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

Dual beam depth profiling strategy has been widely adopted in ToF-SIMS depth profiling, in which two basic operation modes, interlaced mode and non-...
Currently, nuclear wastes are commonly immobilized into glasses because of their long-term durability. Exposure to water for long periods of time,...
We employed deep sequencing technology to identify transcriptional adaptation of the euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002...
Radionuclide 137Cs is one of the major fission products that dominate heat generation in spent fuels over the first 300 hundred years. A durable...
Redox-reactive, biogeochemical phases generated by reductive microbial activity in hyporheic zone sediments from a dynamic groundwater-river...

Science Highlights

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...
Posted: June 13, 2012
Using EMSL capabilities,  scientists at Pacific Northwest National Laboratory determined the wettability—the preference of a rock or other surface...

Instruments

There are no related projects at this time.

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.

ToF-SIMS Depth Profiling Of Insulating Samples, Interlaced Mode Or Non-interlaced Mode?

Abstract: 

Dual beam depth profiling strategy has been widely adopted in ToF-SIMS depth profiling, in which two basic operation modes, interlaced mode and non-interlaced mode, are commonly used. Generally, interlaced mode is recommended for conductive or semi-conductive samples, whereas non-interlaced mode is recommended for insulating samples, where charge compensation can be an issue. Recent publications, however, show that the interlaced mode can be used effectively for glass depth profiling, despite the fact that glass is an insulator. In this study, we provide a simple guide for choosing between interlaced mode and non-interlaced mode for insulator depth profiling. Two representative cases are presented: (1) depth profiling of a leached glass sample, and (2) depth profiling of a single crystal MgO sample. In brief, the interlaced mode should be attempted first, because (1) it may provide reasonable-quality data, and (2) it is time-saving for most cases, and (3) it introduces low H/C/O background. If data quality is the top priority and measurement time is flexible, non-interlaced mode is recommended because interlaced mode may suffer from low signal intensity and poor mass resolution. A big challenge is tracking trace H/C/O in a highly insulating sample (e.g., MgO), because non-interlaced mode may introduce strong H/C/O background but interlaced mode may suffer from low signal intensity. Meanwhile, a C or Au coating is found to be very effective to improve the signal intensity. Surprisingly, the best analyzing location is not on the C or Au coating, but at the edge (outside) of the coating.

Citation: 
Wang Z, K Jin, Y Zhang, F Wang, and Z Zhu.2014."ToF-SIMS Depth Profiling Of Insulating Samples, Interlaced Mode Or Non-interlaced Mode?"Surface and Interface Analysis 46(S1):257-260. doi:10.1002/sia.5419
Authors: 
Z Wang
K Jin
Y Zhang
F Wang
Z Zhu
Volume: 
46
Issue: 
0
Pages: 
257-260
Publication year: 
2014

NanoSIMS Imaging Alternation Layers of a Leached SON68 Glass Via A FIB-made Wedged Crater.

Abstract: 

Currently, nuclear wastes are commonly immobilized into glasses because of their long-term durability. Exposure to water for long periods of time, however, will eventually corrode the waste form and is the leading potential avenue for radionuclide release into the environment. Because such slow processes cannot be experimentally tested, the prediction of release requires a thorough understanding the mechanisms governing glass corrosion. In addition, due to the exceptional durability of glass, much of the testing must be performed on high-surface-area powders. A technique that can provide accurate compositional profiles with very precise depth resolution for non-flat samples would be a major benefit to the field. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling is an excellent tool that has long been used to examine corrosion layers of glass. The roughness of the buried corrosion layers, however, causes the corresponding SIMS depth profiles to exhibit erroneously wide interfaces. In this study, NanoSIMS was used to image the cross-section of the corrosion layers of a leached SON68 glass sample. A wedged crater was prepared by a focused ion beam (FIB) instrument to obtain a 5× improvement in depth resolution for NanoSIMS measurements. This increase in resolution allowed us to confirm that the breakdown of the silica glass network is further from the pristine glass than a second dissolution front for boron, another glass former. The existence of these two distinct interfaces, separated by only ~20 nm distance in depth, was not apparent by traditional ToF-SIMS depth profiling but has been confirmed also by atom probe tomography. This novel sample geometry will be a major benefit to efficient NanoSIMS sampling of irregular interfaces at the nanometer scale that would otherwise be obscured within ToF-SIMS depth profiles.

Citation: 
Wang YC, DK Schreiber, JJ Neeway, S Thevuthasan, JE Evans, JV Ryan, Z Zhu, and W Wei.2014."NanoSIMS Imaging Alternation Layers of a Leached SON68 Glass Via A FIB-made Wedged Crater."Surface and Interface Analysis 46(S1):233-237. doi:10.1002/sia.5585
Authors: 
YC Wang
DK Schreiber
JJ Neeway
S Thevuthasan
JE Evans
JV Ryan
Z Zhu
W Wei
Volume: 
46
Issue: 
Pages: 
233-237
Publication year: 
2014

Inference of Interactions in Cyanobacterial-Heterotrophic Co-Cultures via Transcriptome Sequencing.

Abstract: 

We employed deep sequencing technology to identify transcriptional adaptation of the euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 and the marine facultative aerobe Shewanella putrefaciens W3-18-1 to growth in a co-culture and infer the effect of carbon flux distributions on photoautotroph-heterotroph interactions. The overall transcriptome response of both organisms to co-cultivation was shaped by their respective physiologies and growth constraints. Carbon limitation resulted in the expansion of metabolic capacities which was manifested through the transcriptional upregulation of transport and catabolic pathways. While growth coupling occurred via lactate oxidation or secretion of photosynthetically fixed carbon, there was evidence of specific metabolic interactions between the two organisms. On one hand, the production and excretion of specific amino acids (methionine and alanine) by the cyanobacterium correlated with the putative downregulation of the corresponding biosynthetic machinery of Shewanella W3-18-1. On the other hand, the broad and consistent decrease of mRNA levels for many Fe-regulated Synechococcus 7002 genes during co-cultivation suggested increased Fe availability as well as more facile and energy-efficient mechanisms for Fe acquisition by the cyanobacterium. Furthermore, evidence pointed at potentially novel interactions between oxygenic photoautotrophs and heterotrophs related to the oxidative stress response as transcriptional patterns suggested that Synechococcus 7002 rather than Shewanella W3-18-1 provided scavenging functions for reactive oxygen species under co-culture conditions. This study provides an initial insight into the complexity of photoautotrophic-heterotrophic interactions and brings new perspectives of their role in the robustness and stability of the association.

Citation: 
Beliaev AS, MF Romine, M Serres, HC Bernstein, BE Linggi, LM Markillie, NG Isern, WB Chrisler, LA Kucek, EA Hill, G Pinchuk, DA Bryant, HS Wiley, JK Fredrickson, and A Konopka.2014."Inference of Interactions in Cyanobacterial-Heterotrophic Co-Cultures via Transcriptome Sequencing."The ISME Journal 8(11):2243-2255. doi:10.1038/ismej.2014.69
Authors: 
AS Beliaev
MF Romine
M Serres
HC Bernstein
BE Linggi
LM Markillie
NG Isern
WB Chrisler
LA Kucek
EA Hill
G Pinchuk
DA Bryant
HS Wiley
JK Fredrickson
A Konopka
Facility: 
Volume: 
8
Issue: 
11
Pages: 
2243-2255
Publication year: 
2014

Microstructure and Cs Behavior of Ba-Doped Aluminosilicate Pollucite Irradiated with F+ Ions.

Abstract: 

Radionuclide 137Cs is one of the major fission products that dominate heat generation in spent fuels over the first 300 hundred years. A durable waste form for 137Cs that decays to 137Ba is needed to minimize its environmental impact. Aluminosilicate pollucite CsAlSi2O6 is selected as a model waste form to study the decay-induced structural effects. While Ba-containing precipitates are not present in charge-balanced Cs0.9Ba0.05AlSi2O6, they are found in Cs0.9Ba0.1AlSi2O6 and identified as monoclinic Ba2Si3O8. Pollucite is susceptible to electron irradiation induced amorphization. The threshold density of the electronic energy deposition for amorphization is determined to be ~235 keV/nm3. Pollucite can be readily amorphized under F+ ion irradiation at 673 K. A significant amount of Cs diffusion and release from the amorphized pollucite is observed during the irradiation. However, cesium is immobile in the crystalline structure under He+ ion irradiation at room temperature. The critical temperature for amorphization is not higher than 873 K under F+ ion irradiation. If kept at or above 873 K all the time, the pollucite structure is unlikely to be amorphized; Cs diffusion and release are improbable. A general discussion regarding pollucite as a potential waste form is provided in this report.

Citation: 
Jiang W, L Kovarik, Z Zhu, T Varga, MH Engelhard, ME Bowden, TM Nenoff, and T Garino.2014."Microstructure and Cs Behavior of Ba-Doped Aluminosilicate Pollucite Irradiated with F+ Ions."Journal of Physical Chemistry C 118(31):18160-18169. doi:10.1021/jp5045223
Authors: 
W Jiang
L Kovarik
Z Zhu
T Varga
MH Engelhard
ME Bowden
TM Nenoff
T Garino
Instruments: 
Volume: 
118
Issue: 
31
Pages: 
18160-18169
Publication year: 
2014

Possible Dynamically Gated Conductance along Heme Wires in Bacterial Multiheme Cytochromes.

Abstract: 

The staggered cross decaheme configuration of electron transfer co-factors in the outer-membrane cytochrome MtrF may serve as a prototype for conformationally-gated multi-heme electron transport. Derived from the bacterium Shewanella oneidensis, the staggered cross configuration reveals intersecting c-type octaheme and tetraheme “wires” containing thermodynamic “hills” and “valleys”, suggesting that the protein structure may include a dynamical mechanism for conductance and pathway switching depending on enzymatic functional need. Recent molecular simulations have established the pair-wise electronic couplings, redox potentials, and reorganization energies to predict the maximum conductance along the various heme wire pathways by sequential hopping of a single electron (PNAS (2014) 11,611-616). Here, we expand this information with classical molecular and statistical mechanics calculations of large-amplitude protein dynamics in MtrF, to address its potential to modulate pathway conductance, including assessment of the effect of the total charge state. Explicit solvent molecular dynamics simulations of fully oxidized and fully reduced MtrF employing ten independent 50-ns simulations at 300 K and 1 atm showed that reduced MtrF is more expanded and explores more conformational space than oxidized MtrF, and that heme reduction leads to increased heme solvent exposure. The slowest mode of collective decaheme motion is 90% similar between the oxidized and reduced states, and consists primarily of inter-heme separation with minor rotational contributions. The frequency of this motion is 1.7×107 s 1 for fully-oxidized and fully-reduced MtrF, respectively, slower than the downhill electron transfer rates between stacked heme pairs at the octaheme termini and faster than the electron transfer rates between parallel hemes in the tetraheme chain. This implies that MtrF uses slow conformational fluctuations to modulate electron flow along the octaheme pathway, apparently for the purpose of increasing the residence time of electrons on lowest potential hemes 4 and 9. This apparent gating mechanism should increase the success rate of electron transfer from MtrF to low potential environmental acceptors via these two solvent-exposed hemes.

Citation: 
Smith DMA, and KM Rosso.2014."Possible Dynamically Gated Conductance along Heme Wires in Bacterial Multiheme Cytochromes."Journal of Physical Chemistry B 118(29):8505–8512. doi:10.1021/jp502803y
Authors: 
DMA Smith
KM Rosso
Facility: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Fe(II)- and Sulfide-Facilitated Reduction of 99Tc(VII)O4- in Microbially Reduced Hyporheic Zone Sediments.

Abstract: 

Redox-reactive, biogeochemical phases generated by reductive microbial activity in hyporheic zone sediments from a dynamic groundwater-river interaction zone were evaluated for their ability to reduce soluble pertechnetate [99Tc(VII)O4-] to less soluble Tc(IV). The sediments were bioreduced by indigenous microorganisms that were stimulated by organic substrate addition in synthetic groundwater with or without sulfate. In most treatments, 20 µmol L-1 initial aqueous Tc(VII) was reduced to near or below detection (3.82×10-9 mol L-1) over periods of days to months in suspensions of variable solids concentrations. Native sediments containing significant lithogenic Fe(II) in various phases were, in contrast, unreactive with Tc(VII). The reduction rates in the bioreduced sediments increased with increases in sediment mass, in proportion to weak acid-extractable Fe(II) and sediment-associated sulfide (AVS). The rate of Tc(VII) reduction was first order with respect to both aqueous Tc(VII) concentration and sediment mass, but correlations between specific reductant concentrations and reaction rate were not found. X-ray microprobe measurements revealed a strong correlation between Tc hot spots and Fe-containing mineral particles in the sediment. However, only a portion of Fe-containing particles were Tc-hosts. The Tc-hot spots displayed a chemical signature (by EDXRF) similar to pyroxene. The application of autoradiography and electron microprobe allowed further isolation of Tc-containing particles that were invariably found to be ca 100 µm aggregates of primary mineral material embedded within a fine-grained phyllosilicate matrix. EXAFS spectroscopy revealed that the Tc(IV) within these were a combination of a Tc(IV)O2-like phase and Tc(IV)-Fe surface clusters, with a significant fraction of a TcSx-like phase in sediments incubated with SO42-. AVS was implicated as a more selective reductant at low solids concentration even though its concentration was below that required for stoichiometric reduction of Tc(VII). These results demonstrate that composite mineral aggregates may be redox reaction centers in coarse-textured hyporheic zone sediments regardless of the dominant anoxic biogeochemical processes.

Citation: 
Lee JH, JM Zachara, JK Fredrickson, SM Heald, JP McKinley, AE Plymale, CT Resch, and DA Moore.2014."Fe(II)- and Sulfide-Facilitated Reduction of 99Tc(VII)O4- in Microbially Reduced Hyporheic Zone Sediments."Geochimica et Cosmochimica Acta 136:247-264. doi:10.1016/j.gca.2013.08.017
Authors: 
JH Lee
JM Zachara
JK Fredrickson
SM Heald
JP McKinley
AE Plymale
CT Resch
DA Moore
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations.

Abstract: 

The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products)represents a complex region, both physically and chemically, sandwiched between two distinct boundaries - pristine glass surface at the inner most interface and aqueous solution at the outer most. The physico-chemical processes that control the development of this region have a significant impact on the long-term glass-water reaction. Computational models, spanning different length and time-scales, are currently being developed to improve our understanding of this complex and dynamic process with the goal of accurately describing the pore-scale changes that occur as the system evolves. These modeling approaches include Geochemical Reaction Path simulations, Glass Reactivity in Allowance for Alteration Layer simulations, Monte Carlo simulations, and Molecular Dynamics methods. Discussed in this manuscript are the advances and limitations of each modeling approach placed in the context of the glass water reaction and how collectively these approaches provide insights into the mechanisms that control the formation and evolution of altered layers; thus providing the fundamental data needed to develop pore-scale equations that enable more accurate predictions of nuclear waste glass corrosion in a geologic repository.

Citation: 
Pierce EM, P Frugier, LJ Criscenti, KD Kwon, and SN Kerisit.2014."Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations."International Journal of Applied Glass Science 5(4):421-435. doi:10.1111/ijag.12077
Authors: 
EM Pierce
P Frugier
LJ Criscenti
KD Kwon
SN Kerisit
Volume: 
5
Issue: 
4
Pages: 
421-435
Publication year: 
2014

Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO.

Abstract: 

Bacterial species in the Enterobacteriaceae typically contain multiple paralogues of a small domain of unknown function (DUF1471) from a family of conserved proteins also known as YhcN or BhsA/McbA. Proteins containing DUF1471 may have a
single or three copies of this domain. Representatives of this family have been demonstrated to play roles in several cellular processes including stress response, biofilm formation, and pathogenesis. We have conducted NMR and X-ray crystallographic studies of four DUF1471 domains from Salmonella representing three different paralogous DUF1471 subfamilies: SrfN, YahO, and SssB/YdgH (two of its three DUF1471 domains: the N-terminal domain I (residues 21–91), and the C-terminal domain III (residues 244–314)). Notably, SrfN has been shown to have a role in intracellular infection by Salmonella Typhimurium. These domains share less than 35% pairwise sequence identity. Structures of all four domains show a mixed a+b fold that is most similar to that of bacterial lipoprotein RcsF. However, all four DUF1471 sequences lack the redox sensitive cysteine residues essential for RcsF activity in a phospho-relay pathway, suggesting that DUF1471 domains perform a different function(s). SrfN forms a dimer in contrast to YahO and SssB domains I and III, which are monomers in solution. A putative binding site for oxyanions such as phosphate and sulfate was identified in SrfN, and an interaction between the SrfN dimer and sulfated polysaccharides was demonstrated, suggesting a direct role for this DUF1471 domain at the host-pathogen interface.

Citation: 
Eletsky A, K Michalska, S Houliston, Q Zhang, MD Daily, X Xu, H Cui, A Yee, A Lemak, B Wu, M Garcia, MC Burnet, KM Meyer, UK Aryal, O Sanchez, C Ansong, R Xiao, T Acton, JN Adkins, G Montelione, A Joachimiak, CH Arrowsmith, A Savchenko, T Szyperski, and JR Cort.2014."Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO."PLoS One 9(7):Article No. e101787. doi:10.1371/journal.pone.0101787
Authors: 
A Eletsky
K Michalska
S Houliston
Q Zhang
MD Daily
X Xu
H Cui
A Yee
A Lemak
B Wu
M Garcia
MC Burnet
KM Meyer
UK Aryal
O Sanchez
C Ansong
R Xiao
T Acton
JN Adkins
G Montelione
A Joachimiak
CH Arrowsmith
A Savchenko
T Szyperski
JR Cort
Facility: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

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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...