Research Projects
Cohesion and linkage between projects is facilitated by the SFA hypotheses and a series of Hanford-relevant contamination scenarios that focus multi-scale investigations on a limited set of documented field problems or issues. The first 3-year research projects are listed here.
- Impact of the Local Environment and Electron-Transfer Initiated Transformations of the Structure and Chemical Properties of Mineral and Contaminant Nanoparticulates
(D. Baer, PNNL)
Fundamental information will be obtained on 1) physical and chemical transformations that occur on and within mineral oxide nanoparticulates resulting from electron transfer reactions and other interactions with their local environment and 2) how those transformations alter the reactivity of these particles to impact contaminant transport. The nature of the reactive surfaces, the accessibility of reactive sites, and the structures of the surface and interface layers (or whole nanoparticles) often change significantly as particles respond to and react with their local environment (e.g. surface structure alterations, phase changes, passive layer formation). Although environmentally induced changes occur for bulk materials, the nature and rate for the changes can be more dramatic for nano-sized mineral phases.
This project will focus on obtaining information about these environmentally mediated transformations and how they alter particle reactivity, electron availability and particle mobility. Natural, model, and biogenic nanoparticles will be used to study of phase transformations, interfacial reaction products and particulate reactivity. The particles to be examined include different sizes of magnetite, iron (hydr)oxide, and biogenic/abiotic nanoparticulate contaminant phases. Electron transfer initiated transformations will be examined using carbon tetrachloride, a Hanford Site contaminant, as a probe molecule that reacts to produce soluble reaction products by competing pathways that are believed to be diagnostic of one and two electron transfer reactions. Investigations will rely heavily on surface and nano-scale analysis capabilities available in EMSL including electron microscopy and spectroscopy and reactivity, as well as XAS spectroscopy at the APS and ALS.
- Biomolecular Studies of Microbiological Processes Controlling Contaminant Fate and Transport
(A. Beliaev, PNNL; D. Saffarini, U of Wisconsin-Madison, F. Löffler, Georgia Tech)
Genetic and physiological characterizations DOE and Hanford Site-relevant subsurface microbial isolates and consortia will be performed. Research will focus on single-organism investigations to understand the molecular mechanisms involved in metal and radionuclide biotransformation with the initial emphasis on reduction reactions. Emphasis is on identifying genes, pathways, and subsystems involved in those key reactions, which will ultimately result in developing a comprehensive cross-species model of biological mechanisms. Based on the information and materials derived from the Microbial Ecology project, we will extend our findings to probe key cellular mechanisms involved in contaminant biogeochemical transformations with site-relevant organisms. The ability of indigenous microorganisms to coincidentally catalyze the reduction of key contaminants (U, Tc, and Pu) together with naturally occurring terminal electron acceptors under conditions relevant to Hanford microenvironments will be investigated. Our integrative approach to studying the molecular mechanisms of metal and radionuclide biotransformation will use a combination of genetic, biochemical, and cultivation approaches in conjunction with high-throughput proteomic and genomic technologies.
Using EMSL capabilities will also be critical for ultra-high-resolution imaging and localization of redox active proteins on the cell surfaces that promote electron transfer and interactions with mineral phases. In turn, we will provide resources, information, and materials for molecular- and pore-scale studies, including the identity of macromolecules for in situ probing of key genes/proteins in environmental samples, their subsequent in vitro analyses, and relevant contaminant solids for the nanoparticle project (Baer). Collaborations with Saffarini and Löffler will use their expertise in molecular biology and ecology of metal-reducing organisms, respectively, to identify metal-reducing genes in Hanford-relevant organisms. Our research will be closely coordinated with the molecular scale projects (Rosso, Shi) that will isolate and characterize redox active proteins and pore scale projects that will explore biogeochemical processes controlling speciation of U and Tc in sediments and mineral separates from Hanford (Fredrickson, Liu).
- Chemical Form and Transformation Reactions of Plutonium in Hanford Soils and Sediments
(A. Felmy,PNNL; S. Conradson, LANL)
Fundamental aspects of Pu (bio)geochemistry will be investigated in contaminated Hanford sediments to provide information on causes and mechanisms of anomalous subsurface migration; and insights on its future in-ground stability, phase or speciation transformations, and solid-liquid distribution in various Hanford subsurface microenvironments. The waste cribs at Hanford received effluent generated from plutonium production activities containing hundreds of kilograms of plutonium which have, in certain instances, migrated deep into the subsurface (60-130 feet) with some solutions (discharges to the Z-cribs) high in salts, associated organics (TBP, lard oil) and acidic (pH 2). Access to samples gathered from these sites provides a unique opportunity to evaluate both the chemical form of plutonium in these samples, the aqueous speciation reactions that are likely to occur, and the phase transformations that could occur in neutral to low pH, high salt, potentially reducing microenvironments.
Initial studies will focus on microscale characterization of the chemical form and phase distribution of plutonium present in Z-crib samples using XAS spectroscopy (performed by S.D. Conradson, LANL) as well as TEM, SEM and XPS, and digital autoradiography. Lab studies will focus on kinetic valence and phase transformations, and speciation reactions of plutonium that may occur under both oxidizing and reducing conditions present in Hanford microenvironments of different scale and type. These studies couple with research being performed in the molecular tasks related to: the reactivity of magnetite nanoparticles (Baer), surface reactions of polyvalent contaminants on ferrous-containing Hanford mineral solids of different type (Rosso), and microbial census and functional analyses of subsurface microbes at Hanford sites (including contaminated ones, Konopka) for evaluating relevant redox-transforming microbial populations.
- Pore-Scale Biogeochemical Processes Controlling Contaminant Fate & Transport
(J. Fredrickson, PNNL; K. Kemner, ANL: E. Roden, U of Wisconsin)
Research will probe Hanford/DOE site-relevant biogeochemical processes controlling the subsurface fate and transport of uranium and technetium, building upon knowledge and expertise derived from previous DOE-sponsored research. Using a combination of laboratory and field investigations, we will explore the hypothesis that subsurface microenvironments will be dominant regions of contaminant reaction by focusing on biogeochemical processes that control chemical speciation and physical state of U and Tc in sediments and mineral separates from Hanford as well as in synthetic mineral phases to provide mechanistic insights.
Batch/small reactor experiments will use model organisms and relevant microbial isolates and consortia obtained via the Microbial Ecology project and characterized by the Biomolecular Mechanisms project. Chemical, microscopy, and spectroscopy-based methods will probe contaminant speciation at the bulk scale and as well as their interactions with microbial cells, their reactive macromolecules, and sediment particles. Redox processes at the pore scale where physical/chemical heterogeneity and differences in transport of electron donors and acceptors can influence bulk geochemical reactions will be investigated (Roden). X-ray spectroscopy and microscopy capabilities at APS (Kemner) will be used to determine contaminant chemical speciation and distribution in sediments from laboratory experiments and field samples. Initial research focus will be on reduction-oxidation reactions with relevant electron-accepting and donating species to test the hypothesis regarding reductive valence transformations in microenvironments with active microbial populations and reactive mineral phases. Experimental systems will include those that are well-mixed and those that are static to impose diffusional limitations. This project will coordinate field experimentation with the Microbial Ecology and In-situ field projects and will include biogeochemical characterization of selected Hanford subsurface materials. Research will also be closely coordinated with the Liu Pore-Scale project that will focus on mass transfer (diffusion/advection) processes at the pore scale, the Zachara reactive transport project that will probe biogeochemical reactive transport issues in homogeneous and heterogeneous experimental systems, and the Scheibe reactive transport modeling project to ensure that experiments and results interface with developing models.
- Microbial Ecology
(A. Konopka, PNNL; R. Knight, U of Colorado)
This project will have two primary components: a census of Hanford subsurface microbial communities, and experimental manipulations of microbial communities or relevant single organisms under simulated natural conditions or in situ. The census will use a suite of culture-independent methods (16S rRNA gene analyses, quantitative PCR of specific functional groups of microbes, and proteomic analyses) to assay the relative abundance of different microbes across natural gradients and transition zones and determine the functional proteins expressed by the organisms. Cultivation techniques that emphasize exposure to low nutrient fluxes typical of subsurface environments will be applied in parallel to obtain and characterize Hanford-relevant microbes.
Key outputs from this project will be relevant cultures and processes for detailed investigation and experiments in other SFA projects. Differences in community composition will be related to geological, geochemical and biogeochemical activity features via new data mining tools (Knight). These will form the basis for hypotheses that drive experimental manipulations in which natural communities or Hanford-relevant organisms are incubated in subsurface sediments either in laboratory columns or deployed in boreholes. We anticipate that spatial and temporal heterogeneities in terminal electron acceptors (TEA) (particularly O2 and Fe or Mn oxides) will affect the fate and transport of U or Tc. These experiments will interface with molecular-scale studies to determine the extent to which biogeochemically-reactive cell components identified in the laboratory are expressed under natural conditions. natural conditions that can test their model predictions.
- Microscopic Mass Transfer of U and Tc in Subsurface Sediments
(C. Liu, PNNL; S. Fendorf, Stanford)
Microscopic mass transfer processes and their influence on, and coupling with, geochemical and biogeochemical reactions in subsurface sediments are the target of study. Research will investigate reactive diffusion at pore and sub-pore scales that exerts a fundamental kinetic control on U and Tc reactivity in Hanford sediment microenvironments. Diffusion domains to be considered include intragrain fractures, aggregates, cements, and coating materials with mass flux dominated by abiotic processes; and intra-aggregates and biofilms of microbial agents and minerals with activity/concentration gradients dictated by biological reactions. Molecular dynamic simulations of ions with different size and charge will be performed to determine self-diffusion coefficients in porous media with variable pore sizes and pore surface charges, to provide insights into charge- and species- coupled ion diffusion. Percolation-based analysis will be used to investigate the influence of intragrain pore or fracture connectivity on the apparent diffusion coefficients by integrating molecular self-diffusion coefficients and statistical percolation threshold. Microscopic and spectroscopic measurements of Hanford-sediment diffusion systems will be performed to quantify diffusion properties and validate theoretical calculations. Batch, stirred-flow cell, and short column experiments will be used to evaluate the influence of coupled diffusion and geochemical/biogeochemical reactions in controlling the reactive diffusion rates at the pore-scale (Fendorf). Multi-component, pore-scale reactive diffusion models will be developed to integrate self-diffusion coefficients, charge and species coupling, and pore connectivity effects.
This project will actively collaborate with the Fredrickson pore scale and Zachara reactive transport projects, and will target common contamination scenarios to allow information exchange and upscaling. Sub-pore scale reactive diffusion models will be developed for implementation in SFA reactive transport model (Scheibe). Pore-scale simulations performed by the reactive transport modeling project (Scheibe) will support this effort by providing insights on needed scaling approaches to describe reactive diffusion processes in mineralogically complex Hanford sediments. Research will incrementally increase system complexity in the following order: 1) saturated, microporous environments dominated by abiotic processes, 2) saturated microenvironments with mass flux dictated by biological reactions, and 3) unsaturated microenvironments with mass flux affected by water content and percolation.
- Molecular Scale Mechanisms of Biogeochemical Electron Transfer Underlying Subsurface U/Tc Valence Transformation and Stability
(K. Rosso, PNNL; K. Kemner, ANL; D. Richardson, U of East Anglia)
A molecular-scale understanding will be developed of biogeochemical electron transfer reactions affecting the stability of U and Tc in Hanford-relevant microenvironments. The project will focus a combination of laboratory experiments and molecular modeling on select abiotic and microbial electron transfer reactions in coordination with pore-scale and reactive transport biogeochemistry projects (Zachara, Fredrickson, Felmy), the macromolecular characterization project (Shi), the nanoparticle project (Baer), and the diffusive mass transfer project (Liu). We will initially concentrate on three Hanford-relevant U(VI)/Tc(VII) reduction pathways: i.) reduction by abiotic or biogenic Fe(II) sorbed to mineral matter, ii.) direct enzymatic reduction by cytochromes on the outer-membranes of bacteria, and iii.) reduction by structural Fe(II) available in relevant phases such as basalt glass, magnetite, ilmenite, and clinochlore. This project will supply mechanistic insight, quantitative rates and the relative importance of reaction steps, and molecular details of associated end products. Using Hanford-relevant model mineral surfaces, a suite of high-resolution surface analytical and microscopic tools in the EMSL and via collaboration with APS (Kemner) will be used to characterize the chemical speciation, structure, and distribution of reaction products of heterogeneous abiotic reduction of U(VI) and Tc(VII) by sorbed and/or structural Fe(II) with attention to Hanford-relevant system variables such as pH, [Fe(II/III)], and PO2. In coordination with redox protein function (Shi) and structure determination (Richardson), we will use molecular modeling to develop state-of-the-science simulations of elementary biomolecular electron transfer processes. Molecular modeling will be used as a basis for data interpretation, to test and refine elementary reaction mechanisms, and to assist in the development of kinetic expressions for information transfer to the pore-scale.
- Multiscale Reactive Transport Modeling
(T. Scheibe, PNNL; B. Wood, Oregon State)
Reactive transport simulation models (RTMs) will be an integrating element among the experimental elements of the SFA, in particular integrating information from fundamental scales (molecular and pore) to column and field prediction scales. RTMs will provide support for experimental design, be iteratively updated based on new experimental results, and support post-experimental analysis and interpretation. We will initially focus on the Hanford IFC, for which we will develop a field-scale model of U transport that will systematically incorporate information from SFA experiments at smaller scales. Quantitatively linking across these scales is an ambitious goal, but will be enabled by strong coordination of SFA research and ongoing computational advances. U transport behavior at the IFC is believed to be strongly influenced by both microenvironments and transition zones.
We will formulate pore-scale RTMs of the defined Hanford-relevant contaminant scenarios, that incorporate new information from molecular and pore-scale SFA experiments (Rosso, Liu and Fredrickson) and Hanford microbial characterization data (Konopka). We will develop a stochastic model of the nature and spatial heterogeneity of categorical sediment types (hydrofacies) based on SFA geophysical/geostatistical research (Ward) and other IFC characterization data. For each hydrofacies characteristic particle- and pore-size distributions, pore-scale geometry, and mineralogy will be determined using EMSL and APS facilities (by the SFA collaborative team), and these properties linked with biogeochemical and microscopic process information developed through pore-scale research (Fredrickson and Liu). We will then simulate pore-scale reactive transport using existing modeling capabilities, extended to incorporate relevant processes. Pore-scale model results will be rigorously upscaled using volume averaging (external collaborator Wood) to define continuum-scale models and parameter distributions for each hydrofacies. The upscaled models will be validated using SFA laboratory-scale reactive transport experiments (Zachara), and then used to simulate field-scale reactive transport with an existing continuum code. Predictions will be compared to both SFA and IFC experimental observations to test the models' predictive power and necessary iterations performed. Subsequent modeling focus and development will turn to the biogeochemical behavior of U, Tc, and Pu at other locations and in other sediments (with Felmy, Fredrickson, Liu, and Zachara) that will exhibit different thermodynamic and kinetic behaviors, and associated physical, biologic, and mineralogic controls.
- Functional Characterization of Microbial Macromolecules
(L. Shi, PNNL; D. Richardson; U of East Anglia)
In this project, we will investigate the molecular mechanisms by which microbial macromolecules (e.g., proteins and polysaccharides) influence the subsurface transport of U and Tc. This project will initially focus on i) the mechanism(s) of electron transfer (ET) from these macromolecules to the target contaminants and to Hanford-relevant reactive mineral phases, and ii) the mechanism(s) by which these macromolecules are localized to specific cellular or extracellular compartments to contribute to resolution of the hypothesis addressing reductive valence transformations in microenvironments. Selection of macromolecules for detailed investigation will be based on the results from previous investigations and forthcoming results from the Konopka and Beliaev projects. An integrated approach, which includes genomics, genetic, molecular biology and different chromatographic separation methods, will be used to purify the selected macromolecules.
The biochemical, biophysical, and structural properties of purified macromolecules, especially their ET properties, will be characterized at PNNL, using EMSL and other capabilities, and by the University of East Anglia (Richardson). The structures of these macromolecules and their inter-molecular interactions in solutions will be analyzed with neutron scattering and reflectivity methods at ORNL (as part of ORNL SFA). The characterization results, such as ET rates from the macromolecules to the contaminants and mineral phases and the effects of environmental conditions on the ET rates, will be used in the development and evaluation of molecular models of ET developed by the Rosso project. In turn, the predictions of the models will help generate new hypotheses and design new characterization experiments. The molecular mechanisms that regulate the biosynthesis, distribution and localization of the selected macromolecules in the microbial cells and microsites will be determined by the combined cellular, proteomic, biochemical and nanobiological methods.
- Facies-based Characterization of Hydrogeologic Structures and Reactive Transport Properties
(A. Ward, PNNL; R. Versteeg, INL)
Distribution of sedimentary lithofacies and can be discerned from spatial variations in geophysical responses. This project will develop a theoretical framework for the generation of 3D facies models based on the integration of hydrologic, geophysical, and geostatistical data. The initial focus will be on the development of reliable, physically-based models for predicting medium properties from easily obtained and reliable lithologic input data and high-resolution borehole logs. Whole samples from the IFC, and their component fractions, will be characterized to determine physical, chemical, mineralogical, and electrical properties that will be used to cluster facies according to size and lithology. These data will be used to guide development of pore-scale reactive transport models that will form the basis of the scale integration process (Scheibe).
Broadband (.001-1000 Hz) electrical measurements during batch, stirred-flow cell, and short column experiments (with Fredrickson/Liu) will be used to establish relationships between sediment properties (physical, hydrologic, geochemical, microbiologic), transport parameters, and the electrical response. Time-lapse hydrogeophysical measurements during reactive transport experiments (lab and field, Zachara) will be used to independently characterize the pore-scale lengths that govern mass transfer, such as the surface-area-to pore-volume ratio, self-diffusion coefficients, and the diffusion-limited surface trapping length, as well as geometric indices that control hydraulic properties. Broadband laboratory results will be used to develop correlations between lab- and field-measured geophysical (borehole and surface) responses needed for data interpretation, and to address issues related to the variable resolution of the different geophysical methods.
The IFC site will function as a field laboratory for validating the resulting relationships, and associated laws for up-scaling of flow and reactive transport parameters derived from pore-scale modeling and laboratory transport experiments (Scheibe and Zachara). Surface geophysical measurements will be used to map inter-borehole heterogeneity patterns at the transition zone field laboratory and the IFC monitoring array. This data will be collected at different observation scales and will be merged to develop 3D Markov chain models as necessary to interpret planned SFA and IFC field transport experiments. The geophysical, geostatistical, and hydrologic data will be integrated into a general theoretical framework for generating 3D facies models, and for defining the spatial patterns and connectivity's of associated field scale microenvironments and transition zones.
- Reactive Transport of U and Tc in Sediment Systems Containing Microenvironments and Transition Zones
(J. Zachara, PNNL; J. Davis, USGS; M. Mayes, ORNL)
Larger-scale laboratory and field experiments will be used to investigate how microenvironments and transition zones influence the biogeochemical transport behavior of U and Tc in presence of water advection. Research will link information on contaminant speciation, abiotic and biotic reaction networks of target and co-reactive constituents, and reaction and mass-transfer kinetics, as quantified in pore-scale (Fredrickson) and microscopic transport (Liu) studies of common scenarios, with transport behavior in field-relevant sediment systems. Laboratory column and flow cell experiments ranging from 10 cm to 2 m in size will investigate Hanford-relevant biogeochemical transport scenarios. Experiments will evolve from homogeneous, abiotic sediment studies (in initial research), to more complex structured materials in later years with physical heterogeneities (informed by 3-D facies model(s) of key Hanford subsurface domains, Ward) and active Hanford microorganisms (Konopka and Beliaev). The selected use of undisturbed sediment cores, and excised sediment blocks with preserved in-situ features (Mayes) will provide necessary insights on naturally structured microenvironments. Transport experiments will involve the migration of controlled-composition and tracer-containing solutions through either uncontaminated or contaminated Hanford sediments of well characterized physical, chemical, microbiologic, and mineralogic properties (also shared by other SFA participants). Resulting contaminant and tracer exchanges [and co-reactive constituents such as O2 and Fe(II/III)] with sediment solids will be monitored by in-situ devices along the flow-path, analysis of effluent solutions, and post experiment characterization of solids and microorganisms (if involved). Multi-scale, multi-domain reactive transport modeling (Scheibe) parameterized in part from pore-scale studies (Fredrickson and Liu) will be the primary interpretational tool.
Initial Hanford scenarios to be investigated are: i.) heterogeneous O2 and Tc(VII)/Tc(IV) electron transfer in microenvironments associated with basaltic lithic fragments, both without and with oxygen-consuming microorganisms (with Fredrickson and Beliaev), and ii.) mass-transfer controlled precipitation/dissolution and adsorption/desorption reactions of U(VI) in secondary mineral grain coatings and phyllosilicate aggregates under water saturated and unsaturated conditions (with Liu, and Davis and Mayes). Subsequent laboratory research will investigate the biogeochemical reactivity of U and Tc in transport-controlled, oxic-anoxic transition zones using various IFC cores and model transport systems (with Fredrickson, Konopka, Liu, and Beliaev). The field experimental program will be developed in FY10-11 in collaboration with other SFA participants and the Hanford IFC, beginning with the establishment of the transition zone field laboratory and characterization of its hydrogeologic, geochemical, and microbiologic regime.