Subsurface Flow and Transport

Remediation strategies have been developed for a variety of contaminants by integrating theory, experiment and numerical simulation prior to field-scale studies. Researchers can conduct experiments at various scales, and compare experimental and numerical results to address the nation's most challenging problems in the subsurface related to contaminant transport, carbon cycling, enhanced oil recovery and carbon dioxide sequestration. See a complete list of Subsurface Flow and Transport instruments.

Resources and Techniques

  • Users have access to all the tools—flow cells, simulation programs and analytical instruments from chromatographs to spectrometers—necessary for designing and conducting a subsurface flow and transport experiments.
  • Designing experiments—Simulators such as STOMP (Subsurface Transport Over Multiple Phases) are used to define the boundary and initial conditions of the experiment.
  • Conducting experiments—Micro- to intermediate-flow cells are used with analytical tools to generate data about how contaminants move through the soil.
  • A full suite of analytical tools are available to generate data about samples.

Description

Capability Details

  • Intermediate-scale columns and flow cells
  • Pore-scale microfluidic and imaging capabilities
  • High-pressure/temperature cells for research at reservoir conditions
  • Dual energy gamma radiation system
  • Integrated hydraulic properties apparatus
  • Relative permeability apparatus
  • Analytical tools including ion, liquid and gas chromatographs, inductively coupled plasma-mass spectrometry and carbon analysis tools

Instruments

The carbon analyzer is used to analyze total carbon (TC), inorganic carbon (IC), total organic carbon (TOC), purgeable organic carbon (POC), and non...
Custodian(s): Tom Wietsma
The Agilent 4500 Series inductively coupled plasma mass spectrometer (ICP-MS) is available for all research areas requiring analysis of trace metals...
Custodian(s): Tom Wietsma
This instrument is housed in EMSL.  More details about this instrument will be available soon.
Custodian(s): Tom Wietsma, Mart Oostrom
This ion chromatography capability comprises two Dionex DX-500 modular chromatography systems that can be configured to conduct fully automated...
Custodian(s): Tom Wietsma
The Agilent 1100 Series liquid chromatography system is used for all research areas that require quantitative determination of nonvolatile and...
Custodian(s): Tom Wietsma

Publications

MAX phases (M: early transition metal; A: elements in group 13 or 14; X: C or N), such as titanium silicon carbide (Ti3SiC2), have a unique...
A multi-modal characterization technique, which combines nanoscale secondary ion mass spectroscopy (Nano-SIMS) with a spatial resolution of ~100 nm...
Hysteretic behavior was studied in a series of Fe thin films, grown by molecular beam epitaxy, having different grain sizes and grown on different...
Materials exposed to radiation show structural changes and damages, especially in the nanoscale range. The characterizing equipment involving...
Composite Portland cement-basalt caprock cores with fractures, as well as neat Portland cement columns, were prepared to understand the geochemical...

Science Highlights

Posted: September 01, 2015
The Science Soil contains the largest amount of terrestrial carbon on the planet, so a small change in soil carbon can have a large impact on...
Posted: March 31, 2015
The Science Pore-scale models are useful for studying relationships between fundamental processes at the scale of tens to hundreds of microns—the...
Posted: July 11, 2014
The Science The physical and chemical processes that occur at the scale of individual soil particles dictate the way fluids flow underground over...
Posted: April 21, 2014
A multidisciplinary team of scientists at Pacific Northwest National Laboratory using EMSL resources developed a new approach to simulate water...
Posted: March 19, 2013
One of the most noteworthy concerns for the U.S. Department of Energy is controlling atmospheric carbon dioxide to mitigate its effects on global...

Instruments

At EMSL, a drainage experiment was conducted at 9 MPa and 40 degrees C by injecting supercritical CO2 (scCO2) into the sandstone-analogue pore...
The objective of this work is to utilize the micromodels from EMSL’s Subsurface Flow and Transport Laboratory to evaluate the rate and extent of...

Remediation strategies have been developed for a variety of contaminants by integrating theory, experiment and numerical simulation prior to field-scale studies. Researchers can conduct experiments at various scales, and compare experimental and numerical results to address the nation's most challenging problems in the subsurface related to contaminant transport, carbon cycling, enhanced oil recovery and carbon dioxide sequestration. See a complete list of Subsurface Flow and Transport instruments.

Resources and Techniques

  • Users have access to all the tools—flow cells, simulation programs and analytical instruments from chromatographs to spectrometers—necessary for designing and conducting a subsurface flow and transport experiments.
  • Designing experiments—Simulators such as STOMP (Subsurface Transport Over Multiple Phases) are used to define the boundary and initial conditions of the experiment.
  • Conducting experiments—Micro- to intermediate-flow cells are used with analytical tools to generate data about how contaminants move through the soil.
  • A full suite of analytical tools are available to generate data about samples.

Effects of soluble flavin on heterogeneous electron transfer between surface-exposed bacterial cytochromes and iron oxides.

Abstract: 

Dissimilatory iron-reducing bacteria can utilize insoluble Fe(Mn)-oxides as a terminal electron acceptor under anaerobic conditions. For Shewanella species specifically, some evidence suggests that iron reduction is associated with the secretion of flavin mononucleotide (FMN) and riboflavin that are proposed to mediate electron transfer (Marsili et al., 2008). In this work, we used methyl viologen (MV•+)-encapsulated, porin-cytochrome complex (MtrCAB) embedded liposomes (MELs) as a synthetic model of the Shewanella outer membrane to investigate the proposed mediating behavior of secreted flavins. The reduction kinetics of goethite, hematite and lepidocrocite (200 µM) by MELs ([MV•+] ~ 42 µM and MtrABC ≤ 1 nM) were determined in the presence FMN at pH 7.0 in N2 atmosphere by monitoring the concentrations of MV•+ and FMN through their characteristic UV-visible absorption spectra. Experiments were performed where i) FMN and Fe(III)-oxide were mixed and then reacted with the reduced MELs and ii) FMN was reacted with the reduced MELs followed by addition of Fe(III)-oxide. The redox reactions proceeded in two steps: a fast step that was completed in a few seconds, and a slower one lasting over 400 seconds. For all three Fe(III)-oxides, the initial reaction rate in the presence of a low concentration of FMN (≤ 1 µM) was at least a factor of five faster than those with MELs alone, and orders of magnitude faster than those by FMNH2, suggesting that FMN may serve as a co-factor that enhances electron transfer from outer-membrane c-cytochromes to Fe(III)-oxides. The rate and extent of the initial reaction followed the order of lepidocrocite > hematite > goethite, the same as their reduction potentials, implying thermodynamic control on reaction rate. However, at higher FMN concentrations (> 1 µM), the reaction rates for both steps decreased and varied inversely with FMN concentration, indicating that FMN inhibited the MEL to Fe(III)-oxide electron transfer reaction. The implications of the observed kinetic behaviors to flavin-mediated Fe(III) oxide reduction in natural environments are discussed.

Citation: 
Wang Z, Z Shi, L Shi, GF White, DJ Richardson, TA Clarke, JK Fredrickson, and JM Zachara.2015."Effects of soluble flavin on heterogeneous electron transfer between surface-exposed bacterial cytochromes and iron oxides."Geochimica et Cosmochimica Acta 163:299-310. doi:10.1016/j.gca.2015.03.039
Authors: 
Wang Zheming
Wang Z
Z Shi
L Shi
GF White
DJ Richardson
TA Clarke
JK Fredrickson
JM Zachara
Facility: 
Volume: 
Issue: 
Pages: 
Publication year: 
2015

Nitrate bioreduction in redox-variable low permeability sediments.

Abstract: 

Denitrification is a microbial process that reduces nitrate and nitrite to nitrous oxide (N2O) or dinitrogen (N2) with a strong implication to global nitrogen cycling and climate change. This paper reports the effect of sediment redox conditions on the rate and end product of denitrification. The sediments were collected from a redox transition zone consisting of oxic and reduced layers at US Department of Energy’s Hanford Site where N2O was locally accumulated in groundwater. The results revealed that denitrification rate and end product varied significantly with initial sediment redox state. The denitrification rate was relatively faster, limited by organic carbon content and bioavailability in the oxic sediment. In contrast, the rate was much slower in the reduced sediment, limited by biomass and microbial function. A significant amount of N2O was accumulated in the reduced sediment; while in the oxic sediment, N2O was further reduced to N2. RT-PCR analysis revealed that nosZ, the gene that codes for N2O reductase, was below detection in the reduced sediment. The results implied that redox transition zones can be important sinks or sources of N2O depending on local biogeochemical and microbial conditions, and are important systems for understanding and modeling denitrification in subsurface environments.

Citation: 
Yan S, Y Liu, C Liu, L Shi, J Shang, H Shan, JM Zachara, JK Fredrickson, DW Kennedy, CT Resch, CJ Thompson, and SJ Fansler.2015."Nitrate bioreduction in redox-variable low permeability sediments."Science of the Total Environment 539:185-195. doi:10.1016/j.scitotenv.2015.08.122
Authors: 
S Yan
Y Liu
C Liu
L Shi
J Shang
H Shan
JM Zachara
JK Fredrickson
DW Kennedy
CT Resch
CJ Thompson
SJ Fansler
Facility: 
Volume: 
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Pages: 
Publication year: 
2015

Argon Cluster Sputtering Source for ToF-SIMS Depth Profiling of InsulatingMaterials: High Sputter Rate and Accurate Interfacial

Abstract: 

For the first time, the use of an argon cluster ion sputtering source has been demonstrated to perform superiorly relative to traditional oxygen and cesium ion sputtering sources for ToF-SIMS depth profiling of insulating materials. The superior performance has been attributed to effective alleviation of surface charging. A simulated nuclear waste glass, SON68, and layered hole-perovskite oxide thin films were selected as model systems due to their fundamental and practical significance. Our study shows that if the size of analysis areas is same, the highest sputter rate of argon cluster sputtering can be 2-3 times faster than the highest sputter rates of oxygen or cesium sputtering. More importantly, high quality data and high sputter rates can be achieved simultaneously for argon cluster sputtering while this is not the case for cesium and oxygen sputtering. Therefore, for deep depth profiling of insulating samples, the measurement efficiency of argon cluster sputtering can be about 6-15 times better than traditional cesium and oxygen sputtering. Moreover, for a SrTiO3/SrCrO3 bi-layer thin film on a SrTiO3 substrate, the true 18O/16O isotopic distribution at the interface is better revealed when using the argon cluster sputtering source. Therefore, the implementation of an argon cluster sputtering source can significantly improve the measurement efficiency of insulating materials, and thus can expand the application of ToF-SIMS to the study of glass corrosion, perovskite oxide thin films, and many other potential systems.

Citation: 
Wang Z, B Liu, E Zhao, K Jin, Y Du, JJ Neeway, JV Ryan, D Hu, H Zhang, M Hong, S Le Guernic, S Thevuthasan, F Wang, and Z Zhu.2015."Argon Cluster Sputtering Source for ToF-SIMS Depth Profiling of InsulatingMaterials: High Sputter Rate and Accurate Interfacial Information."Journal of the American Society for Mass Spectrometry 26(8):1283-1290. doi:10.1007/s13361-015-1159-1
Authors: 
Du Yingge
Dehong Hu
Zihua Zhu
Wang Z
B Liu
E Zhao
K Jin
Y Du
JJ Neeway
JV Ryan
D Hu
H Zhang
M Hong
S Le Guernic
S Thevuthasan
F Wang
Z Zhu
Volume: 
26
Issue: 
8
Pages: 
1283-1290
Publication year: 
2015

The Fate Of Silicon During Glass Corrosion Under Alkaline Conditions: A Mechanistic And Kinetic Study With The International

Abstract: 

International Simple Glass - a six oxide borosilicate glass selected by the international nuclear glass community to improve the understanding of glass corrosion mechanisms and kinetics - was altered at 90°C in a solution initially saturated with respect to amorphous 29-SiO2. The pH90°C, was fixed at 9 at the start of the experiment and raised to 11.5 after 209 d by the addition of KOH. Isotope sensitive analytical techniques were used to analyze the solution and altered glass samples, helping to understand the driving forces and rate limiting processes controlling long-term glass alteration. At pH 9, the corrosion rate continuously drops and the glass slowly transforms into a uniform, homogeneous and isovolumic amorphous alteration layer. The mechanisms responsible for this transformation are water diffusion through the growing alteration layer and ion exchange. We demonstrate that this amorphous alteration layer is not a precipitate resulting from the hydrolysis of the silicate network; it inherits from the glass structure from which the most weakly bonded cations (Na, Ca and B) have been released. At pH 11.5, the alteration process is very different: the high solubility of glass network formers (Si, Al, Zr) triggers the rapid and complete dissolution of the glass (dissolution becomes congruent) and precipitation of amorphous and crystalline phases. Unlike at pH 9 where glass corrosion rate decreased by 3 orders of magnitude likely due to transport-limiting phenomenon within the amorphous alteration layer, the rate at pH 11.5 is maintained at a value close to the forward rate due to both the hydrolysis of the silicate network and the precipitation of CSH and zeolites. This study provides key information for a unified model for glass dissolution.

Citation: 
Gin S, P Jollivet, M Fournie, C Berthon, Z Wang, AV Mitroshkov, Z Zhu, and JV Ryan.2015."The Fate Of Silicon During Glass Corrosion Under Alkaline Conditions: A Mechanistic And Kinetic Study With The International Simple Glass."Geochimica et Cosmochimica Acta 151:68-85. doi:10.1016/j.gca.2014.12.009
Authors: 
Zhu Zihua
Gin S
P Jollivet
M Fournie
C Berthon
Z Wang
AV Mitroshkov
Z Zhu
JV Ryan
Volume: 
Issue: 
Pages: 
Publication year: 
2015

Pore and Continuum Scale Study of the Effect of Subgrid Transport Heterogeneity on Redox Reaction Rates .

Abstract: 

A micromodel system with a pore structure for heterogeneous flow and transport was used to investigate the effect of subgrid transport heterogeneity on redox reaction rates. Hematite reductive dissolution by injecting a reduced form of flavin mononucleotide (FMNH2) at variable flow rates was used as an example to probe the variations of redox reaction rates in different subgrid transport domains. Experiments, pore-scale simulations, and macroscopic modeling were performed to measure and simulate in-situ hematite reduction and to evaluate the scaling behavior of the redox reaction rates from the pore to macroscopic scales. The results indicated that the measured pore-scale rates of hematite reduction were consistent with the predictions from a pore scale reactive transport model. A general trend is that hematite reduction followed reductant transport pathways, starting from the advection-dominated pores toward the interior of diffusion-dominated domains. Two types of diffusion domains were considered in the micromodel: a micropore diffusion domain, which locates inside solid grains or aggregates where reactant transport is limited by diffusion; and a macropore diffusion domain, which locates at wedged, dead-end pore spaces created by the grain-grain contacts. The rate of hematite reduction in the advection-dominated domain was faster than those in the diffusion-controlled domains, and the rate in the macropore diffusion domain was faster than that in the micropore domain. The reduction rates in the advection and macropore diffusion domains increased with increasing flow rate, but were affected by different mechanisms. The rate increase in the advection domain was controlled by the mass action effect as a faster flow supplied more reactants, and the rate increase in the macropore domain was more affected by the rate of mass exchange with the advection domain, which increased with increasing flow rate. The hematite reduction rate in the micropore domain was, however, not affected by the flow rate because molecular diffusion limits reductant supply to the micropore domain interior. Domain-based macroscopic models were evaluated to scale redox reaction rates from the pore to macroscopic scales. A single domain model, which ignores subgrid transport heterogeneity deviated significantly from the pore-scale results. Further analysis revealed that the rate expression for hematite reduction was not scalable from the pore to porous media using the single domain model. A three-domain model, which effectively considers subgrid reactive diffusion in the micropore and macropore domains, significantly improved model description. Overall this study revealed the importance of subgrid transport heterogeneity in the manifestation of redox reaction rates in porous media and in scaling reactions from the pore to porous media. The research also supported that the domain-based scaling approach can be used to directly scale redox reactions in porous media with subgrid transport heterogeneity.

Citation: 
Liu Y, C Liu, C Zhang, X Yang, and JM Zachara.2015."Pore and Continuum Scale Study of the Effect of Subgrid Transport Heterogeneity on Redox Reaction Rates ."Geochimica et Cosmochimica Acta 163:140-155. doi:10.1016/j.gca.2015.04.039
Authors: 
Liu Chongxuan
Liu Y
C Liu
C Zhang
X Yang
JM Zachara
Facility: 
Volume: 
Issue: 
Pages: 
Publication year: 
2015

Multi-heme Cytochromes in Shewanella oneidensis MR-1: Structures, functions and opportunities.

Abstract: 

Multi-heme cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometers. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-heme cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-heme cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward there are opportunities to engage multi-heme cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-heme cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-heme cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.

Citation: 
Breuer M, KM Rosso, J Blumberger, and JN Butt.2015."Multi-heme Cytochromes in Shewanella oneidensis MR-1: Structures, functions and opportunities."Journal of the Royal Society Interface 12(102):Article No. 20141117. doi:10.1098/rsif.2014.1117
Authors: 
M Kevin
Breuer M
KM Rosso
J Blumberger
JN Butt
Facility: 
Volume: 
Issue: 
Pages: 
Publication year: 
2015

Pore-Scale and Multiscale Numerical Simulation of Flow and Transport in a Laboratory-Scale Column.

Abstract: 

Pore-scale models are useful for studying relationships between fundamental processes and phenomena at larger (i.e., Darcy) scales. However, the size of domains that can be simulated with explicit pore-scale resolution is limited by computational and observational constraints. Direct numerical simulation of pore-scale flow and transport is typically performed on millimeter-scale volumes at which X-ray computed tomography (XCT), often used to characterize pore geometry, can achieve micrometer resolution. In contrast, the scale at which a continuum approximation of a porous medium is valid is usually larger, on the order of centimeters to decimeters. Furthermore, laboratory experiments that measure continuum properties are typically performed on decimeter-scale columns. At this scale, XCT resolution is coarse (tens to hundreds of micrometers) and prohibits characterization of small pores and grains. We performed simulations of pore-scale processes over a decimeter-scale volume of natural porous media with a wide range of grain sizes, and compared to results of column experiments using the same sample. Simulations were conducted using high-performance codes executed on a supercomputer. Two approaches to XCT image segmentation were evaluated, a binary (pores and solids) segmentation and a ternary segmentation that resolved a third category (porous solids with pores smaller than the imaged resolution). We used a mixed Stokes-Darcy simulation method to simulate the combination of Stokes flow in large open pores and Darcy-like flow in porous solid regions. Simulations based on the ternary segmentation provided results that were consistent with experimental observations, demonstrating our ability to successfully model pore-scale flow over a column-scale domain.

Citation: 
Scheibe TD, WA Perkins, MC Richmond, MI McKinley, PDJ Romero Gomez, M Oostrom, TW Wietsma, JA Serkowski, and JM Zachara.2015."Pore-Scale and Multiscale Numerical Simulation of Flow and Transport in a Laboratory-Scale Column."Water Resources Research 51(2):1023-1035. doi:10.1002/2014WR015959
Authors: 
D Timothy
Martinus Oostrom
Thomas W Wietsma
Scheibe TD
WA Perkins
MC Richmond
MI McKinley
PDJ Romero Gomez
M Oostrom
TW Wietsma
JA Serkowski
JM Zachara
Facility: 
Volume: 
51
Issue: 
2
Pages: 
1023-1035
Publication year: 
2015

Monte Carlo Simulations of Coupled Diffusion and Surface Reactions during the Aqueous Corrosion of Borosilicate Glasses.

Abstract: 

Borosilicate nuclear waste glasses develop complex altered layers as a result of coupled processes such as hydrolysis of network species, condensation of Si species, and diffusion. However, diffusion has often been overlooked in Monte Carlo models of the aqueous corrosion of borosilicate glasses. Therefore, three different models for dissolved Si diffusion in the altered layer were implemented in a Monte Carlo model and evaluated for glasses in the compositional range (75-x) mol% SiO2 (12.5+x/2) mol% B2O3 and (12.5+x/2) mol% Na2O, where 0 ≤ x ≤ 20%, and corroded in static conditions at a surface-to-volume ratio of 1000 m-1. The three models considered instantaneous homogenization (M1), linear concentration gradients (M2), and concentration profiles determined by solving Fick’s 2nd law using a finite difference method (M3). Model M3 revealed that concentration profiles in the altered layer are not linear and show changes in shape and magnitude as corrosion progresses, unlike those assumed in model M2. Furthermore, model M3 showed that, for borosilicate glasses with a high forward dissolution rate compared to the diffusion rate, the gradual polymerization and densification of the altered layer is significantly delayed compared to models M1 and M2. Models M1 and M2 were found to be appropriate models only for glasses with high release rates such as simple borosilicate glasses with low ZrO2 content.

Citation: 
Kerisit SN, EM Pierce, and JV Ryan.2015."Monte Carlo Simulations of Coupled Diffusion and Surface Reactions during the Aqueous Corrosion of Borosilicate Glasses."Journal of Non-crystalline Solids 408:142-149. doi:10.1016/j.jnoncrysol.2014.07.020
Authors: 
SN Kerisit
EM Pierce
JV Ryan
Volume: 
Issue: 
Pages: 
Publication year: 
2015

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(509) 371-7816

Dr. Bowden joined EMSL in 2009 and currently manages EMSL's optical spectroscopy and diffraction, subsurface flow and transport, and microfabrication and deposition capabilities. He is responsible for the X-ray diffraction facility and assists...