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 JEOL JEM-3000SFF was designed for high-resolution cryogenic transmission electron microscopy (cryo-EM) of biological samples and expands EMSL/...
This time-lapse fluorescence microscope with single molecule detection sensitivity is used to follow individual molecules or organelles in their...
Custodian(s): Galya Orr

Publications

The microstructure and chemistry of SmCo2Fe2B melt-spun alloy after multistage annealing was investigated using high resolution transmission electron...
Grain growth of nanocrystalline materials is generally thermally activated, but can also be driven by irradiation at much lower temperature. In...
14YWT oxide dispersion strengthened (ODS) ferritic steel was irradiated with of 5 MeV Ni2+ ions, at 300 °C, 450 °C, and 600 °...
Dual beam depth profiling strategy has been widely adopted in ToF-SIMS depth profiling, in which two basic operation modes, interlaced mode and non-...
Melanoma is a malignant tumor of melanocytes. Although extensive investigations have been done to study metabolic changes in primary melanoma in...

Science Highlights

Posted: March 30, 2015
The Science Lipids derived from oil-rich microorganisms such as bacteria, yeast and microalgae offer a promising source of renewable fuels and...
Posted: March 24, 2015
To understand a lithium battery at the nanoscale, scientists with EMSL and other organizations at the Department of Energy’s Joint Center for Energy...
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...

Instruments

There are no related projects at this time.

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.

1H NMR Metabolomics Study of Metastatic Melanoma in C57BL/6J Mouse Spleen.

Abstract: 

Melanoma is a malignant tumor of melanocytes. Although extensive investigations have been done to study metabolic changes in primary melanoma in vivo and in vitro, little effort has been devoted to metabolic profiling of metastatic tumors in organs other than lymph nodes. In this work, NMR-based metabolomics combined with multivariate data analysis is used to study metastatic B16-F10 melanoma in C57BL/6J mouse spleen. Principal Component Analysis (PCA), an unsupervised multivariate data analysis method, is used to detect possible outliers, while Orthogonal Projection to Latent Structure (OPLS), a supervised multivariate data analysis method, is employed to find important metabolites responsible for discriminating the control and the melanoma groups. Two different strategies, i.e., spectral binning and spectral deconvolution, are used to reduce the original spectral data before statistical analysis. Spectral deconvolution is found to be superior for identifying a set of discriminatory metabolites between the control and the melanoma groups, especially when the sample size is small. OPLS results show that the melanoma group can be well separated from its control group. It is found that taurine, glutamate, aspartate, O-Phosphoethanolamine, niacinamide ,ATP, lipids and glycerol derivatives are decreased statistically and significantly while alanine, malate, xanthine, histamine, dCTP, GTP, thymidine, 2'-Deoxyguanosine are statistically and significantly elevated. These significantly changed metabolites are associated with multiple biological pathways and may be potential biomarkers for metastatic melanoma in spleen.

Citation: 
Wang X, MY Hu, J Feng, M Liu, and JZ Hu.2014."1H NMR Metabolomics Study of Metastatic Melanoma in C57BL/6J Mouse Spleen."Metabolomics 10(6):1129-1144. doi:10.1007/s11306-014-0652-z
Authors: 
X Wang
MY Hu
J Feng
M Liu
JZ Hu
Volume: 
10
Issue: 
6
Pages: 
1129-1144
Publication year: 
2014

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

Stability Of Nanoclusters In 14YWT Oxide Dispersion Strengthened Steel Under Heavy Ion-irradiation By Atom Probe Tomography.

Abstract: 

14YWT oxide dispersion strengthened (ODS) ferritic steel was irradiated with of 5 MeV Ni2+ ions, at 300 °C, 450 °C, and 600 °C to a damage level of 100 dpa. The stability of Ti–Y–O nanoclusters was investigated by applying atom probe tomography (APT) in voltage mode, of the samples before and after irradiations. The average size and number density of the nanoclusters was determined using the maximum separation method. These techniques allowed for the imaging of nanoclusters to sizes well below the resolution limit of conventional transmission electron microscopy techniques. The most significant changes were observed for samples irradiated at 300 °C where the size (average Guinier radius) and number density of nanoclusters were observed to decrease from 1.1 nm to 0.8 nm and 12 × 1023 to 3.6 × 1023, respectively. In this study, the nanoclusters are more stable at higher temperature.

Citation: 
He J, F Wan, K Sridharan, TR Allen, AG Certain, V Shutthanandan, and Y Wu.2014."Stability Of Nanoclusters In 14YWT Oxide Dispersion Strengthened Steel Under Heavy Ion-irradiation By Atom Probe Tomography."Journal of Nuclear Materials 455(1-3):41-45. doi:10.1016/j.jnucmat.2014.03.024
Authors: 
He J
F Wan
K Sridharan
TR Allen
AG Certain
V Shutthanan
Y Wu
Instruments: 
Volume: 
455
Issue: 
0
Pages: 
41-45
Publication year: 
2014

The Effect of Eectronic Energy Loss on Irradiation-Induced Grain Growth in Nanocrystalline Oxides.

Abstract: 

Grain growth of nanocrystalline materials is generally thermally activated, but can also be driven by irradiation at much lower temperature. In nanocrystalline ceria and zirconia, contributions from both displacement damage and ionization to the grain growth are identified. Our atomistic simulations have revealed fast grain boundary (GB) movements due to the high density of disorder near GBs. Our experimental results have shown that irradiation-induced grain growth is a function of total energy deposited, where the excitation of target electrons and displacement of lattice atoms both contribute to the overall disorder and both play important roles in grain growth. The coupling of energy deposition to the electronic and lattice structures should both be taken into consideration when engineering nanostructural materials.

Citation: 
Zhang Y, DS Aidhy, T Varga, S Moll, PD Edmondson, F Namavar, K Jin, CN Ostrouchov, and WJ Weber.2014."The Effect of Eectronic Energy Loss on Irradiation-Induced Grain Growth in Nanocrystalline Oxides."Physical Chemistry Chemical Physics. PCCP 16(17):8051-8059. doi:10.1039/c4cp00392f
Authors: 
Y Zhang
DS Aidhy
T Varga
S Moll
PD Edmondson
F Namavar
K Jin
CN Ostrouchov
WJ Weber
Volume: 
16
Issue: 
17
Pages: 
8051-8059
Publication year: 
2014

Microstructure of Multistage Annealed Nanocrystalline SmCo2Fe2B Alloy with Enhanced Magnetic Properties.

Abstract: 

The microstructure and chemistry of SmCo2Fe2B melt-spun alloy after multistage annealing was investigated using high resolution transmission electron microscopy (HRTEM) and 3D atom probe tomography. The multistage annealing resulted in an increase in both the coercivity and magnetization. The presence of Sm(Co,Fe)4B (1:4:1) and Sm2(Co,Fe)17Bx (2:17:x) magnetic phases were confirmed using both techniques. Fe2B at a scale of ∼5 nm was found by HRTEM precipitating within the 1:4:1 phase after the second-stage annealing. Ordering within the 2:17:x phase was directly identified both by the presence of antiphase boundaries observed by TEM and the interconnected isocomposition surface network found in 3D atom probe results in addition to radial distribution function analysis. The variations in the local chemistry after the secondary annealing were considered pivotal in improving the magnetic properties.

Citation: 
Jiang X, A Devaraj, B Balamurugan, J Cui, and JE Shield.2014."Microstructure of Multistage Annealed Nanocrystalline SmCo2Fe2B Alloy with Enhanced Magnetic Properties."Journal of Applied Physics 115(6):Article No. 063902. doi:10.1063/1.4865298
Authors: 
X Jiang
A Devaraj
B Balamurugan
J Cui
JE Shield
Volume: 
0
Issue: 
0
Pages: 
0
Publication year: 
2014

Impact of a Mixed Oxide’s Surface Composition and Structure on Its Adsorptive Properties: Case of the (Fe,Cr)3O4(111)

Abstract: 

Characterization of an α-(Fe0.75,Cr0.25)2O3(0001) mixed oxide single crystal surface was conducted using x-ray photoelectron spectroscopy (XPS), secondary ion mass spectrometry (SIMS), low energy electron diffraction (LEED) and temperature programmed desorption (TPD). After sputter/anneal cleaning in ultra-high vacuum (UHV), the mixed oxide surface became terminated with a magnetite-(111) structure based on the presence of (2x2) spots in LEED and Fe2+ in XPS. The composition of the surface was close to that of M3O4 based on XPS, with the metal (M) content of Fe2+/3+ and Cr3+ being close to 1.4:1, despite the fact that the film’s bulk was 3:1 with respect to the metal cations. The enrichment of the surface with Cr was not altered by high temperature oxidation in UHV, but could be returned to that of the bulk film composition by exposure to the ambient. Adsorption of various probe molecules (NO, O2, CO2 and H2O) was used to identify the active cation sites present in the (Fe,Cr)3O4(111) terminated surface. Although XPS and SIMS both indicated that the near-surface region was enriched in Cr3+, no adsorption states typically associated with Cr3+ sites on -Cr2O3 single crystal surfaces were detected. Instead, the TPD behaviors of O2 and CO2 pointed toward the main active sites being Fe2+ and Fe3+, with O2 preferentially adsorbing at the former and CO2 at the latter. NO was observed to bind at both Fe2+ and Fe3+ sites, and H2O TPD looked nearly identical to that for H2O on the Fe3O4(111) surface. Competition for adsorption sites between coadsorbed combinations of CO2, O2, H2O and NO corroborated these assignments. These results indicate that the surface composition of a mixed oxide can vary significantly from its bulk composition depending on the treatment conditions. Even then, the surface composition does not necessarily provide direct insight into the active adsorption sites. In the case of the (Fe,Cr)3O4(111) termination of the α-(Fe0.75,Cr0.25)2O3(0001) surface, Cr3+ cations in the near-surface region appear to be fully coordinated and unavailable for adsorbing molecules. The authors thank Drs. Sara Chamberlin and Scott Chambers for supplying the film used in this work. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. The research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

Citation: 
Henderson MA, and MH Engelhard.2014."Impact of a Mixed Oxide’s Surface Composition and Structure on Its Adsorptive Properties: Case of the (Fe,Cr)3O4(111) Termination of the ?-(Fe,Cr)2O3(0001) Surface."Journal of Physical Chemistry C 118(50):29058-29067. doi:10.1021/jp5038975
Authors: 
MA Henderson
MH Engelhard
Facility: 
Volume: 
118
Issue: 
50
Pages: 
29058-29067
Publication year: 
2014

Dendrimer-Encapsulated Ruthenium Nanoparticles as Catalysts for Lithium-O2 Batteries.

Abstract: 

Dendrimer-encapsulated ruthenium nanoparticles (DEN-Ru) have been used as catalysts in lithium-O2 batteries for the first time. Results obtained from UV-vis spectroscopy, electron microscopy and X-ray photoelectron spectroscopy show that the nanoparticles synthesized by the dendrimer template method are ruthenium oxide instead of metallic ruthenium reported earlier by other groups. The DEN-Ru significantly improve the cycling stability of lithium (Li)-O2 batteries with carbon black electrodes and decrease the charging potential even at low catalyst loading. The monodispersity, porosity and large number of surface functionalities of the dendrimer template prevent the aggregation of the ruthenium nanoparticles making their entire surface area available for catalysis. The potential of using DEN-Ru as stand-alone cathode materials for Li-O2 batteries is also explored.

Citation: 
Bhattacharya P, EN Nasybulin, MH Engelhard, L Kovarik, ME Bowden, S Li, DJ Gaspar, W Xu, and J Zhang.2014."Dendrimer-Encapsulated Ruthenium Nanoparticles as Catalysts for Lithium-O2 Batteries."Advanced Functional Materials 24(47):7510-7519. doi:10.1002/adfm.201402701
Authors: 
P Bhattacharya
EN Nasybulin
MH Engelhard
L Kovarik
ME Bowden
S Li
DJ Gaspar
W Xu
J Zhang
Facility: 
Volume: 
24
Issue: 
47
Pages: 
7510-7519
Publication year: 
2014

In Situ Study of CO2 and H2O Partitioning Between Na-Montmorillonite and Variably Wet Supercritical Carbon Dioxide.

Abstract: 

Shale formations play fundamental roles in large-scale geologic carbon sequestration (GCS) aimed primarily to mitigate climate change, and in smaller-scale GCS targeted mainly for CO2-enhanced gas recovery operations. In both technologies, CO2 is injected underground as a supercritical fluid (scCO2), where interactions with shale minerals could influence successful GCS implementation. Reactive components of shales include expandable clays, such as montmorillonites and mixed-layer illite/smectite clays. In this work, we used in situ X-ray diffraction (XRD) and in situ infrared (IR) spectroscopy to investigate the swelling/shrinkage and water/CO2 sorption of a pure montmorillonite, Na-SWy-2, when the clay is exposed to variably hydrated scCO2 at 50 °C and 90 bar. Measured interlayer spacings and sorbed water concentrations at varying levels of scCO2 hydration are similar to previously reported values measured in air at ambient pressure over a range of relative humidities. IR spectra show evidence of both water and CO2 intercalation, and variations in peak shapes and positions suggest multiple sorbed types with distinct chemical environments. Based on the intensity of the asymmetric CO stretching band of the CO2 associated with the Na-SWy-2, we observed a significant increase in sorbed CO2 as the clay expands from a 0W to a 1W state, suggesting that water props open the interlayer so that CO2 can enter. However, as the clay transitions from a 1W to a 2W state, CO2 desorbs sharply. These observations were placed in the context of two conceptual models concerning hydration mechanisms for expandable clays and were also discussed in light of recent theoretical studies on CO2-H2O-clay interactions. The swelling/shrinkage of expandable clays could affect solid volume, porosity, and permeability of shales. Consequently, the results from this work could aid predictions of shale caprock integrity in large-scale GCS, as well as methane transmissivity in enhanced gas recovery operations.

Citation: 
Loring JS, ES Ilton, J Chen, CJ Thompson, PF Martin, P Benezeth, KM Rosso, AR Felmy, and HT Schaef.2014."In Situ Study of CO2 and H2O Partitioning Between Na-Montmorillonite and Variably Wet Supercritical Carbon Dioxide."Langmuir 30(21):6120-6128. doi:10.1021/la500682t
Authors: 
JS Loring
ES Ilton
J Chen
CJ Thompson
PF Martin
P Benezeth
KM Rosso
AR Felmy
HT Schaef
Volume: 
30
Issue: 
21
Pages: 
6120-6128
Publication year: 
2014

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Dr. Lea has over 20 years of experience with research related to surface science. His primary focus areas are related to the application of electron spectroscopy and scanning probes to study chemical and geochemical processes, biomolecular...