
  Abstract
  This proposal is to request computational resources in the Chinook cluster for the coming three fiscal years. Our intention is to continue studies on actinide materials that we started with an open-call proposal funded starting in May 2011. The performance of pure density functionals and hybrid (HSE) in predictions of crystal structure and electronic structure has been assessed for: uranium oxides and carbides, neptunium oxides, and plutonium oxides. In this proposal we request computational resources to continue these studies in what constitutes a three-year effort. We first want to assess the effect of spin-orbital interaction in the predicted crystal structure and electronic structure of these materials. We want to also complete the series of oxides, sesquioxides, carbides, and nitrides in our studies. Then move to the evaluation of metallic system, such as pure plutonium, PuCoGa5, PuCoIn5 and their relative alloys with uranium and cerium. Once these studies are complete we will move our focus to materials with magnetic properties such as lanthanide oxides and transition-metal ferromagnets.
• Direct atomic level structural analysis of metallic and bimetallic catalytic clusters and their interaction with catalytic support under in-situ and ex-situ conditions
  Project Lead: Libor Kovarik
  Project Lead Institution: Environmental Molecular Sciences Laboratory
  Abstract
  This project will focus on probing the structure-property relationship of heterogeneous catalytic clusters under dynamic operating conditions. The key issue is to develop a detailed understanding of the atomistic nature of metal and bimetallic clusters and their interaction with catalysts support under ambient and catalytic conditions. We will investigate a class of transition metal (TM) clusters (e.g., Pt, Ir, Pd) supported by ?-Al2O3 and MgAl2O4 substrates. The atomic nature of the catalysts will be studied with environmental aberration-corrected high-resolution transmission electron microscopy (ETEM) and scanning transmission electron microscope STEM in high-angle annular dark field (HAADF) imaging. Due to the complexity of these catalytic systems, the results obtained from STEM/TEM will be complemented by XAS, infrared (IR), and Raman spectroscopy techniques, and the combined experimental results will be integrated with DFT methods to create quantitative models in order to directly relate the structure and catalytic performance. The in situ and ex-situ studies are expected to advance the fundamental understanding of catalytic properties of metal and bimetallic metals clusters supported by various oxide ?-Al2O3, MgAl2O4 substrates. The results will have impact on design and optimization of new heterogeneous catalyst systems.
• Cluster Model Studies of Condensed Phase Phenomena
  Project Lead: Xuebin Wang
  Project Lead Institution: Pacific Northwest National Laboratory
  Abstract
  This is a request for continuing a previous program (proposal ID 44676) which was closed on September 30, 2012. This program is focused on obtaining a microscopic understanding of solution chemistry and solvation of negatively charged ions using cluster models in the gas phase via combined low temperature photoelectron spectroscopy (PES) and theoretical computations. Electrospray ionization (ESI) is used to produce solvated clusters from solution samples. Our focus is on the solvation of complex multiply charged anions, and molecular ionic clusters. Microscopic information on the solvation and stabilization of these anions is important for understanding solution chemistry and properties of inorganic materials or atmospheric aerosols. We have extended our research by developing an ESI-PES apparatus with a capability of cooling and controlling ion temperature. We have applied this new apparatus to systematically study the electronic stability of a series of multiply-charged anions. High-resolution PES spectra of anions important to the environment and biology were recorded at low temperatures. Temperature dependent PES investigations of solvated anions manifest many essential factors dictating the solvation energetic and dynamics, such as entropy effect, confirmation change and the balance between the anion-solvent, solvent-solvent interactions.
• Directed Mesoscale Synthesis of Tunnel Structured Materials for Energy Applications
  Project Lead: Eugene Ilton
  Project Lead Institution: Pacific Northwest National Laboratory
  Abstract
  Many materials for energy applications function by reversibly absorbing and releasing charge carriers. Conventional synthesis of these materials typically results in complex aggregates of nano-scale crystallites with inconsistent properties and unpredictable performance. Further, these complex morphologies and aggregate structures render it difficult to distinguish the effects of intrinsic structure/composition on a targeted property such as the diffusion of charge carriers. In this regard, we propose to develop a novel synthesis capability and expertise for extended single crystal epitaxial films of tunnel-structured manganese oxides, an important class of energy materials, to enable fundamental experimental studies that probe intrinsic structure-property relationships. This has never been successfully implemented before and will lay the ground work for studying other energy materials with complex structures. An immediate scientific issue of interest, and one of the primary goals of this work, is to understand the influence of tunnel size and composition on coupled electron/(H+)ion diffusion and charge storage. We will take advantage of EMSL’s unique combination of capabilities in epitaxial synthesis, computational chemistry (including ab initio thermodynamics), and characterization methods as outlined schematically in the Figure. The outcome can then be leveraged for anticipated funding opportunities in mesoscale science through BES. As discussed in a following section “Mesoscale Science” includes epitaxial films which span a monolayer to 100’s of nanometers. In this sense, we intend to probe “intra-crystalline” mesoscale processes. This fundamental advance is necessary to eventually tackle the full range of mesoscale phenomena in nano-crystalline aggregates, and is aligned with BES programmatic growth targets.
• Multiscale Analysis of Phase Change Memory
  Project Lead: M.P. Anantram
  Project Lead Institution: University of Washington
  Abstract
  The ever increasing demands for energy-efficient, high-density, and fast-speed information technology have spurred extensive research interests in non-silicon resistor-based technologies. The most noteworthy example is the phase change memory (PCM), which has emerged as a promising technology for next-generation logic/memory design. Due to its superb scalability and high energy efficiency, the nonvolatile PCM has the potential to offer much more powerful and greener solution to build information centers and various commodity electronic devices than the existing silicon based device technologies. However, compared to the thorough understanding of the silicon based devices, the fundamental understanding of the emerging PCM devices is still missing. This is why the PCM-oriented Technology CAD (TCAD) methodology is still at its infancy stage, compared to the maturity of the silicon based TCAD tools. This project aims at developing hierarchical multiscale PCM analysis methodologies, by combining experiment and simulation. The general purposes are: (1) enriching the fundamental understanding of PCM device operation, especially the PCM mesoscopic electron transport mechanism; (2) investigating fundamental physical scaling limit of PCM technology; and (3) developing the multiscale PCM-oriented TCAD methodology to assist future-generation PCM device design.
• Catalytic Reformation of the Bio-oil Aqueous Fraction: Reforming Catalyst Development
  Project Lead: Robert Dagle
  Project Lead Institution: Pacific Northwest National Laboratory
  Abstract
  Bio-oils must be upgraded if they are to be used as a replacement diesel and gasoline fuel. The overall goal of this project is to examine the feasibility of steam reforming the aqueous fraction of the bio-oil. Fast pyrolysios bio-oils can be separated into aqueous and organic fraction by the addition of water or a solvent or hydrotreating to less than 20wt % O. While other liquefaction technologies such as, hydrothermal liquefaction and some permutations of catalytic pyrolysis directly yield biphasic (predominantly aqueous and predominantly organic) bio-oils. The loss of organic species in the aqueous phase that would need to be treated in order to reclaim the water is potentially a negative economic impact. The higher value predominantly organic fraction can be used to make chemicals or upgraded to provide gasoline, diesel, or jet fuels. The lower value predominantly aqueous fraction can be converted into syngas by steam reforming, producing hydrogen which can be recycled in-plant for hydrogenation purposes (e.g. hydrodeoxygenation upgrading). Process hydrogen would otherwise be supplied from either natural gas, or steam reforming of the entire bio-oil, which includes the higher value organic fraction. Reformation of the bio-oil aqueous fraction would increase overall biomass carbon utilization, decrease hydrogen requirement for the overall liquefaction process, and reduce aqueous stream waste processing cost. The steam reforming of model biomass compounds, including acetic acid, acetone, phenol, cresol, ethanol, and sugars, has been carried out with Ni and noble metal catalysts, including Pt, Rh, and Pd. Coking problems have largely been reported on the Ni catalyst surfaces. The steam reforming of model compounds over noble metal catalysts have been reported with some degree of success, given suitable operating conditions. Temperature, steam-to-carbon ratios, and space velocity are important operating parameters. Steam-to-carbon molar ratio in excess of 6 has been reported as typically necessary to avoid coking. Since water addition to the bio-oil is necessary, in order to separate the aqueous and organic fraction, allowing use of the dilute aqueous stream with no water removal required prior to reforming is advantageous. However, there is a trade-off with the energy penalty associated with water vaporization. Thus, robust reforming catalysts are desired that allow stable reforming operation at low steam-to-carbon ratios. Little has been reported for the steam reforming of actual aqueous fraction of the products that result from direct liquefaction processes (fast pyrolysis, catalytic fast pyrolysis, hydro-pyrolysis and hydrothermal liquefaction). At the same time, very little characterization data has been published on the composition of these aqueous streams. This project will leverage other projects being performed at PNNL that will produce and characterize bio-oil aqueous fractions. In this project catalysts will be developed for the steam reforming of species specifically found in the aqueous fraction of the bio-oil. This project will also leverage previous work at PNNL engaged in developing active and stable noble metal based catalysts for light hydrocarbon and tar reforming of gasifier-derived syngas.
• Surface-supported sub-nano clusters as catalysts
  Project Lead: Anastassia Alexandrova
  Project Lead Institution: University of California, Los Angeles
  Abstract
  The ultimate objective of the proposed research is fundamental understanding and design of novel catalytic interfaces based on ultra-small, sub-nano surface-deposited clusters, with a particular application to CO oxidation. Small deposited clusters are very promising new catalysts, because of the unique electronic structure effects in them, such as presence of corner and edge sites, strain energy, dangling orbitals, separation of bands into MOs, and yet small HOMO-LUMO gaps. The electronic structure – property dependence is prominent, apparently erratic, and highly tunable, at small catalytic unit size. At the most fundamental level, all materials properties, including catalytic activity, arise from the bonding and interactions of the constituent atoms. Thus, in order to approach catalyst design rationally and with a reasonable degree of predictability, it is critical to have a qualitative understanding of chemical bonding motifs attainable in materials, along with their resultant structure / properties. This understanding is the key feature of the proposed theoretical research. It is proposed to study, using electronic structure calculations, both existing and new catalytic systems: clusters of Pd, pure and doped with Au, on such surfaces as stoichiometric and defected titania, and known topological insulators, such as Bi2Se3. For systems where catalytic behavior was observed experimentally, we will explain the size/composition/activity dependences, as well as cluster shapes and stability, in terms of chemical bonding within the cluster, between the cluster and the surface, and between the catalytic interface and the substrate of the catalyzed reaction. After that, we will advance our research toward new catalytic systems, such as Au-doped clusters of Pd, and also clusters deposited on topological insulators. The former are expected to yield bifunctional catalysts. The latter are completely new systems, hitherto unexplored in catalysis. They are expected to be even better catalysts than clusters deposited on semiconductors, due to the robust nature of the high energy electronic states on their surfaces. This research will be facilitated by existing electronic structure methods, as well as new theoretical methodologies. The deliverables of the proposed research include fundamental understanding of selected catalytic systems from the chemical bonding prospective, which will be instrumental in further interpretation of experimental data, and catalyst design. Additionally, new catalytic systems will arise. We request computer time at the EMSL Chinook machine to make this research possible.
• Computational Study of Colicin Dynamics in Lipid Bilayers
  Project Lead: H. Peter Lu
  Project Lead Institution: Bowling Green State University
  Abstract
  We plan to study the colicin ion channel open-close dynamics involving in protein domains diffuse across the biological membrane under an external electric field. Our work will serve as an adequate computational template enabling further investigations on mechanisms of ion channel protein and receptor protein dynamics in vitro and in living cells.
• Structure-property relationships in pure and doped epitaxial tungsten trioxide thin films
  Project Lead: Yingge Du
  Project Lead Institution: Environmental Molecular Sciences Laboratory
  Abstract
  The primary objective of this project is to investigate the structure-property relationships of well-defined epitaxial tungsten trioxide (WO3) films with and without dopants, and thereby provide fundamental insights into the catalytic and photocatalytic properties. Our hypothesis is that through systematic studies of molybdenum (Mo) and nitrogen (N) doped WO3 films, we can understand the fundamental principles and determine the extent to which: (1) Mo doping can change the alcohol dehydration chemistry of WO3, and (2) N doping can redshift the 2.8 eV band gap deeper into the visible region. It is anticipated that such a fundamental understanding of the structure-property relationship in epitaxial pure and doped films will help us to derive a general model that will be applicable to a large class of dopants in WO3. We propose to grow structurally excellent epitaxial WO3 films on appropriately symmetry- and lattice-matched oxide substrates using the next-generation ozone-assisted molecular beam epitaxy (MBE) system equipped with high-sensitivity in-situ atomic absorption flux sensors recently developed at PNNL. The team consisting of PNNL staff and university collaborators will take full advantage of the unique suite of capabilities available at EMSL and collaborators’ sites, including deposition and microfabrication, spectroscopy and diffraction, microscopy, and high performance computing. The proposed research is of significant interest in catalysis and photocatalysis, and fits very well with the EMSL mission, in particular, the integration of experiments and theory to solve complex scientific problems.