Microscopy

Advancement in energy, environment and biology research relies heavily on micro-, nano- and atomic-scale chemical and structural imaging. Many microscopy instruments have high-resolution imaging capabilities including complementary chemical, structural and phase information, in-situ imaging in native environments and imaging of dynamic processes with high temporal-resolution. See a complete list of Microscopy instruments.

Resources and Techniques

  • Nanoscale and sub-nanoscale imaging allows users to elucidate chemical processes and acquire structural data for a variety of samples such as nanostructures and cell-surface proteins.
  • Tomography yields three-dimensional reconstruction of transmission electron microscopy images generated for biological samples as well as for soft materials and samples with 3D structural heterogeneity.
  • Environmental particle analysis offers knowledge about non-volatile atmospheric particle composition and hydration properties using high-pressure scanning electron microscopy equipped with energy-dispersive x-ray analysis capability.
  • Environmental mode imaging techniques enable sample preservation to eliminate extensive preparation procedures that can introduce artifacts and make possible live-cell imaging and in situ imaging in liquids or controlled gas environments with high resolution microscopy.
  • Dynamic imaging capability enables real-time studies of nanosecond-scale dynamic processes with unprecedented spatial resolution, such as protein-protein interactions, with contrast at the single-molecule level.

Quiet Wing for Advanced Microscopy
Seven microscopes are housed in the Quiet Wing, a space specially designed to reduce external factors, such as vibrations and electromagnetic fields, that can impede capture of high-resolution images. Read more about the Quiet Wing and its instrumentation.

Description

Capability Details

• Electron microscopes with tomography, cryo, scanning, photoemission and high-resolution (sub-nanometer) imaging capabilities
• Focused ion beam/scanning electron microscopes for specialized sample preparation and three-dimensional topographic and chemical imaging
• Nuclear magnetic resonance microscopy with 10-40-_m resolution to study the anatomy, metabolism and transport processes of live cell cultures, biofilms and tissue samples
• Dual Raman confocal microscope for analysis of radiological samples
• Single-molecule fluorescence tools to study molecular interactions in real time
• Scanning probe microscopy with capabilities ranging from examination of dynamic nanoscale processes in condensed environments to high resolution studies of catalysis materials in ultra-high vacuum.

 

Instruments

The Asylum MFP-3D BIO is a versatile atomic force microscope (AFM) that combines molecular resolution imaging and picoNewton force-based...
Custodian(s): Kevin M. Rosso
Housed in EMSL's Radiochemistry Annex, the field emission electron microprobe (EMP) enables chemical analysis and imaging of radionuclides with high...
Custodian(s): Bruce Arey
The environmental scanning electron microscope (ESEM) is a new-generation SEM that can image samples under controlled environments and temperatures...
Custodian(s): Alexander Laskin, Scott Lea
The X-ray photoelectron spectroscopy (XPS) imaging system provides fast, uantitative, real-time parallel imaging with highest resolution...
The JEOL JEM-3000SFF was designed for high-resolution cryogenic transmission electron microscopy (cryo-EM) of biological samples and expands EMSL/...

Publications

We analyzed proteomes of colon and rectal tumors previously characterized by the Cancer Genome Atlas (TCGA) and performed integrated proteogenomic...
Complementary methods of high-resolution mass spectrometry and micro-spectroscopy were utilized for molecular analysis of secondary organic aerosol (...
The effects of laser wavelength (355 nm and 532 nm) and laser pulse energy on the quantitative accuracy of atom probe tomography (APT) examinations...
Control of the reactivity of the nickel center of the [NiFe] hydrogenase and other metalloproteins commonly involves outer coordination sphere...
A method termed vapor-phase tomography has recently been proposed to characterize the distribution of volatile organic contaminant mass in vadose-...

Science Highlights

Posted: January 13, 2015
The Science Lithium (Li) metal has long been considered one of the most attractive anode materials, but large-scale application of high-energy...
Posted: December 09, 2014
The Science Rechargeable lithium ion batteries are common in portable electronics and in some vehicles, but they cannot store enough energy for the...
Posted: November 20, 2014
Aluminum oxide, or alumina, has numerous industrial uses, including as a catalyst and a catalytic support. Characterizing alumina has been difficult...
Posted: October 07, 2014
The Science Steam reforming is a method for converting biomass-derived light hydrocarbons and aromatics into a mixture of carbon monoxide and...
Posted: September 22, 2014
Phototrophs are organisms that use sunlight to convert inorganic materials to organic materials. Researchers are studying these organisms’...

Advancement in energy, environment and biology research relies heavily on micro-, nano- and atomic-scale chemical and structural imaging. Many microscopy instruments have high-resolution imaging capabilities including complementary chemical, structural and phase information, in-situ imaging in native environments and imaging of dynamic processes with high temporal-resolution. See a complete list of Microscopy instruments.

Resources and Techniques

  • Nanoscale and sub-nanoscale imaging allows users to elucidate chemical processes and acquire structural data for a variety of samples such as nanostructures and cell-surface proteins.
  • Tomography yields three-dimensional reconstruction of transmission electron microscopy images generated for biological samples as well as for soft materials and samples with 3D structural heterogeneity.
  • Environmental particle analysis offers knowledge about non-volatile atmospheric particle composition and hydration properties using high-pressure scanning electron microscopy equipped with energy-dispersive x-ray analysis capability.
  • Environmental mode imaging techniques enable sample preservation to eliminate extensive preparation procedures that can introduce artifacts and make possible live-cell imaging and in situ imaging in liquids or controlled gas environments with high resolution microscopy.
  • Dynamic imaging capability enables real-time studies of nanosecond-scale dynamic processes with unprecedented spatial resolution, such as protein-protein interactions, with contrast at the single-molecule level.

Quiet Wing for Advanced Microscopy
Seven microscopes are housed in the Quiet Wing, a space specially designed to reduce external factors, such as vibrations and electromagnetic fields, that can impede capture of high-resolution images. Read more about the Quiet Wing and its instrumentation.

Molecular Selectivity of Brown Carbon Chromophores.

Abstract: 

Complementary methods of high-resolution mass spectrometry and micro-spectroscopy were utilized for molecular analysis of secondary organic aerosol (SOA) generated from ozonolysis of two structural monoterpene isomers: D-limonene (LSOA) and a-pinene (PSOA). Laboratory simulated aging of LSOA and PSOA, through conversion of carbonyls into imines mediated by NH3 vapors in humid air, resulted in selective browning of the LSOA sample, while the PSOA sample remained white. Comparative analysis of the reaction products in the aged LSOA and PSOA samples provided insights into chemistry relevant to formation of brown carbon chromophores. A significant fraction of carbonyl-imine conversion products with identical molecular formulas were detected in both samples. This reflects the high level of similarity in the molecular composition of these two closely related SOA materials. Several highly conjugated products were detected exclusively in the brown LSOA sample and were identified as potential chromophores responsible for the observed color change. The majority of the unique products in the aged LSOA sample with the highest number of double bonds contain two nitrogen atoms. We conclude that chromophores characteristic of the carbonyl- imine chemistry in LSOA are highly conjugated oligomers of secondary imines (Schiff bases) present at relatively low concentrations. Formation of this type of conjugated compounds in PSOA is hindered by the structural rigidity of the a-pinene oxidation products. Our results suggest that the overall light-absorbing properties of SOA may be determined by trace amounts of strong brown carbon chromophores.

Citation: 
Laskin J, A Laskin, S Nizkorodov, PJ Roach, PA Eckert, MK Gilles, B Wang, HJ Lee, and Q Hu.2014."Molecular Selectivity of Brown Carbon Chromophores."Environmental Science & Technology 48(20):12047-12055. doi:10.1021/es503432r
Authors: 
J Laskin
A Laskin
S Nizkorodov
PJ Roach
PA Eckert
MK Gilles
B Wang
HJ Lee
Q Hu
Volume: 
48
Issue: 
20
Pages: 
12047-12055
Publication year: 
2014

Proteogenomic characterization of human colon and rectal cancer.

Abstract: 

We analyzed proteomes of colon and rectal tumors previously characterized by the Cancer Genome Atlas (TCGA) and performed integrated proteogenomic analyses. Protein sequence variants encoded by somatic genomic variations displayed reduced expression compared to protein variants encoded by germline variations. mRNA transcript abundance did not reliably predict protein expression differences between tumors. Proteomics identified five protein expression subtypes, two of which were associated with the TCGA "MSI/CIMP" transcriptional subtype, but had distinct mutation and methylation patterns and associated with different clinical outcomes. Although CNAs showed strong cis- and trans-effects on mRNA expression, relatively few of these extend to the protein level. Thus, proteomics data enabled prioritization of candidate driver genes. Our analyses identified HNF4A, a novel candidate driver gene in tumors with chromosome 20q amplifications. Integrated proteogenomic analysis provides functional context to interpret genomic abnormalities and affords novel insights into cancer biology.

Citation: 
Zhang B, J Wang, X Wang, J Zhu, Q Liu, Z Shi, MC Chambers, LJ Zimmerman, KF Shaddox, S Kim, S Davies, S Wang, P Wang, C Kinsinger, R Rivers, H Rodriguez, R Townsend, M Ellis, SA Carr, DL Tabb, RJ Coffey, R Slebos, and D Liebler.2014."Proteogenomic characterization of human colon and rectal cancer."Nature 513(7518):382-387. doi:10.1038/nature13438
Authors: 
B Zhang
J Wang
X Wang
J Zhu
Q Liu
Z Shi
MC Chambers
LJ Zimmerman
KF Shaddox
S Kim
S Davies
S Wang
P Wang
C Kinsinger
R Rivers
H Rodriguez
R Townsend
M Ellis
SA Carr
DL Tabb
RJ Coffey
R Slebos
D Liebler
Facility: 
Instruments: 
Volume: 
513
Issue: 
7518
Pages: 
382-387
Publication year: 
2014

Modulation of Active Site Electronic Structure by the Protein Matrix to Control [NiFe] Hydrogenase Reactivity .

Abstract: 

Control of the reactivity of the nickel center of the [NiFe] hydrogenase and other metalloproteins commonly involves outer coordination sphere ligands that act to modify the geometry and physical properties of the active site metal centers. We carried out a combined set of classical molecular dynamics and quantum/classical mechanics calculations to provide quantitative estimates of how dynamic fluctuations of the active site within the protein matrix modulate the electronic structure at the
catalytic center. Specifically we focused on the dynamics of the inner and outer coordination spheres of the cysteinate-bound Ni–Fe cluster in the catalytically active Ni-C state. There are correlated movements of the cysteinate ligands and the surrounding hydrogen-bonding network, which modulate the electron affinity at the active site and the proton affinity of a terminal cysteinate. On the basis of these findings, we hypothesize a coupling between protein dynamics and electron and proton transfer reactions critical to dihydrogen production.

Citation: 
Smith DMA, S Raugei, and TC Squier.2014."Modulation of Active Site Electronic Structure by the Protein Matrix to Control [NiFe] Hydrogenase Reactivity ."Physical Chemistry Chemical Physics. PCCP 16(43):24026-24033. doi:10.1039/c4cp03518f
Authors: 
DMA Smith
S Raugei
TC Squier
Facility: 
Volume: 
16
Issue: 
43
Pages: 
24026-24033
Publication year: 
2014

Effects of Laser Energy and Wavelength on the Analysis of LiFePO4 Using Laser Assisted Atom Probe Tomography.

Abstract: 

The effects of laser wavelength (355 nm and 532 nm) and laser pulse energy on the quantitative accuracy of atom probe tomography (APT) examinations of LiFePO4 (LFP) are considered. A systematic investigation of ultraviolet (UV, 355 nm) and green (532 nm) laser assisted APT of LFP has revealed distinctly different behaviors. With the use of UV laser the major issue was identified as the preferential loss of oxygen (up to 10 at. %) while other elements (Li, Fe and P) were observed to be close to nominal ratios. Lowering the laser energy per pulse to 1 pJ increased the observed oxygen concentration to near its correct stoichiometry and was well correlated with systematically higher concentrations of 16O2+ ions. This observation supports the premise that lower laser energies lead to a higher probability of oxygen molecule ionization. Conversely, at higher laser energies the resultant lower effective electric field reduces the probability of oxygen molecule ionization. Green laser assisted field evaporation led to the selective loss of Li (~50% deficiency) and correct ratios of the remaining elements, including the oxygen concentration. The loss of Li is explained by selective dc evaporation of lithium between laser pulses and relatively negligible oxygen loss as neutrals during green-laser pulsing. Lastly, plotting of multihit events on a Saxey plot for the straight-flight path data (green laser only) revealed a surprising dynamic recombination process for some molecular ions mid-flight.

Citation: 
Santhanagopalan D, DK Schreiber, DE Perea, R Martens, Y Janssen, P Kalifah, and YS Meng.2015."Effects of Laser Energy and Wavelength on the Analysis of LiFePO4 Using Laser Assisted Atom Probe Tomography."Ultramicroscopy 148:57-66. doi:10.1016/j.ultramic.2014.09.004
Authors: 
D Santhanagopalan
DK Schreiber
DE Perea
R Martens
Y Janssen
P Kalifah
YS Meng
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2015

Fe/SSZ-13 as an NH3-SCR Catalyst: A Reaction Kinetics and FTIR/Mössbauer Spectroscopic Study.

Abstract: 

Using a traditional aqueous solution ion-exchange method under a protecting atmosphere of N2, an Fe/SSZ-13 catalyst active in NH3-SCR was synthesized. Mössbauer and FTIR spectroscopies were used to probe the nature of the Fe sites. In the fresh sample, the majority of Fe species are extra-framework cations. The likely monomeric and dimeric ferric ions in hydrated form are [Fe(OH)2]+ and [HO-Fe-O-Fe-OH]2+, based on Mössbauer measurements. During the severe hydrothermal aging (HTA) applied in this study, a majority of cationic Fe species convert to FeAlOx and clustered FeOx species, accompanied by severe dealumination of the SSZ-13 framework. The clustered FeOx species do not give a sextet Mössbauer spectrum, indicating that these are highly disordered. However, some Fe species in cationic positions remain after aging as determined from Mössbauer measurements and CO/NO FTIR titrations. NO/NH3 oxidation reaction tests reveal that dehydrated cationic Fe are substantially more active in catalyzing oxidation reactions than the hydrated ones. For NH3-SCR, enhancement of NO oxidation under ‘dry’ conditions promotes SCR rates below ~300 C. This is due mainly to contribution from the “fast” SCR channel. Above ~300 C, enhancement of NH3 oxidation under ‘dry’ conditions, however, becomes detrimental to NOx conversions. The HTA sample loses much of the SCR activity below ~300 C; however, above ~400 C much of the activity remains. This may suggest that the FeAlOx and FeOx species become active at such elevated temperatures. Alternatively, the high-temperature activity may be maintained by the remaining extra-framework cationic species. For potential practical applications, Fe/SSZ-13 may be used as a co-catalyst for Cu/CHA as integral aftertreatment SCR catalysts on the basis of the stable high temperature activity after hydrothermal aging. The authors gratefully acknowledge the US Department of Energy (DOE), Energy Efficiency and Renewable Energy, Vehicle Technologies Office for the support of this work. The research described in this paper was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle.

Citation: 
Gao F, M Kollar, RK Kukkadapu, NM Washton, Y Wang, J Szanyi, and CHF Peden.2015."Fe/SSZ-13 as an NH3-SCR Catalyst: A Reaction Kinetics and FTIR/Mössbauer Spectroscopic Study."Applied Catalysis. B, Environmental 164:407-419. doi:10.1016/j.apcatb.2014.09.031
Authors: 
F Gao
M Kollar
RK Kukkadapu
NM Washton
Y Wang
J Szanyi
CHF Peden
Volume: 
Issue: 
Pages: 
Publication year: 
2015

Measuring Spatial Variability of Vapor Flux to Characterize Vadose-zone VOC Sources: Flow-cell Experiments.

Abstract: 

A method termed vapor-phase tomography has recently been proposed to characterize the distribution of volatile organic contaminant mass in vadose-zone source areas, and to measure associated three-dimensional distributions of local contaminant mass discharge. The method is based on measuring the spatial variability of vapor flux, and thus inherent to its effectiveness is the premise that the magnitudes and temporal variability of vapor concentrations measured at different monitoring points within the interrogated area will be a function of the geospatial positions of the points relative to the source location. A series of flow-cell experiments was conducted to evaluate this premise. A well-defined source zone was created by injection and extraction of a non-reactive gas (SF6). Spatial and temporal concentration distributions obtained from the tests were compared to simulations produced with a mathematical model describing advective and diffusive transport. Tests were conducted to characterize both areal and vertical components of the application. Decreases in concentration over time were observed for monitoring points located on the opposite side of the source zone from the local–extraction point, whereas increases were observed for monitoring points located between the local–extraction point and the source zone. The results illustrate that comparison of temporal concentration profiles obtained at various monitoring points gives a general indication of the source location with respect to the extraction and monitoring points.

Citation: 
Mainhagu J, C Morrison, MJ Truex, M Oostrom, and M Brusseau.2014."Measuring Spatial Variability of Vapor Flux to Characterize Vadose-zone VOC Sources: Flow-cell Experiments."Journal of Contaminant Hydrology 167:32-43. doi:10.1016/j.jconhyd.2014.07.007
Authors: 
J Mainhagu
C Morrison
MJ Truex
M Oostrom
M Brusseau
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Ion-induced swelling of ODS ferritic alloy MA957 tubing to 500 dpa.

Abstract: 

In order to study the potential swelling behavior of the ODS ferritic alloy MA957 at very high dpa levels, specimens were prepared from pressurized tubes that were unirradiated archives of tubes previously irradiated in FFTF to doses as high at 110 dpa. These unirradiated specimens were irradiated with 1.8 MeV Cr+ ions to doses ranging from 100 to 500 dpa and examined by transmission electron microscopy. No coinjection of helium or hydrogen was employed. It was shown that compared to several ferritic/martensitic steels irradiated in the same facility, these tubes were rather resistant to void swelling, reaching a maximum value of only 4.5% at 500 dpa and 450°C. In this fine-grained material, the distribution of swelling was strongly influenced by the presence of void denuded zones along the grain boundaries.

Citation: 
Toloczko MB, FA Garner, V Voyevodin, VV Bryk, OV Borodin, VV Melnichenko, and AS Kalchenko.2014."Ion-induced swelling of ODS ferritic alloy MA957 tubing to 500 dpa."Journal of Nuclear Materials 453(1-3):323-333. doi:10.1016/j.jnucmat.2014.06.011
Authors: 
MB Toloczko
FA Garner
V Voyevodin
VV Bryk
OV Borodin
VV Melnichenko
AS Kalchenko
Volume: 
453
Issue: 
Pages: 
323-333
Publication year: 
2014

Fe(II)-catalyzed Recrystallization of Goethite Revisited.

Abstract: 

Results from enriched 57Fe isotope tracer experiments have shown that atom exchange can occur between structural Fe in Fe(III) oxides and aqueous Fe(II) with no formation of secondary minerals or change in particle size or shape. Here we derive a mass balance model to quantify the extent of Fe atom exchange between goethite and aqueous Fe(II) that accounts for different Fe pool sizes. We use this model to reinterpret our previous work and to quantify the influence of particle size and pH on extent of goethite exchange with aqueous Fe(II). Consistent with our previous interpretation, substantial exchange of goethite occurred at pH 7.5 (≈ 90%) and we observed little effect of particle size between nanogoethite (81 x 11 nm) and microgoethite (590 x 42 nm). Despite ≈ 90% of the bulk goethite exchanging at pH 7.5, we found no change in mineral phase, particle size, crystallinity, or reactivity after reaction with aqueous Fe(II). At a lower pH of 5.0, no net sorption of Fe(II) was observed and significantly less exchange occurred accounting for less than the estimated proportion of surface Fe atoms in the particles. Particle size appears to influence the amount of exchange at pH 5.0 and we suggest that aggregation and surface area may play a role. Results from sequential chemical extractions indicate that 57Fe accumulates in extracted Fe(III) goethite components. Isotopic compositions of the extracts indicate that a gradient of 57Fe develops within the goethite with more accumulation of 57Fe occurring in the more easily extracted Fe(III) that may be nearer to the surface. We interpret our particle size, pH, and sequential extraction findings as consistent with the mechanism of interfacial electron transfer and bulk conduction previously proposed to explain the substantial Fe atom exchange observed in goethite in contact with aqueous Fe(II).

Citation: 
Handler R, AJ Frierdich, C Johnson, KM Rosso, B Beard, CM Wang, D Latta, A Neumann, TS Pasakarnis, WAPJ Premaratne, and M Scherer.2014."Fe(II)-catalyzed Recrystallization of Goethite Revisited."Environmental Science & Technology 48(19):11302-11311. doi:10.1021/es503084u
Authors: 
R Hler
AJ Frierdich
C Johnson
KM Rosso
B Beard
CM Wang
D Latta
A Neumann
TS Pasakarnis
WAPJ Premaratne
M Scherer
Volume: 
48
Issue: 
19
Pages: 
11302-11311
Publication year: 
2014

Grain boundary depletion and migration during selective oxidation of Cr in a Ni-5Cr binary alloy exposed to high-temperature

Abstract: 

High-resolution microscopy of a high-purity Ni-5Cr alloy exposed to 360°C hydrogenated water reveals intergranular selective oxidation of Cr accompanied by local Cr depletion and diffusion-induced grain boundary migration (DIGM). The corrosion-product oxide consists of a porous, interconnected network of Cr2O3 platelets with no further O ingress into the metal ahead. Extensive grain boundary depletion of Cr (to <0.05at.%) is observed typically 20–100 nm wide as a result of DIGM and reaching depths of many micrometers beyond the oxidation front.

Citation: 
Schreiber DK, MJ Olszta, and SM Bruemmer.2014."Grain boundary depletion and migration during selective oxidation of Cr in a Ni-5Cr binary alloy exposed to high-temperature hydrogenated water."Scripta Materialia 89:41-44. doi:10.1016/j.scriptamat.2014.06.022
Authors: 
DK Schreiber
MJ Olszta
SM Bruemmer
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Microstructure Based Modeling of β Phase Influence on Mechanical Response of Cast AM Series Mg Alloys.

Abstract: 

Magnesium alloys have become popular alternatives to aluminums and steels for the purpose of vehicle light-weighting. However, Mg alloys are hindered from wider application due to limited ductility as well as poor creep and corrosion performance. Understanding the impact of microstructural features on bulk response is key to improving Mg alloys for more widespread use and for moving towards truly predicting modeling capabilities. This study focuses on modeling the intrinsic features, particularly volume fraction and morphology of beta phase present, of cast Mg alloy microstructure and quantifying their impact on bulk performance. Computational results are compared to experimental measurements of cast plates of Mg alloy with varying aluminum content.

Citation: 
Barker EI, KS Choi, X Sun, E Deda, J Allison, M Li, J Forsmark, J Zindel, and L Godlewski.2014."Microstructure Based Modeling of ? Phase Influence on Mechanical Response of Cast AM Series Mg Alloys."Computational Materials Science 92:353-3612. doi:10.1016/j.commatsci.2014.03.010
Authors: 
EI Barker
KS Choi
X Sun
E Deda
J Allison
M Li
J Forsmark
J Zindel
L Godlewski
Volume: 
Issue: 
Pages: 
Publication year: 
2014

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